Starting phenix.real_space_refine
on Wed Feb 12 07:42:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ox6_17258/02_2025/8ox6_17258.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ox6_17258/02_2025/8ox6_17258.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.39
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ox6_17258/02_2025/8ox6_17258.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ox6_17258/02_2025/8ox6_17258.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ox6_17258/02_2025/8ox6_17258.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ox6_17258/02_2025/8ox6_17258.cif"
  }
  resolution = 2.39
  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=   1.000
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: 7
    Type Number    sf(0)   Gaussians
     Al      1      5.89       5
     Mg      1      5.21       5
     S      32      5.16       5
     C    4817      2.51       5
     N    1193      2.21       5
     O    1311      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7359
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4643
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 575, 4643
          Classifications: {'peptide': 575}
          Link IDs: {'PTRANS': 16, 'TRANS': 558}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2642
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 2642
          Classifications: {'peptide': 328}
          Link IDs: {'PTRANS': 25, 'TRANS': 302}
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 6
          Unusual residues: {' MG': 1, 'ALF': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 4.45, per 1000 atoms: 0.60
  Number of scatterers: 7359
  At special positions: 0
  Unit cell: (71.4288, 93.168, 136.646, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      32     16.00
     Al      1     13.00
     Mg      1     11.99
     F       4      9.00
     O    1311      8.00
     N    1193      7.00
     C    4817      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  91 " - pdb=" SG  CYS B 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  94 " - pdb=" SG  CYS B 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 157 " - pdb=" SG  CYS B 171 " distance=2.04

  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
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
    NAG-ASN
      " NAG B 401 " - " ASN B 107 "
      " NAG B 402 " - " ASN B 294 "
      " NAG C   1 " - " ASN B 180 "
  Time building additional restraints: 1.84
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1696

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 6 sheets defined
      59.4% alpha, 7.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 107 through 116
      removed outlier: 3.844A  pdb=" N   ASN A 111 " --> pdb=" O   PHE A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 131
      removed outlier: 3.510A  pdb=" N   LEU A 122 " --> pdb=" O   ARG A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 174
      Proline residue:  A 147  - end of helix
      removed outlier: 4.245A  pdb=" N   ASP A 162 " --> pdb=" O   LYS A 158 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ILE A 173 " --> pdb=" O   MET A 169 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ASN A 174 " --> pdb=" O   ASP A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 366
    Processing helix  chain 'A' and resid 370 through 374
    Processing helix  chain 'A' and resid 380 through 396
      removed outlier: 3.569A  pdb=" N   PHE A 389 " --> pdb=" O   GLY A 385 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   TRP A 390 " --> pdb=" O   PHE A 386 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   GLY A 391 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 400
    Processing helix  chain 'A' and resid 403 through 422
      removed outlier: 3.599A  pdb=" N   ILE A 419 " --> pdb=" O   GLN A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 447
    Processing helix  chain 'A' and resid 713 through 724
    Processing helix  chain 'A' and resid 734 through 744
      removed outlier: 3.557A  pdb=" N   THR A 738 " --> pdb=" O   ASP A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 744 through 749
    Processing helix  chain 'A' and resid 869 through 885
      removed outlier: 3.697A  pdb=" N   VAL A 880 " --> pdb=" O   VAL A 876 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 894 through 896
      No H-bonds generated for 'chain 'A' and resid 894 through 896'
    Processing helix  chain 'A' and resid 897 through 904
      removed outlier: 3.718A  pdb=" N   THR A 903 " --> pdb=" O   ASN A 899 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 928 through 930
      No H-bonds generated for 'chain 'A' and resid 928 through 930'
    Processing helix  chain 'A' and resid 931 through 937
    Processing helix  chain 'A' and resid 938 through 963
      removed outlier: 3.545A  pdb=" N   TYR A 956 " --> pdb=" O   ARG A 952 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   PHE A 961 " --> pdb=" O   LYS A 957 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 963 through 970
      removed outlier: 3.907A  pdb=" N   PHE A 970 " --> pdb=" O   PHE A 966 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 981 through 989
      removed outlier: 3.685A  pdb=" N   THR A 986 " --> pdb=" O   ASP A 982 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LEU A 987 " --> pdb=" O   TRP A 983 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   ASN A 989 " --> pdb=" O   ILE A 985 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 994 through 1004
    Processing helix  chain 'A' and resid 1008 through 1015
    Processing helix  chain 'A' and resid 1016 through 1018
      No H-bonds generated for 'chain 'A' and resid 1016 through 1018'
    Processing helix  chain 'A' and resid 1019 through 1024
      removed outlier: 3.546A  pdb=" N   GLN A1023 " --> pdb=" O   TYR A1019 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1030 through 1057
      removed outlier: 3.965A  pdb=" N   PHE A1034 " --> pdb=" O   TYR A1030 " (cutoff:3.500A)
      Proline residue:  A1051  - end of helix
    Processing helix  chain 'A' and resid 1068 through 1092
    Processing helix  chain 'A' and resid 1097 through 1119
      removed outlier: 3.686A  pdb=" N   PHE A1115 " --> pdb=" O   PHE A1111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1119 through 1126
      removed outlier: 3.574A  pdb=" N   HIS A1123 " --> pdb=" O   SER A1119 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   VAL A1124 " --> pdb=" O   ALA A1120 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   LEU A1125 " --> pdb=" O   GLY A1121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1134 through 1140
    Processing helix  chain 'A' and resid 1142 through 1156
    Processing helix  chain 'A' and resid 1157 through 1171
    Processing helix  chain 'A' and resid 1173 through 1181
      removed outlier: 3.638A  pdb=" N   HIS A1181 " --> pdb=" O   LYS A1177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 75
      removed outlier: 4.306A  pdb=" N   ILE B  53 " --> pdb=" O   THR B  49 " (cutoff:3.500A)
      Proline residue:  B  63  - end of helix
    Processing helix  chain 'B' and resid 91 through 96
    Processing helix  chain 'B' and resid 131 through 137
      removed outlier: 3.634A  pdb=" N   SER B 137 " --> pdb=" O   ARG B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 144
    Processing helix  chain 'B' and resid 146 through 152
      removed outlier: 3.738A  pdb=" N   LEU B 151 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 161
      Proline residue:  B 159  - end of helix
    Processing helix  chain 'B' and resid 172 through 177
    Processing helix  chain 'B' and resid 206 through 212
    Processing helix  chain 'B' and resid 222 through 227
      removed outlier: 3.839A  pdb=" N   PHE B 227 " --> pdb=" O   GLU B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 253
      removed outlier: 3.994A  pdb=" N   ILE B 253 " --> pdb=" O   ASN B 250 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 250 through 253'
    Processing helix  chain 'B' and resid 254 through 262
    Processing helix  chain 'B' and resid 322 through 350
      removed outlier: 3.579A  pdb=" N   PHE B 337 " --> pdb=" O   GLY B 333 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   VAL B 345 " --> pdb=" O   VAL B 341 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 426 through 427
    Processing sheet with id=AA2, first strand: chain 'A' and resid 727 through 730
      removed outlier: 5.996A  pdb=" N   ILE A 451 " --> pdb=" O   TRP A 729 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   TYR A 450 " --> pdb=" O   LEU A 889 " (cutoff:3.500A)
      removed outlier: 7.483A  pdb=" N   ILE A 891 " --> pdb=" O   TYR A 450 " (cutoff:3.500A)
      removed outlier: 5.911A  pdb=" N   PHE A 452 " --> pdb=" O   ILE A 891 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   THR A 888 " --> pdb=" O   ILE A 906 " (cutoff:3.500A)
      removed outlier: 8.027A  pdb=" N   VAL A 908 " --> pdb=" O   THR A 888 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   ALA A 890 " --> pdb=" O   VAL A 908 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1095 through 1096
    Processing sheet with id=AA4, first strand: chain 'B' and resid 78 through 81
      removed outlier: 5.949A  pdb=" N   TYR B 122 " --> pdb=" O   LEU B 272 " (cutoff:3.500A)
      removed outlier: 5.713A  pdb=" N   LEU B 272 " --> pdb=" O   TYR B 122 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   LEU B 124 " --> pdb=" O   ARG B 270 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   ARG B 270 " --> pdb=" O   LEU B 124 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 103
      removed outlier: 3.985A  pdb=" N   CYS B 102 " --> pdb=" O   TYR B 297 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 102 through 103
      removed outlier: 3.985A  pdb=" N   CYS B 102 " --> pdb=" O   TYR B 297 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   ARG B 290 " --> pdb=" O   ILE B 188 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   THR B 182 " --> pdb=" O   THR B 296 " (cutoff:3.500A)

    362 hydrogen bonds defined for protein.
    1026 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: 1.96

  Time building geometry restraints manager: 2.18 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2249
        1.34 -     1.46: 1944
        1.46 -     1.58: 3303
        1.58 -     1.70: 0
        1.70 -     1.82: 57
  Bond restraints: 7553
  Sorted by residual:
  bond pdb=" F2  ALF A1202 "
       pdb="AL   ALF A1202 "
    ideal  model  delta    sigma   weight residual
    1.685  1.807 -0.122 2.00e-02 2.50e+03 3.73e+01
  bond pdb=" F3  ALF A1202 "
       pdb="AL   ALF A1202 "
    ideal  model  delta    sigma   weight residual
    1.685  1.791 -0.106 2.00e-02 2.50e+03 2.83e+01
  bond pdb=" F4  ALF A1202 "
       pdb="AL   ALF A1202 "
    ideal  model  delta    sigma   weight residual
    1.686  1.790 -0.104 2.00e-02 2.50e+03 2.68e+01
  bond pdb=" F1  ALF A1202 "
       pdb="AL   ALF A1202 "
    ideal  model  delta    sigma   weight residual
    1.684  1.779 -0.095 2.00e-02 2.50e+03 2.24e+01
  bond pdb=" C1  BMA C   3 "
       pdb=" C2  BMA C   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.560 -0.041 2.00e-02 2.50e+03 4.26e+00
  ... (remaining 7548 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    14.03: 10257
       14.03 -    28.06: 4
       28.06 -    42.08: 0
       42.08 -    56.11: 0
       56.11 -    70.14: 2
  Bond angle restraints: 10263
  Sorted by residual:
  angle pdb=" F1  ALF A1202 "
        pdb="AL   ALF A1202 "
        pdb=" F2  ALF A1202 "
      ideal   model   delta    sigma   weight residual
     108.68  178.82  -70.14 3.00e+00 1.11e-01 5.47e+02
  angle pdb=" F3  ALF A1202 "
        pdb="AL   ALF A1202 "
        pdb=" F4  ALF A1202 "
      ideal   model   delta    sigma   weight residual
     109.63  179.77  -70.14 3.00e+00 1.11e-01 5.47e+02
  angle pdb=" F2  ALF A1202 "
        pdb="AL   ALF A1202 "
        pdb=" F4  ALF A1202 "
      ideal   model   delta    sigma   weight residual
     110.21   89.76   20.45 3.00e+00 1.11e-01 4.65e+01
  angle pdb=" F1  ALF A1202 "
        pdb="AL   ALF A1202 "
        pdb=" F4  ALF A1202 "
      ideal   model   delta    sigma   weight residual
     109.02   89.31   19.71 3.00e+00 1.11e-01 4.32e+01
  angle pdb=" F2  ALF A1202 "
        pdb="AL   ALF A1202 "
        pdb=" F3  ALF A1202 "
      ideal   model   delta    sigma   weight residual
     109.59   90.37   19.22 3.00e+00 1.11e-01 4.10e+01
  ... (remaining 10258 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.59: 4162
       21.59 -    43.18: 289
       43.18 -    64.77: 24
       64.77 -    86.36: 10
       86.36 -   107.95: 4
  Dihedral angle restraints: 4489
    sinusoidal: 1846
      harmonic: 2643
  Sorted by residual:
  dihedral pdb=" CA  GLN A1131 "
           pdb=" C   GLN A1131 "
           pdb=" N   PHE A1132 "
           pdb=" CA  PHE A1132 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.46   22.54     0      5.00e+00 4.00e-02 2.03e+01
  dihedral pdb=" CA  PRO B  90 "
           pdb=" C   PRO B  90 "
           pdb=" N   CYS B  91 "
           pdb=" CA  CYS B  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.22   21.78     0      5.00e+00 4.00e-02 1.90e+01
  dihedral pdb=" CB  CYS B  91 "
           pdb=" SG  CYS B  91 "
           pdb=" SG  CYS B 104 "
           pdb=" CB  CYS B 104 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   59.46   33.54     1      1.00e+01 1.00e-02 1.60e+01
  ... (remaining 4486 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 974
       0.053 -    0.106: 161
       0.106 -    0.159: 22
       0.159 -    0.212: 0
       0.212 -    0.265: 1
  Chirality restraints: 1158
  Sorted by residual:
  chirality pdb=" C5  BMA C   3 "
            pdb=" C4  BMA C   3 "
            pdb=" C6  BMA C   3 "
            pdb=" O5  BMA C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.26 2.00e-01 2.50e+01 1.75e+00
  chirality pdb=" CA  ILE A 728 "
            pdb=" N   ILE A 728 "
            pdb=" C   ILE A 728 "
            pdb=" CB  ILE A 728 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.02e-01
  chirality pdb=" CA  VAL A 400 "
            pdb=" N   VAL A 400 "
            pdb=" C   VAL A 400 "
            pdb=" CB  VAL A 400 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.64e-01
  ... (remaining 1155 not shown)

  Planarity restraints: 1276
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 169 "   -0.030 5.00e-02 4.00e+02   4.54e-02 3.30e+00
        pdb=" N   PRO B 170 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO B 170 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 170 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A1126 "    0.029 5.00e-02 4.00e+02   4.37e-02 3.06e+00
        pdb=" N   PRO A1127 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A1127 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A1127 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 217 "   -0.028 5.00e-02 4.00e+02   4.22e-02 2.85e+00
        pdb=" N   PRO B 218 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO B 218 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 218 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1273 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.50: 73
        2.50 -     3.10: 5970
        3.10 -     3.70: 11576
        3.70 -     4.30: 17803
        4.30 -     4.90: 28676
  Nonbonded interactions: 64098
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 454 "
            pdb=" OG1 THR A 458 "
     model   vdw
     1.906 3.040
  nonbonded pdb=" O   LEU A 441 "
            pdb=" OH  TYR A 924 "
     model   vdw
     1.939 3.040
  nonbonded pdb=" O   LEU A 445 "
            pdb=" OH  TYR A1019 "
     model   vdw
     1.952 3.040
  nonbonded pdb=" O   ASN A 989 "
            pdb=" O   HOH A1301 "
     model   vdw
     1.991 3.040
  nonbonded pdb=" OH  TYR B 134 "
            pdb=" OG  SER B 177 "
     model   vdw
     1.995 3.040
  ... (remaining 64093 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.610
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.750
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:11.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7172
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      :  0.004   0.122   7553  Z= 0.269
  Angle     :  1.196  70.139  10263  Z= 0.456
  Chirality :  0.040   0.265   1158
  Planarity :  0.004   0.045   1273
  Dihedral  : 14.224 107.953   2784
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  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: -0.40 (0.29), residues: 893
  helix:  0.28 (0.25), residues: 459
  sheet:  1.06 (0.61), residues: 89
  loop : -1.31 (0.35), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 260 
 HIS   0.002   0.000   HIS A 965 
 PHE   0.019   0.001   PHE A1132 
 TYR   0.027   0.002   TYR A 968 
 ARG   0.006   0.000   ARG B 307 

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  981 GLU cc_start: 0.7977 (tt0) cc_final: 0.7447 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.8956
  time to fit residues: 130.5478
Evaluate side-chains
  96 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 45 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9980
   chunk 69 optimal weight:    5.9990
   chunk 26 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 80 optimal weight:    0.6980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 117 ASN
B 142 GLN
** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 211 ASN
B 254 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.170281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.134685 restraints weight = 9653.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.3697 rms_B_bonded: 2.55
r_work: 0.3581 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6835
moved from start:          0.1645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   7553  Z= 0.312
  Angle     :  0.974  29.922  10263  Z= 0.429
  Chirality :  0.047   0.254   1158
  Planarity :  0.005   0.039   1273
  Dihedral  :  8.553  75.053   1088
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 11.25 %
    Favored  : 86.22 %
  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: -0.10 (0.29), residues: 893
  helix:  0.52 (0.24), residues: 462
  sheet:  1.34 (0.61), residues: 88
  loop : -1.19 (0.36), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 260 
 HIS   0.003   0.001   HIS A 167 
 PHE   0.024   0.002   PHE A1132 
 TYR   0.017   0.002   TYR A1110 
 ARG   0.005   0.001   ARG B 307 

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 0.820 
Fit side-chains
REVERT: A  427 TYR cc_start: 0.7786 (t80) cc_final: 0.7493 (t80)
REVERT: A  875 MET cc_start: 0.5307 (tmm) cc_final: 0.4944 (tmm)
  outliers start: 20
  outliers final: 9
  residues processed: 117
  average time/residue: 0.7328
  time to fit residues: 94.1011
Evaluate side-chains
  104 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue 1133 THR
Chi-restraints excluded: chain A residue 1144 TYR
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  238 LYS
Chi-restraints excluded: chain B residue  295 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 76 optimal weight:    0.6980
   chunk 46 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   chunk 73 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
A 167 HIS
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1131 GLN
A1138 ASN
B 117 ASN
B 129 GLN
** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 235 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.170053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.134446 restraints weight = 9780.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.3695 rms_B_bonded: 2.54
r_work: 0.3579 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6822
moved from start:          0.2142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7553  Z= 0.283
  Angle     :  0.935  29.350  10263  Z= 0.402
  Chirality :  0.045   0.268   1158
  Planarity :  0.004   0.033   1273
  Dihedral  :  6.677  56.429   1088
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 14.54 %
    Favored  : 81.29 %
  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: -0.07 (0.29), residues: 893
  helix:  0.57 (0.24), residues: 465
  sheet:  1.34 (0.59), residues: 88
  loop : -1.25 (0.36), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 260 
 HIS   0.004   0.001   HIS A 167 
 PHE   0.022   0.002   PHE A1132 
 TYR   0.018   0.002   TYR A1110 
 ARG   0.004   0.001   ARG B 307 

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 113
  time to evaluate  : 0.829 
Fit side-chains
REVERT: A  427 TYR cc_start: 0.7753 (t80) cc_final: 0.7402 (t80)
REVERT: A  875 MET cc_start: 0.5194 (tmm) cc_final: 0.4755 (tmm)
REVERT: A 1057 GLN cc_start: 0.6774 (OUTLIER) cc_final: 0.6252 (mp10)
REVERT: A 1178 ILE cc_start: 0.7460 (pt) cc_final: 0.7216 (pp)
REVERT: B   29 ASP cc_start: 0.7398 (t0) cc_final: 0.7153 (t0)
REVERT: B  129 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8091 (tt0)
REVERT: B  228 LYS cc_start: 0.6901 (mmpt) cc_final: 0.6278 (mmpt)
  outliers start: 33
  outliers final: 11
  residues processed: 133
  average time/residue: 0.7345
  time to fit residues: 106.9313
Evaluate side-chains
  116 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  409 GLU
Chi-restraints excluded: chain A residue 1057 GLN
Chi-restraints excluded: chain A residue 1133 THR
Chi-restraints excluded: chain A residue 1144 TYR
Chi-restraints excluded: chain B residue   53 ILE
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  129 GLN
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  295 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 80 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 22 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 85 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 117 ASN
B 129 GLN
** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.170275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.134650 restraints weight = 9742.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3701 rms_B_bonded: 2.54
r_work: 0.3584 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6816
moved from start:          0.2356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7553  Z= 0.255
  Angle     :  0.921  29.495  10263  Z= 0.390
  Chirality :  0.044   0.266   1158
  Planarity :  0.004   0.033   1273
  Dihedral  :  6.088  56.529   1088
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 15.80 %
    Favored  : 80.03 %
  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: -0.00 (0.29), residues: 893
  helix:  0.66 (0.24), residues: 463
  sheet:  1.26 (0.59), residues: 88
  loop : -1.22 (0.36), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 260 
 HIS   0.002   0.001   HIS A 965 
 PHE   0.016   0.001   PHE B 179 
 TYR   0.018   0.002   TYR A 123 
 ARG   0.003   0.000   ARG A 412 

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 112
  time to evaluate  : 0.948 
Fit side-chains
REVERT: A  716 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6433 (pp20)
REVERT: A  875 MET cc_start: 0.5474 (tmm) cc_final: 0.5171 (tmm)
REVERT: A  983 TRP cc_start: 0.7839 (m100) cc_final: 0.7618 (m100)
REVERT: A 1057 GLN cc_start: 0.6624 (OUTLIER) cc_final: 0.6120 (mp10)
REVERT: A 1178 ILE cc_start: 0.7505 (pt) cc_final: 0.7252 (pp)
REVERT: B   29 ASP cc_start: 0.7389 (t0) cc_final: 0.7072 (t0)
REVERT: B  165 ASP cc_start: 0.7528 (p0) cc_final: 0.7149 (m-30)
REVERT: B  228 LYS cc_start: 0.6800 (mmpt) cc_final: 0.6122 (mmpt)
  outliers start: 33
  outliers final: 14
  residues processed: 135
  average time/residue: 0.7893
  time to fit residues: 116.4024
Evaluate side-chains
  118 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  409 GLU
Chi-restraints excluded: chain A residue  716 GLU
Chi-restraints excluded: chain A residue  869 THR
Chi-restraints excluded: chain A residue 1057 GLN
Chi-restraints excluded: chain A residue 1133 THR
Chi-restraints excluded: chain A residue 1144 TYR
Chi-restraints excluded: chain B residue   53 ILE
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  171 CYS
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  295 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 11 optimal weight:    0.2980
   chunk 1 optimal weight:    0.1980
   chunk 64 optimal weight:    4.9990
   chunk 5 optimal weight:    0.5980
   chunk 79 optimal weight:    0.0570
   chunk 29 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.3698

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

Flipped N/Q/H residues before XYZ refinement:
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1061 GLN
B 117 ASN
B 142 GLN
B 144 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.173116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.138059 restraints weight = 9618.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.3742 rms_B_bonded: 2.53
r_work: 0.3624 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6768
moved from start:          0.2651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7553  Z= 0.179
  Angle     :  0.894  29.502  10263  Z= 0.372
  Chirality :  0.042   0.257   1158
  Planarity :  0.004   0.034   1273
  Dihedral  :  5.589  56.357   1088
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 17.45 %
    Favored  : 78.76 %
  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:  0.20 (0.29), residues: 893
  helix:  0.83 (0.24), residues: 471
  sheet:  1.81 (0.61), residues: 82
  loop : -1.27 (0.36), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 207 
 HIS   0.002   0.000   HIS A 167 
 PHE   0.012   0.001   PHE A1072 
 TYR   0.019   0.001   TYR A1110 
 ARG   0.003   0.000   ARG B 262 

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 130
  time to evaluate  : 0.862 
Fit side-chains
REVERT: A  122 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6735 (pt)
REVERT: A  149 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7673 (mt)
REVERT: A  377 GLU cc_start: 0.6392 (mp0) cc_final: 0.6041 (mp0)
REVERT: A  427 TYR cc_start: 0.7788 (t80) cc_final: 0.7553 (t80)
REVERT: A  875 MET cc_start: 0.5074 (tmm) cc_final: 0.4765 (tmm)
REVERT: A  983 TRP cc_start: 0.7717 (m100) cc_final: 0.7491 (m100)
REVERT: A 1057 GLN cc_start: 0.6548 (OUTLIER) cc_final: 0.5951 (mp10)
REVERT: A 1114 MET cc_start: 0.7250 (ttp) cc_final: 0.7015 (ttm)
REVERT: B   29 ASP cc_start: 0.7404 (t0) cc_final: 0.7064 (t0)
REVERT: B  144 ASN cc_start: 0.6471 (OUTLIER) cc_final: 0.6066 (m-40)
REVERT: B  165 ASP cc_start: 0.7530 (p0) cc_final: 0.7235 (m-30)
REVERT: B  228 LYS cc_start: 0.6704 (mmpt) cc_final: 0.6056 (mmpt)
REVERT: B  248 ASP cc_start: 0.7628 (t70) cc_final: 0.7313 (t70)
REVERT: B  270 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.8083 (ptp-170)
  outliers start: 30
  outliers final: 14
  residues processed: 150
  average time/residue: 0.7306
  time to fit residues: 120.0959
Evaluate side-chains
  135 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  409 GLU
Chi-restraints excluded: chain A residue  869 THR
Chi-restraints excluded: chain A residue 1057 GLN
Chi-restraints excluded: chain A residue 1062 ASP
Chi-restraints excluded: chain A residue 1064 GLU
Chi-restraints excluded: chain A residue 1133 THR
Chi-restraints excluded: chain A residue 1144 TYR
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  144 ASN
Chi-restraints excluded: chain B residue  171 CYS
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  270 ARG
Chi-restraints excluded: chain B residue  295 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 88 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 7 optimal weight:   10.0000
   chunk 40 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0670
   chunk 74 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.7318

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

Flipped N/Q/H residues before XYZ refinement:
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 977 GLN
B 117 ASN
B 144 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.171469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.136157 restraints weight = 9624.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.3716 rms_B_bonded: 2.49
r_work: 0.3598 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6793
moved from start:          0.2744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7553  Z= 0.221
  Angle     :  0.906  29.506  10263  Z= 0.377
  Chirality :  0.043   0.263   1158
  Planarity :  0.004   0.037   1273
  Dihedral  :  5.527  56.382   1088
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 18.58 %
    Favored  : 77.50 %
  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:  0.26 (0.29), residues: 893
  helix:  0.86 (0.24), residues: 471
  sheet:  1.92 (0.60), residues: 82
  loop : -1.25 (0.36), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 260 
 HIS   0.002   0.001   HIS A 167 
 PHE   0.019   0.001   PHE B 179 
 TYR   0.019   0.002   TYR A1110 
 ARG   0.002   0.000   ARG A 412 

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 118
  time to evaluate  : 0.782 
Fit side-chains
REVERT: A  149 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7676 (mt)
REVERT: A  875 MET cc_start: 0.5102 (tmm) cc_final: 0.4529 (tmm)
REVERT: A  879 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6711 (mp)
REVERT: A  916 MET cc_start: 0.7382 (tmm) cc_final: 0.7181 (tpp)
REVERT: A  983 TRP cc_start: 0.7796 (m100) cc_final: 0.7536 (m100)
REVERT: A 1057 GLN cc_start: 0.6661 (OUTLIER) cc_final: 0.6080 (mp10)
REVERT: A 1114 MET cc_start: 0.7244 (ttp) cc_final: 0.6992 (ttm)
REVERT: B   29 ASP cc_start: 0.7434 (t0) cc_final: 0.7078 (t0)
REVERT: B  165 ASP cc_start: 0.7609 (p0) cc_final: 0.7182 (m-30)
REVERT: B  228 LYS cc_start: 0.6722 (mmpt) cc_final: 0.6066 (mmpt)
REVERT: B  270 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.8117 (ptp-170)
  outliers start: 31
  outliers final: 18
  residues processed: 138
  average time/residue: 0.7860
  time to fit residues: 118.2174
Evaluate side-chains
  136 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  409 GLU
Chi-restraints excluded: chain A residue  869 THR
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue 1013 LEU
Chi-restraints excluded: chain A residue 1057 GLN
Chi-restraints excluded: chain A residue 1062 ASP
Chi-restraints excluded: chain A residue 1133 THR
Chi-restraints excluded: chain A residue 1144 TYR
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  171 CYS
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  270 ARG
Chi-restraints excluded: chain B residue  295 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 24 optimal weight:   20.0000
   chunk 76 optimal weight:    5.9990
   chunk 32 optimal weight:    0.4980
   chunk 52 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 88 optimal weight:    0.7980
   chunk 12 optimal weight:    4.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 167 HIS
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 977 GLN
B 117 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.170997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.135450 restraints weight = 9559.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.3707 rms_B_bonded: 2.49
r_work: 0.3589 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6802
moved from start:          0.2846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7553  Z= 0.222
  Angle     :  0.907  29.517  10263  Z= 0.379
  Chirality :  0.043   0.265   1158
  Planarity :  0.004   0.038   1273
  Dihedral  :  5.470  56.405   1088
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 18.96 %
    Favored  : 76.99 %
  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 (0.29), residues: 893
  helix:  0.93 (0.24), residues: 466
  sheet:  1.85 (0.59), residues: 82
  loop : -1.18 (0.36), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 207 
 HIS   0.002   0.001   HIS A 359 
 PHE   0.019   0.001   PHE B 179 
 TYR   0.021   0.002   TYR A1110 
 ARG   0.003   0.000   ARG A 118 

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 115
  time to evaluate  : 0.814 
Fit side-chains
REVERT: A  377 GLU cc_start: 0.6893 (mp0) cc_final: 0.6542 (mp0)
REVERT: A  875 MET cc_start: 0.5193 (tmm) cc_final: 0.4630 (tmm)
REVERT: A  879 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6970 (mp)
REVERT: A  916 MET cc_start: 0.7408 (tmm) cc_final: 0.7121 (tmm)
REVERT: A  983 TRP cc_start: 0.7834 (m100) cc_final: 0.7596 (m100)
REVERT: A 1057 GLN cc_start: 0.6638 (OUTLIER) cc_final: 0.6078 (mp10)
REVERT: A 1106 SER cc_start: 0.8183 (m) cc_final: 0.7971 (m)
REVERT: A 1114 MET cc_start: 0.7296 (ttp) cc_final: 0.7026 (ttm)
REVERT: A 1144 TYR cc_start: 0.8293 (OUTLIER) cc_final: 0.7789 (m-80)
REVERT: B   29 ASP cc_start: 0.7438 (t0) cc_final: 0.7090 (t0)
REVERT: B  228 LYS cc_start: 0.6690 (mmpt) cc_final: 0.6069 (mmpt)
REVERT: B  270 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.8129 (ptp-170)
  outliers start: 32
  outliers final: 17
  residues processed: 139
  average time/residue: 0.7691
  time to fit residues: 117.0846
Evaluate side-chains
  130 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 109
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  167 HIS
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  409 GLU
Chi-restraints excluded: chain A residue  869 THR
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue 1057 GLN
Chi-restraints excluded: chain A residue 1062 ASP
Chi-restraints excluded: chain A residue 1133 THR
Chi-restraints excluded: chain A residue 1144 TYR
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  171 CYS
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  270 ARG
Chi-restraints excluded: chain B residue  295 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 59 optimal weight:    0.3980
   chunk 62 optimal weight:    0.8980
   chunk 24 optimal weight:    5.9990
   chunk 31 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 86 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   chunk 22 optimal weight:    0.0170
   chunk 68 optimal weight:    0.4980
   overall best weight:    0.5018

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

Flipped N/Q/H residues before XYZ refinement:
A 167 HIS
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 977 GLN
B 117 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.171684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.136366 restraints weight = 9714.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.3721 rms_B_bonded: 2.51
r_work: 0.3603 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6788
moved from start:          0.2928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7553  Z= 0.195
  Angle     :  0.899  29.469  10263  Z= 0.374
  Chirality :  0.042   0.262   1158
  Planarity :  0.004   0.039   1273
  Dihedral  :  5.396  56.344   1088
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 19.22 %
    Favored  : 76.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.22 (0.29), residues: 893
  helix:  0.89 (0.24), residues: 473
  sheet:  1.78 (0.59), residues: 82
  loop : -1.33 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 207 
 HIS   0.002   0.000   HIS A 359 
 PHE   0.015   0.001   PHE B 179 
 TYR   0.021   0.002   TYR A1110 
 ARG   0.002   0.000   ARG B 262 

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 111
  time to evaluate  : 0.773 
Fit side-chains
REVERT: A  875 MET cc_start: 0.5252 (OUTLIER) cc_final: 0.4685 (tmm)
REVERT: A  879 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.7044 (mp)
REVERT: A  916 MET cc_start: 0.7386 (tmm) cc_final: 0.7135 (tpp)
REVERT: A  983 TRP cc_start: 0.7812 (m100) cc_final: 0.7567 (m100)
REVERT: A 1057 GLN cc_start: 0.6612 (OUTLIER) cc_final: 0.6047 (mp10)
REVERT: A 1106 SER cc_start: 0.8157 (m) cc_final: 0.7947 (m)
REVERT: A 1114 MET cc_start: 0.7266 (ttp) cc_final: 0.6973 (ttm)
REVERT: A 1144 TYR cc_start: 0.8251 (OUTLIER) cc_final: 0.7731 (m-80)
REVERT: B   29 ASP cc_start: 0.7433 (t0) cc_final: 0.7104 (t0)
REVERT: B  165 ASP cc_start: 0.7346 (p0) cc_final: 0.6992 (m-30)
REVERT: B  202 LYS cc_start: 0.7276 (tppt) cc_final: 0.7057 (tptt)
REVERT: B  228 LYS cc_start: 0.6621 (mmpt) cc_final: 0.6077 (mmpt)
REVERT: B  270 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.8105 (ptp-170)
  outliers start: 31
  outliers final: 16
  residues processed: 134
  average time/residue: 0.7389
  time to fit residues: 108.5379
Evaluate side-chains
  132 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  167 HIS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  409 GLU
Chi-restraints excluded: chain A residue  869 THR
Chi-restraints excluded: chain A residue  875 MET
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue 1057 GLN
Chi-restraints excluded: chain A residue 1062 ASP
Chi-restraints excluded: chain A residue 1133 THR
Chi-restraints excluded: chain A residue 1144 TYR
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  171 CYS
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  270 ARG
Chi-restraints excluded: chain B residue  295 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 84 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 54 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0040
   chunk 0 optimal weight:    6.9990
   chunk 21 optimal weight:    6.9990
   chunk 58 optimal weight:    0.4980
   chunk 47 optimal weight:    0.5980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.4992

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

Flipped N/Q/H residues before XYZ refinement:
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 977 GLN
B 117 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.170959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.135779 restraints weight = 9706.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3728 rms_B_bonded: 2.48
r_work: 0.3610 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6806
moved from start:          0.3014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7553  Z= 0.191
  Angle     :  0.898  29.476  10263  Z= 0.372
  Chirality :  0.042   0.262   1158
  Planarity :  0.004   0.039   1273
  Dihedral  :  5.340  56.323   1088
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 19.85 %
    Favored  : 76.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.29), residues: 893
  helix:  0.92 (0.24), residues: 473
  sheet:  1.79 (0.59), residues: 82
  loop : -1.36 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 207 
 HIS   0.003   0.001   HIS A 359 
 PHE   0.018   0.001   PHE A 345 
 TYR   0.021   0.001   TYR A1110 
 ARG   0.004   0.000   ARG A 166 

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 113
  time to evaluate  : 0.775 
Fit side-chains
REVERT: A  716 GLU cc_start: 0.6440 (pp20) cc_final: 0.6135 (pm20)
REVERT: A  875 MET cc_start: 0.5295 (OUTLIER) cc_final: 0.4735 (tmm)
REVERT: A  879 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6875 (mp)
REVERT: A  916 MET cc_start: 0.7370 (tmm) cc_final: 0.7136 (tpp)
REVERT: A  983 TRP cc_start: 0.7807 (m100) cc_final: 0.7529 (m100)
REVERT: A 1057 GLN cc_start: 0.6665 (OUTLIER) cc_final: 0.6033 (mp10)
REVERT: A 1106 SER cc_start: 0.8162 (m) cc_final: 0.7955 (m)
REVERT: A 1114 MET cc_start: 0.7262 (ttp) cc_final: 0.6957 (ttm)
REVERT: A 1144 TYR cc_start: 0.8261 (OUTLIER) cc_final: 0.7728 (m-80)
REVERT: B   29 ASP cc_start: 0.7442 (t0) cc_final: 0.7125 (t0)
REVERT: B  202 LYS cc_start: 0.7219 (tppt) cc_final: 0.6980 (tptt)
REVERT: B  228 LYS cc_start: 0.6517 (mmpt) cc_final: 0.6005 (mmpt)
REVERT: B  270 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.8054 (ptp-170)
  outliers start: 30
  outliers final: 16
  residues processed: 136
  average time/residue: 0.7736
  time to fit residues: 114.8832
Evaluate side-chains
  130 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 109
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  409 GLU
Chi-restraints excluded: chain A residue  869 THR
Chi-restraints excluded: chain A residue  875 MET
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue 1057 GLN
Chi-restraints excluded: chain A residue 1062 ASP
Chi-restraints excluded: chain A residue 1133 THR
Chi-restraints excluded: chain A residue 1144 TYR
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue  171 CYS
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  270 ARG
Chi-restraints excluded: chain B residue  295 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 58 optimal weight:    0.3980
   chunk 30 optimal weight:    5.9990
   chunk 40 optimal weight:    0.0670
   chunk 55 optimal weight:    0.6980
   chunk 10 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 84 optimal weight:    0.7980
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 977 GLN
B 117 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.172022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.136877 restraints weight = 9756.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 2.51
r_work: 0.3607 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6800
moved from start:          0.3035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7553  Z= 0.200
  Angle     :  0.905  29.493  10263  Z= 0.378
  Chirality :  0.043   0.262   1158
  Planarity :  0.004   0.039   1273
  Dihedral  :  5.326  56.328   1088
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 20.48 %
    Favored  : 76.23 %
  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:  0.27 (0.29), residues: 893
  helix:  0.96 (0.24), residues: 473
  sheet:  1.80 (0.59), residues: 82
  loop : -1.36 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 207 
 HIS   0.003   0.001   HIS A 359 
 PHE   0.017   0.001   PHE A 345 
 TYR   0.024   0.002   TYR A 123 
 ARG   0.002   0.000   ARG A 412 

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 112
  time to evaluate  : 0.789 
Fit side-chains
REVERT: A  716 GLU cc_start: 0.6426 (pp20) cc_final: 0.6134 (pm20)
REVERT: A  875 MET cc_start: 0.5433 (OUTLIER) cc_final: 0.4836 (tmm)
REVERT: A  879 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6866 (mp)
REVERT: A  983 TRP cc_start: 0.7793 (m100) cc_final: 0.7548 (m100)
REVERT: A 1106 SER cc_start: 0.8153 (m) cc_final: 0.7946 (m)
REVERT: A 1114 MET cc_start: 0.7250 (ttp) cc_final: 0.6949 (ttm)
REVERT: A 1144 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.7719 (m-80)
REVERT: B   29 ASP cc_start: 0.7432 (t0) cc_final: 0.7114 (t0)
REVERT: B  228 LYS cc_start: 0.6521 (mmpt) cc_final: 0.5998 (mmpt)
REVERT: B  270 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.8041 (ptp-170)
  outliers start: 26
  outliers final: 16
  residues processed: 129
  average time/residue: 0.7709
  time to fit residues: 108.4710
Evaluate side-chains
  130 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  409 GLU
Chi-restraints excluded: chain A residue  869 THR
Chi-restraints excluded: chain A residue  875 MET
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue 1062 ASP
Chi-restraints excluded: chain A residue 1133 THR
Chi-restraints excluded: chain A residue 1144 TYR
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  171 CYS
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  270 ARG
Chi-restraints excluded: chain B residue  295 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 21 optimal weight:    0.0030
   chunk 85 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   chunk 57 optimal weight:    0.0870
   chunk 42 optimal weight:    0.5980
   chunk 72 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0970
   chunk 7 optimal weight:    7.9990
   chunk 23 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.2766

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

Flipped N/Q/H residues before XYZ refinement:
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 977 GLN
B 117 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.173944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.139500 restraints weight = 9639.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3756 rms_B_bonded: 2.48
r_work: 0.3638 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6755
moved from start:          0.3221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7553  Z= 0.177
  Angle     :  0.911  29.563  10263  Z= 0.380
  Chirality :  0.042   0.257   1158
  Planarity :  0.004   0.040   1273
  Dihedral  :  5.249  56.239   1088
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 20.86 %
    Favored  : 76.49 %
  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 (0.29), residues: 893
  helix:  1.07 (0.24), residues: 473
  sheet:  1.84 (0.59), residues: 82
  loop : -1.41 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 207 
 HIS   0.004   0.000   HIS A 359 
 PHE   0.012   0.001   PHE B 179 
 TYR   0.041   0.002   TYR A 123 
 ARG   0.003   0.000   ARG A 867 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5392.46 seconds
wall clock time: 95 minutes 56.54 seconds (5756.54 seconds total)