Starting phenix.real_space_refine
on Fri Aug 22 15:39:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qtv_18654/08_2025/8qtv_18654.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qtv_18654/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qtv_18654/08_2025/8qtv_18654.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qtv_18654/08_2025/8qtv_18654.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qtv_18654/08_2025/8qtv_18654.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qtv_18654/08_2025/8qtv_18654.map"
  }
  resolution = 3.25
  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    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): 0.01s

  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: 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: 1.81, per 1000 atoms: 0.36
  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: 0.45
  Conformation dependent library (CDL) restraints added in 226.5 milliseconds
  
  Enol-peptide restraints added in 953.7 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:
      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: 0.20
  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: 0.76

  Time building geometry restraints manager: 0.57 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: 0.01
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:             1.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.250
  Find NCS groups from input model:        0.040
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.860
-------------------------------------------------------------------------------
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 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: -0.99 (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
 ARG   0.001   0.000   ARG B 996 
 TYR   0.004   0.000   TYR A 906 
 PHE   0.003   0.000   PHE A1135 
 TRP   0.004   0.000   TRP A1090 
 HIS   0.001   0.000   HIS B1147 

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

*********************** 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  : 0.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.1000
  time to fit residues: 4.7415
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  : 0.183 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.3980
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.6786

-------------------------------------------------------------------------------
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 = 0.3271 r_free = 0.3271 target = 0.071225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.050293 restraints weight = 14756.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.2732 rms_B_bonded: 5.02
r_work: 0.2546 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.2546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8498
moved from start:          0.1402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5213  Z= 0.161
  Angle     :  0.526   6.458   7114  Z= 0.271
  Chirality :  0.044   0.128    760
  Planarity :  0.003   0.021    934
  Dihedral  :  3.366  21.718    712
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 15.71 %
    Favored  : 82.86 %
  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: -0.55 (0.33), residues: 658
  helix:  1.58 (0.47), residues: 116
  sheet: -0.01 (0.48), residues: 126
  loop : -1.10 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1050 
 TYR   0.008   0.001   TYR A1167 
 PHE   0.005   0.001   PHE B1028 
 TRP   0.005   0.001   TRP A1014 
 HIS   0.002   0.000   HIS B1147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 5184)
  covalent geometry    : angle       0.52302 ( 7056)
  SS BOND              : bond        0.00286 (   29)
  SS BOND              : angle       0.77622 (   58)
  hydrogen bonds       : bond        0.03863 (  164)
  hydrogen bonds       : angle       4.17548 (  444)

*********************** 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  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  931 GLN cc_start: 0.7779 (tm-30) cc_final: 0.7288 (tm-30)
REVERT: A  942 ASP cc_start: 0.8706 (t0) cc_final: 0.8344 (t0)
REVERT: B  931 GLN cc_start: 0.7280 (tm-30) cc_final: 0.7054 (tm-30)
REVERT: B  942 ASP cc_start: 0.8672 (t0) cc_final: 0.8449 (t0)
  outliers start: 8
  outliers final: 4
  residues processed: 32
  average time/residue: 0.0740
  time to fit residues: 3.2532
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  : 0.203 
-------------------------------------------------------------------------------
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 32 optimal weight:    8.9990
   chunk 21 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   overall best weight:    1.9988

-------------------------------------------------------------------------------
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 = 0.3249 r_free = 0.3249 target = 0.070212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.049045 restraints weight = 14676.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.2695 rms_B_bonded: 5.04
r_work: 0.2506 rms_B_bonded: 4.96 restraints_weight: 0.5000
r_work (final): 0.2506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.1831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5213  Z= 0.182
  Angle     :  0.528   5.197   7114  Z= 0.275
  Chirality :  0.043   0.129    760
  Planarity :  0.003   0.022    934
  Dihedral  :  3.680  21.357    712
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 17.14 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.36 (0.33), residues: 658
  helix:  1.83 (0.46), residues: 116
  sheet:  0.18 (0.48), residues: 124
  loop : -1.02 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B1050 
 TYR   0.010   0.001   TYR A 993 
 PHE   0.006   0.001   PHE A1164 
 TRP   0.004   0.001   TRP A1014 
 HIS   0.002   0.001   HIS A 910 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 5184)
  covalent geometry    : angle       0.52509 ( 7056)
  SS BOND              : bond        0.00303 (   29)
  SS BOND              : angle       0.81081 (   58)
  hydrogen bonds       : bond        0.04221 (  164)
  hydrogen bonds       : angle       4.13635 (  444)

*********************** 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
  39 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 25
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  942 ASP cc_start: 0.8757 (t0) cc_final: 0.8517 (t0)
REVERT: B  931 GLN cc_start: 0.7550 (tm-30) cc_final: 0.7286 (tm-30)
REVERT: B  942 ASP cc_start: 0.8701 (t0) cc_final: 0.8369 (t0)
  outliers start: 14
  outliers final: 6
  residues processed: 38
  average time/residue: 0.0690
  time to fit residues: 3.6447
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  : 0.148 
-------------------------------------------------------------------------------
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 12 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 22 optimal weight:    6.9990
   chunk 63 optimal weight:    7.9990
   chunk 4 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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 = 0.3240 r_free = 0.3240 target = 0.070002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2727 r_free = 0.2727 target = 0.047848 restraints weight = 14957.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.2669 rms_B_bonded: 5.18
r_work: 0.2482 rms_B_bonded: 5.01 restraints_weight: 2.0000
r_work (final): 0.2482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.2200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   5213  Z= 0.231
  Angle     :  0.584   6.409   7114  Z= 0.301
  Chirality :  0.044   0.152    760
  Planarity :  0.003   0.023    934
  Dihedral  :  4.017  21.063    712
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 16.96 %
    Favored  : 80.18 %
  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: -0.38 (0.34), residues: 658
  helix:  1.83 (0.45), residues: 116
  sheet:  0.02 (0.47), residues: 124
  loop : -0.98 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B1190 
 TYR   0.008   0.001   TYR A1167 
 PHE   0.006   0.001   PHE B1217 
 TRP   0.003   0.001   TRP A1014 
 HIS   0.002   0.001   HIS A 910 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 ( 5184)
  covalent geometry    : angle       0.57698 ( 7056)
  SS BOND              : bond        0.00347 (   29)
  SS BOND              : angle       1.17415 (   58)
  hydrogen bonds       : bond        0.04404 (  164)
  hydrogen bonds       : angle       4.13251 (  444)

*********************** 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
  40 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 24
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  942 ASP cc_start: 0.8822 (t0) cc_final: 0.8572 (t0)
REVERT: B  931 GLN cc_start: 0.7635 (tm-30) cc_final: 0.7259 (tm-30)
REVERT: B  942 ASP cc_start: 0.8732 (t0) cc_final: 0.8458 (t0)
  outliers start: 16
  outliers final: 13
  residues processed: 40
  average time/residue: 0.0650
  time to fit residues: 3.7176
Evaluate side-chains
  35 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 22
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 37 optimal weight:    8.9990
   chunk 23 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 36 optimal weight:    0.8980
   chunk 29 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    3.3788

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.068542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.047314 restraints weight = 15060.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.2651 rms_B_bonded: 5.01
r_work: 0.2461 rms_B_bonded: 4.90 restraints_weight: 0.5000
r_work (final): 0.2461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start:          0.2531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.034   5213  Z= 0.297
  Angle     :  0.652   9.078   7114  Z= 0.341
  Chirality :  0.046   0.192    760
  Planarity :  0.003   0.024    934
  Dihedral  :  4.447  20.515    712
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 17.68 %
    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 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: -0.49 (0.33), residues: 658
  helix:  1.69 (0.45), residues: 116
  sheet: -0.16 (0.47), residues: 124
  loop : -1.01 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1190 
 TYR   0.010   0.001   TYR A1167 
 PHE   0.008   0.001   PHE A1217 
 TRP   0.002   0.001   TRP A1065 
 HIS   0.003   0.001   HIS A 910 

Details of bonding type rmsd
  covalent geometry    : bond        0.00663 ( 5184)
  covalent geometry    : angle       0.63867 ( 7056)
  SS BOND              : bond        0.00408 (   29)
  SS BOND              : angle       1.57049 (   58)
  hydrogen bonds       : bond        0.04895 (  164)
  hydrogen bonds       : angle       4.34140 (  444)

*********************** 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: 22
    poor density    : 22
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  942 ASP cc_start: 0.8855 (t0) cc_final: 0.8556 (t0)
REVERT: B  942 ASP cc_start: 0.8748 (t0) cc_final: 0.8499 (t0)
  outliers start: 22
  outliers final: 15
  residues processed: 42
  average time/residue: 0.0876
  time to fit residues: 4.7752
Evaluate side-chains
  38 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 23
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
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 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 1020 ILE
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 6 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 49 optimal weight:    7.9990
   chunk 19 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 9 optimal weight:    9.9990
   overall best weight:    2.9588

-------------------------------------------------------------------------------
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 = 0.3216 r_free = 0.3216 target = 0.068743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.047471 restraints weight = 15173.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.2654 rms_B_bonded: 5.01
r_work: 0.2465 rms_B_bonded: 4.90 restraints_weight: 0.5000
r_work (final): 0.2465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.2697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.029   5213  Z= 0.261
  Angle     :  0.614   5.567   7114  Z= 0.321
  Chirality :  0.046   0.121    760
  Planarity :  0.004   0.032    934
  Dihedral  :  4.480  19.796    712
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 17.14 %
    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 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: -0.52 (0.33), residues: 658
  helix:  1.69 (0.44), residues: 116
  sheet: -0.19 (0.48), residues: 124
  loop : -1.02 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B1187 
 TYR   0.009   0.001   TYR A 993 
 PHE   0.009   0.001   PHE B1217 
 TRP   0.002   0.001   TRP A1090 
 HIS   0.003   0.001   HIS B 910 

Details of bonding type rmsd
  covalent geometry    : bond        0.00585 ( 5184)
  covalent geometry    : angle       0.60747 ( 7056)
  SS BOND              : bond        0.00362 (   29)
  SS BOND              : angle       1.17396 (   58)
  hydrogen bonds       : bond        0.04567 (  164)
  hydrogen bonds       : angle       4.32308 (  444)

*********************** 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
  44 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 24
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  942 ASP cc_start: 0.8862 (t0) cc_final: 0.8531 (t0)
REVERT: B  942 ASP cc_start: 0.8765 (t0) cc_final: 0.8474 (t0)
REVERT: B 1157 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8183 (p)
REVERT: B 1201 ARG cc_start: 0.9077 (ptp-170) cc_final: 0.8339 (mtt90)
  outliers start: 20
  outliers final: 15
  residues processed: 42
  average time/residue: 0.0779
  time to fit residues: 4.4211
Evaluate side-chains
  40 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 24
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
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 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 1020 ILE
Chi-restraints excluded: chain B residue 1157 THR
Chi-restraints excluded: chain B residue 1181 CYS
Chi-restraints excluded: chain B residue 1200 VAL
Chi-restraints excluded: chain B residue 1228 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 57 optimal weight:    3.9990
   chunk 42 optimal weight:    0.7980
   chunk 50 optimal weight:    0.2980
   chunk 48 optimal weight:    8.9990
   chunk 63 optimal weight:    5.9990
   chunk 29 optimal weight:    8.9990
   chunk 11 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    1.4186

-------------------------------------------------------------------------------
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 = 0.3254 r_free = 0.3254 target = 0.070692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.049386 restraints weight = 14626.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.2733 rms_B_bonded: 5.03
r_work: 0.2545 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.2545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8563
moved from start:          0.2576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5213  Z= 0.142
  Angle     :  0.555   5.738   7114  Z= 0.287
  Chirality :  0.044   0.127    760
  Planarity :  0.003   0.026    934
  Dihedral  :  4.096  18.837    712
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 18.39 %
    Favored  : 78.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.40 (0.34), residues: 658
  helix:  1.98 (0.45), residues: 114
  sheet: -0.18 (0.48), residues: 124
  loop : -0.96 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B1187 
 TYR   0.007   0.001   TYR A 993 
 PHE   0.004   0.001   PHE A1061 
 TRP   0.004   0.001   TRP A1090 
 HIS   0.001   0.000   HIS B1147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 5184)
  covalent geometry    : angle       0.55227 ( 7056)
  SS BOND              : bond        0.00246 (   29)
  SS BOND              : angle       0.84135 (   58)
  hydrogen bonds       : bond        0.03478 (  164)
  hydrogen bonds       : angle       4.06173 (  444)

*********************** 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
  48 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 29
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  942 ASP cc_start: 0.8860 (t0) cc_final: 0.8486 (t0)
REVERT: A 1157 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8020 (p)
REVERT: B  942 ASP cc_start: 0.8759 (t0) cc_final: 0.8402 (t0)
  outliers start: 19
  outliers final: 14
  residues processed: 47
  average time/residue: 0.0877
  time to fit residues: 5.1883
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  : 0.135 
-------------------------------------------------------------------------------
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  998 MET
Chi-restraints excluded: chain A residue 1010 LEU
Chi-restraints excluded: chain A residue 1067 LEU
Chi-restraints excluded: chain A residue 1157 THR
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 1189 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 5 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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 = 0.3227 r_free = 0.3227 target = 0.069295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.047784 restraints weight = 14878.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.2655 rms_B_bonded: 5.10
r_work: 0.2463 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.2463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8556
moved from start:          0.2734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   5213  Z= 0.232
  Angle     :  0.604   5.461   7114  Z= 0.316
  Chirality :  0.045   0.124    760
  Planarity :  0.003   0.026    934
  Dihedral  :  4.333  18.141    712
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 18.04 %
    Favored  : 78.57 %
  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: -0.35 (0.34), residues: 658
  helix:  1.77 (0.45), residues: 116
  sheet:  0.01 (0.48), residues: 120
  loop : -0.92 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B1187 
 TYR   0.007   0.001   TYR B 993 
 PHE   0.006   0.001   PHE B1217 
 TRP   0.002   0.001   TRP A1065 
 HIS   0.003   0.001   HIS B 910 

Details of bonding type rmsd
  covalent geometry    : bond        0.00526 ( 5184)
  covalent geometry    : angle       0.59918 ( 7056)
  SS BOND              : bond        0.00344 (   29)
  SS BOND              : angle       1.01390 (   58)
  hydrogen bonds       : bond        0.04394 (  164)
  hydrogen bonds       : angle       4.15656 (  444)

*********************** 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
  45 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 26
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  942 ASP cc_start: 0.8871 (t0) cc_final: 0.8538 (t0)
REVERT: A 1157 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8128 (p)
REVERT: A 1201 ARG cc_start: 0.9107 (ptp-170) cc_final: 0.8299 (mtt90)
REVERT: B  942 ASP cc_start: 0.8794 (t0) cc_final: 0.8492 (t0)
REVERT: B 1201 ARG cc_start: 0.9127 (ptp-170) cc_final: 0.8310 (mtt90)
  outliers start: 19
  outliers final: 16
  residues processed: 44
  average time/residue: 0.0968
  time to fit residues: 5.3914
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  : 0.241 
-------------------------------------------------------------------------------
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 1157 THR
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 1189 CYS
Chi-restraints excluded: chain B residue 1200 VAL
Chi-restraints excluded: chain B residue 1228 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 48 optimal weight:    8.9990
   chunk 22 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 62 optimal weight:    9.9990
   overall best weight:    0.9988

-------------------------------------------------------------------------------
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 = 0.071505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.049698 restraints weight = 14608.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.2699 rms_B_bonded: 5.13
r_work: 0.2508 rms_B_bonded: 5.05 restraints_weight: 2.0000
r_work (final): 0.2508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.2602

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= 0.113
  Angle     :  0.555   5.646   7114  Z= 0.285
  Chirality :  0.044   0.133    760
  Planarity :  0.003   0.027    934
  Dihedral  :  4.019  17.899    712
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  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 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: -0.34 (0.34), residues: 658
  helix:  2.04 (0.45), residues: 114
  sheet: -0.18 (0.48), residues: 124
  loop : -0.91 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1193 
 TYR   0.007   0.001   TYR A 993 
 PHE   0.005   0.001   PHE A1217 
 TRP   0.004   0.001   TRP A1090 
 HIS   0.001   0.000   HIS B1147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 5184)
  covalent geometry    : angle       0.55326 ( 7056)
  SS BOND              : bond        0.00214 (   29)
  SS BOND              : angle       0.74064 (   58)
  hydrogen bonds       : bond        0.03124 (  164)
  hydrogen bonds       : angle       3.96291 (  444)

*********************** 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
  47 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 31
  time to evaluate  : 0.226 
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: 0.8837 (t0) cc_final: 0.8411 (t0)
REVERT: B  942 ASP cc_start: 0.8752 (t0) cc_final: 0.8369 (t0)
  outliers start: 16
  outliers final: 15
  residues processed: 46
  average time/residue: 0.0904
  time to fit residues: 5.3632
Evaluate side-chains
  43 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 28
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
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  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 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
Chi-restraints excluded: chain B residue 1228 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   chunk 57 optimal weight:    7.9990
   chunk 15 optimal weight:    5.9990
   chunk 6 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   overall best weight:    2.1186

-------------------------------------------------------------------------------
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 = 0.3237 r_free = 0.3237 target = 0.070078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2744 r_free = 0.2744 target = 0.048559 restraints weight = 14766.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.2671 rms_B_bonded: 5.07
r_work: 0.2479 rms_B_bonded: 4.96 restraints_weight: 0.5000
r_work (final): 0.2479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.2709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5213  Z= 0.194
  Angle     :  0.580   5.429   7114  Z= 0.302
  Chirality :  0.045   0.125    760
  Planarity :  0.003   0.026    934
  Dihedral  :  4.187  18.053    712
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 18.57 %
    Favored  : 78.57 %
  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: -0.39 (0.34), residues: 658
  helix:  1.84 (0.45), residues: 116
  sheet: -0.20 (0.48), residues: 124
  loop : -0.92 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1050 
 TYR   0.008   0.001   TYR B 993 
 PHE   0.005   0.001   PHE A1217 
 TRP   0.002   0.001   TRP A1090 
 HIS   0.002   0.000   HIS B 910 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 ( 5184)
  covalent geometry    : angle       0.57696 ( 7056)
  SS BOND              : bond        0.00306 (   29)
  SS BOND              : angle       0.90280 (   58)
  hydrogen bonds       : bond        0.03981 (  164)
  hydrogen bonds       : angle       4.05564 (  444)

********************** 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
  41 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 25
  time to evaluate  : 0.121 
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: 0.8853 (t0) cc_final: 0.8492 (t0)
REVERT: A 1157 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8086 (p)
REVERT: B  942 ASP cc_start: 0.8778 (t0) cc_final: 0.8409 (t0)
  outliers start: 16
  outliers final: 14
  residues processed: 40
  average time/residue: 0.0788
  time to fit residues: 4.0804
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  : 0.142 
-------------------------------------------------------------------------------
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 1157 THR
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
Chi-restraints excluded: chain B residue 1228 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   chunk 55 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 56 optimal weight:    0.3980
   chunk 50 optimal weight:    0.4980
   overall best weight:    1.1784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.071307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.049412 restraints weight = 14879.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.2696 rms_B_bonded: 5.18
r_work: 0.2505 rms_B_bonded: 5.06 restraints_weight: 2.0000
r_work (final): 0.2505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.2630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5213  Z= 0.126
  Angle     :  0.574   7.790   7114  Z= 0.297
  Chirality :  0.045   0.131    760
  Planarity :  0.003   0.027    934
  Dihedral  :  4.052  21.797    712
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 18.75 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.39 (0.34), residues: 658
  helix:  2.00 (0.45), residues: 114
  sheet: -0.20 (0.48), residues: 124
  loop : -0.96 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B1050 
 TYR   0.007   0.001   TYR B 993 
 PHE   0.004   0.001   PHE B1061 
 TRP   0.004   0.001   TRP A1090 
 HIS   0.002   0.000   HIS B1147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 5184)
  covalent geometry    : angle       0.57216 ( 7056)
  SS BOND              : bond        0.00226 (   29)
  SS BOND              : angle       0.74066 (   58)
  hydrogen bonds       : bond        0.03248 (  164)
  hydrogen bonds       : angle       3.97050 (  444)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1269.06 seconds
wall clock time: 22 minutes 26.98 seconds (1346.98 seconds total)