Starting phenix.real_space_refine
on Sun Apr 27 17:55:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9m0d_63543/04_2025/9m0d_63543.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9m0d_63543/04_2025/9m0d_63543.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.41
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9m0d_63543/04_2025/9m0d_63543.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9m0d_63543/04_2025/9m0d_63543.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9m0d_63543/04_2025/9m0d_63543.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9m0d_63543/04_2025/9m0d_63543.cif"
  }
  resolution = 3.41
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.039
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 35 atoms to isotropic.
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
     P       3      5.49       5
     S      13      5.16       5
     C    3928      2.51       5
     N    1157      2.21       5
     O    1211      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 6312
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "R"
      Number of atoms: 1293
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1293
          Classifications: {'peptide': 254}
          Incomplete info: {'truncation_to_alanine': 216}
          Link IDs: {'PTRANS': 6, 'TRANS': 247}
          Chain breaks: 6
          Unresolved chain link angles: 6
          Unresolved non-hydrogen bonds: 802
          Unresolved non-hydrogen angles: 1057
          Unresolved non-hydrogen dihedrals: 677
          Unresolved non-hydrogen chiralities: 99
          Planarities with less than four sites: {'GLN:plan1': 3, 'TPO:plan-1': 1, 'ARG:plan': 11, 'TYR:plan': 16, 'ASN:plan1': 11, 'TRP:plan': 4, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 4, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 414
    Chain: "B"
      Number of atoms: 2389
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 361, 2389
          Classifications: {'peptide': 361}
          Incomplete info: {'truncation_to_alanine': 134}
          Link IDs: {'PTRANS': 28, 'TRANS': 332}
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 483
          Unresolved non-hydrogen angles: 602
          Unresolved non-hydrogen dihedrals: 387
          Unresolved non-hydrogen chiralities: 41
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 21, 'ARG:plan': 13}
          Unresolved non-hydrogen planarities: 263
    Chain: "D"
      Number of atoms: 1371
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1371
          Classifications: {'peptide': 219}
          Incomplete info: {'truncation_to_alanine': 97}
          Link IDs: {'PTRANS': 11, 'TRANS': 207}
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 286
          Unresolved non-hydrogen angles: 365
          Unresolved non-hydrogen dihedrals: 238
          Unresolved non-hydrogen chiralities: 31
          Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 122
    Chain: "Q"
      Number of atoms: 1259
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 1259
          Classifications: {'peptide': 210}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 119}
          Link IDs: {'PTRANS': 11, 'TRANS': 198}
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 368
          Unresolved non-hydrogen angles: 465
          Unresolved non-hydrogen dihedrals: 302
          Unresolved non-hydrogen chiralities: 36
          Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 179
  Time building chain proxies: 5.12, per 1000 atoms: 0.81
  Number of scatterers: 6312
  At special positions: 0
  Unit cell: (77.9, 95.94, 159.08, 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)
     S      13     16.00
     P       3     15.00
     O    1211      8.00
     N    1157      7.00
     C    3928      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  45 " - pdb=" SG  CYS D 119 " distance=2.03
    Simple disulfide: pdb=" SG  CYS Q  44 " - pdb=" SG  CYS Q 109 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.86
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1974

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 16 sheets defined
      26.6% alpha, 21.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.07
  Creating SS restraints...
    Processing helix  chain 'R' and resid 60 through 90
      removed outlier: 4.114A  pdb=" N   ARG R  90 " --> pdb=" O   PHE R  86 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 100 through 129
      Proline residue:  R 121  - end of helix
    Processing helix  chain 'R' and resid 141 through 171
    Processing helix  chain 'R' and resid 184 through 201
    Processing helix  chain 'R' and resid 230 through 265
      Proline residue:  R 248  - end of helix
      removed outlier: 4.001A  pdb=" N   VAL R 265 " --> pdb=" O   ASN R 261 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 300 through 327
      Proline residue:  R 318  - end of helix
    Processing helix  chain 'R' and resid 335 through 367
      Proline residue:  R 361  - end of helix
      removed outlier: 4.099A  pdb=" N   VAL R 367 " --> pdb=" O   LEU R 363 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 368 through 382
      removed outlier: 3.732A  pdb=" N   LEU R 382 " --> pdb=" O   THR R 378 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 96 through 108
      removed outlier: 3.652A  pdb=" N   GLN B 100 " --> pdb=" O   LEU B  96 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ARG B 102 " --> pdb=" O   ARG B  98 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LYS B 105 " --> pdb=" O   GLU B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 162
      removed outlier: 3.873A  pdb=" N   SER B 162 " --> pdb=" O   LYS B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 192
    Processing helix  chain 'D' and resid 110 through 114
    Processing helix  chain 'D' and resid 186 through 188
      No H-bonds generated for 'chain 'D' and resid 186 through 188'
    Processing helix  chain 'Q' and resid 100 through 104
    Processing helix  chain 'Q' and resid 142 through 149
    Processing helix  chain 'Q' and resid 170 through 174
      removed outlier: 3.533A  pdb=" N   ASN Q 173 " --> pdb=" O   LYS Q 170 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 204 through 210
      removed outlier: 3.580A  pdb=" N   GLU Q 208 " --> pdb=" O   LYS Q 204 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 8 through 11
    Processing sheet with id=AA2, first strand: chain 'B' and resid 75 through 77
    Processing sheet with id=AA3, first strand: chain 'B' and resid 75 through 77
      removed outlier: 3.857A  pdb=" N   TYR B 143 " --> pdb=" O   ILE B 167 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ILE B 167 " --> pdb=" O   TYR B 143 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 185 through 187
      removed outlier: 3.950A  pdb=" N   ARG B 187 " --> pdb=" O   LEU B 196 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   LEU B 196 " --> pdb=" O   ARG B 187 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   HIS B 197 " --> pdb=" O   THR B 220 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   VAL B 217 " --> pdb=" O   LYS B 269 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   SER B 265 " --> pdb=" O   ASN B 221 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 246 through 257
      removed outlier: 6.538A  pdb=" N   VAL B 234 " --> pdb=" O   VAL B 252 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   MET B 254 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   ILE B 232 " --> pdb=" O   MET B 254 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   GLU B 256 " --> pdb=" O   ILE B 230 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   ILE B 230 " --> pdb=" O   GLU B 256 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LYS B 229 " --> pdb=" O   VAL B 327 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   LYS B 231 " --> pdb=" O   LYS B 325 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   TYR B 320 " --> pdb=" O   PHE B 348 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 29 through 30
    Processing sheet with id=AA7, first strand: chain 'D' and resid 33 through 35
      removed outlier: 6.515A  pdb=" N   ILE D  57 " --> pdb=" O   SER D  73 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   SER D  73 " --> pdb=" O   ILE D  57 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   TRP D  59 " --> pdb=" O   VAL D  71 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 33 through 35
      removed outlier: 4.134A  pdb=" N   TYR D 132 " --> pdb=" O   ARG D 121 " (cutoff:3.500A)
      removed outlier: 8.066A  pdb=" N   ARG D 123 " --> pdb=" O   LEU D 130 " (cutoff:3.500A)
      removed outlier: 8.139A  pdb=" N   LEU D 130 " --> pdb=" O   ARG D 123 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 152 through 154
      removed outlier: 4.380A  pdb=" N   GLY D 169 " --> pdb=" O   LEU D 154 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 180 through 184
    Processing sheet with id=AB2, first strand: chain 'D' and resid 199 through 200
    Processing sheet with id=AB3, first strand: chain 'Q' and resid 26 through 27
    Processing sheet with id=AB4, first strand: chain 'Q' and resid 31 through 33
      removed outlier: 6.387A  pdb=" N   VAL Q  54 " --> pdb=" O   TYR Q  70 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   TYR Q  70 " --> pdb=" O   VAL Q  54 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   TRP Q  56 " --> pdb=" O   LEU Q  68 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'Q' and resid 84 through 85
    Processing sheet with id=AB6, first strand: chain 'Q' and resid 137 through 138
      removed outlier: 6.304A  pdb=" N   TYR Q 194 " --> pdb=" O   ASN Q 159 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'Q' and resid 150 through 151

    334 hydrogen bonds defined for protein.
    900 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: 1.91

  Time building geometry restraints manager: 2.17 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2227
        1.34 -     1.46: 1022
        1.46 -     1.58: 3135
        1.58 -     1.70: 3
        1.70 -     1.82: 18
  Bond restraints: 6405
  Sorted by residual:
  bond pdb=" OG1 TPO R 407 "
       pdb=" P   TPO R 407 "
    ideal  model  delta    sigma   weight residual
    1.717  1.591  0.126 2.00e-02 2.50e+03 3.96e+01
  bond pdb=" O3P SEP R 409 "
       pdb=" P   SEP R 409 "
    ideal  model  delta    sigma   weight residual
    1.610  1.511  0.099 2.00e-02 2.50e+03 2.45e+01
  bond pdb=" O2P SEP R 410 "
       pdb=" P   SEP R 410 "
    ideal  model  delta    sigma   weight residual
    1.610  1.512  0.098 2.00e-02 2.50e+03 2.40e+01
  bond pdb=" O3P SEP R 410 "
       pdb=" P   SEP R 410 "
    ideal  model  delta    sigma   weight residual
    1.610  1.513  0.097 2.00e-02 2.50e+03 2.35e+01
  bond pdb=" O2P SEP R 409 "
       pdb=" P   SEP R 409 "
    ideal  model  delta    sigma   weight residual
    1.610  1.514  0.096 2.00e-02 2.50e+03 2.32e+01
  ... (remaining 6400 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 8622
        1.80 -     3.59: 184
        3.59 -     5.39: 27
        5.39 -     7.18: 6
        7.18 -     8.98: 4
  Bond angle restraints: 8843
  Sorted by residual:
  angle pdb=" C   SEP R 409 "
        pdb=" N   SEP R 410 "
        pdb=" CA  SEP R 410 "
      ideal   model   delta    sigma   weight residual
     121.70  114.99    6.71 1.80e+00 3.09e-01 1.39e+01
  angle pdb=" CA  PRO D  37 "
        pdb=" N   PRO D  37 "
        pdb=" CD  PRO D  37 "
      ideal   model   delta    sigma   weight residual
     112.00  107.55    4.45 1.40e+00 5.10e-01 1.01e+01
  angle pdb=" N   PRO D  37 "
        pdb=" CD  PRO D  37 "
        pdb=" CG  PRO D  37 "
      ideal   model   delta    sigma   weight residual
     103.20   98.81    4.39 1.50e+00 4.44e-01 8.55e+00
  angle pdb=" CB  SEP R 409 "
        pdb=" OG  SEP R 409 "
        pdb=" P   SEP R 409 "
      ideal   model   delta    sigma   weight residual
     110.00  118.77   -8.77 3.00e+00 1.11e-01 8.54e+00
  angle pdb=" N   SEP R 409 "
        pdb=" CA  SEP R 409 "
        pdb=" C   SEP R 409 "
      ideal   model   delta    sigma   weight residual
     111.20  103.25    7.95 2.80e+00 1.28e-01 8.07e+00
  ... (remaining 8838 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 3512
       16.01 -    32.02: 174
       32.02 -    48.03: 43
       48.03 -    64.04: 20
       64.04 -    80.05: 6
  Dihedral angle restraints: 3755
    sinusoidal: 719
      harmonic: 3036
  Sorted by residual:
  dihedral pdb=" CD  ARG B   6 "
           pdb=" NE  ARG B   6 "
           pdb=" CZ  ARG B   6 "
           pdb=" NH1 ARG B   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   46.15  -46.15     1      1.00e+01 1.00e-02 2.95e+01
  dihedral pdb=" CB  CYS D  45 "
           pdb=" SG  CYS D  45 "
           pdb=" SG  CYS D 119 "
           pdb=" CB  CYS D 119 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -127.42   41.42     1      1.00e+01 1.00e-02 2.40e+01
  dihedral pdb=" CA  GLN D 105 "
           pdb=" C   GLN D 105 "
           pdb=" N   MET D 106 "
           pdb=" CA  MET D 106 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.04   15.96     0      5.00e+00 4.00e-02 1.02e+01
  ... (remaining 3752 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 782
       0.039 -    0.078: 227
       0.078 -    0.117: 84
       0.117 -    0.156: 10
       0.156 -    0.195: 2
  Chirality restraints: 1105
  Sorted by residual:
  chirality pdb=" CG  LEU D 104 "
            pdb=" CB  LEU D 104 "
            pdb=" CD1 LEU D 104 "
            pdb=" CD2 LEU D 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.78    0.19 2.00e-01 2.50e+01 9.47e-01
  chirality pdb=" CA  SEP R 410 "
            pdb=" N   SEP R 410 "
            pdb=" C   SEP R 410 "
            pdb=" CB  SEP R 410 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.50    2.35    0.16 2.00e-01 2.50e+01 6.17e-01
  chirality pdb=" CB  TPO R 407 "
            pdb=" CA  TPO R 407 "
            pdb=" OG1 TPO R 407 "
            pdb=" CG2 TPO R 407 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.64   -0.16 2.00e-01 2.50e+01 6.04e-01
  ... (remaining 1102 not shown)

  Planarity restraints: 1193
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B   6 "   -0.785 9.50e-02 1.11e+02   3.52e-01 7.53e+01
        pdb=" NE  ARG B   6 "    0.048 2.00e-02 2.50e+03
        pdb=" CZ  ARG B   6 "    0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG B   6 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG B   6 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE D 196 "    0.041 5.00e-02 4.00e+02   6.20e-02 6.16e+00
        pdb=" N   PRO D 197 "   -0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO D 197 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO D 197 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 180 "   -0.038 5.00e-02 4.00e+02   5.87e-02 5.52e+00
        pdb=" N   PRO B 181 "    0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO B 181 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 181 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 1190 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 65
        2.63 -     3.20: 5755
        3.20 -     3.77: 9505
        3.77 -     4.33: 11860
        4.33 -     4.90: 20645
  Nonbonded interactions: 47830
  Sorted by model distance:
  nonbonded pdb=" O   PRO B 123 "
            pdb=" OH  TYR B 143 "
     model   vdw
     2.064 3.040
  nonbonded pdb=" CG1 VAL B  36 "
            pdb=" CB  PHE B 116 "
     model   vdw
     2.100 3.860
  nonbonded pdb=" O   ALA B 262 "
            pdb=" OG  SER B 265 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   ASP Q 103 "
            pdb=" OH  TYR Q 107 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" O   ILE R 359 "
            pdb=" N   LEU R 363 "
     model   vdw
     2.261 3.120
  ... (remaining 47825 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     21.140
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7250
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      :  0.005   0.126   6407  Z= 0.243
  Angle     :  0.664   8.980   8847  Z= 0.370
  Chirality :  0.042   0.195   1105
  Planarity :  0.011   0.352   1193
  Dihedral  : 12.641  80.051   1775
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 20.18 %
    Favored  : 79.24 %
  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: -1.04 (0.27), residues: 1018
  helix:  3.08 (0.31), residues: 237
  sheet: -2.03 (0.30), residues: 281
  loop : -1.78 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  70 
 HIS   0.004   0.001   HIS B 352 
 PHE   0.010   0.001   PHE B 267 
 TYR   0.009   0.001   TYR D 127 
 ARG   0.004   0.001   ARG D  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19159 (  325)
  hydrogen bonds       : angle       8.61366 (  900)
  SS BOND              : bond        0.00362 (    2)
  SS BOND              : angle       0.99718 (    4)
  covalent geometry    : bond        0.00479 ( 6405)
  covalent geometry    : angle       0.66340 ( 8843)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.669 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 55
  average time/residue: 0.1575
  time to fit residues: 12.3745
Evaluate side-chains
  53 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 51
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  411 ASN
Chi-restraints excluded: chain B residue  289 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    0.0370
   chunk 78 optimal weight:    0.2980
   chunk 43 optimal weight:    0.4980
   chunk 26 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 80 optimal weight:   50.0000
   chunk 31 optimal weight:    0.0670
   chunk 49 optimal weight:    0.0980
   chunk 60 optimal weight:    0.5980
   chunk 93 optimal weight:    5.9990
   overall best weight:    0.1996

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

Flipped N/Q/H residues before XYZ refinement:
R 406 HIS
B 280 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4609 r_free = 0.4609 target = 0.211945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.187306 restraints weight = 8625.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.4360 rms_B_bonded: 1.25
r_work: 0.4177 rms_B_bonded: 1.44 restraints_weight: 0.5000
r_work: 0.4012 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.4012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.1059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   6407  Z= 0.101
  Angle     :  0.495   6.642   8847  Z= 0.269
  Chirality :  0.042   0.132   1105
  Planarity :  0.004   0.053   1193
  Dihedral  :  5.699  83.483   1087
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 17.25 %
    Favored  : 78.65 %
  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: -0.79 (0.27), residues: 1018
  helix:  3.00 (0.30), residues: 243
  sheet: -1.82 (0.33), residues: 255
  loop : -1.61 (0.27), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  70 
 HIS   0.004   0.001   HIS D  58 
 PHE   0.011   0.001   PHE Q 160 
 TYR   0.010   0.001   TYR B 143 
 ARG   0.014   0.001   ARG B   6 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03908 (  325)
  hydrogen bonds       : angle       5.57010 (  900)
  SS BOND              : bond        0.00122 (    2)
  SS BOND              : angle       0.96872 (    4)
  covalent geometry    : bond        0.00196 ( 6405)
  covalent geometry    : angle       0.49451 ( 8843)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 48
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
  outliers start: 14
  outliers final: 11
  residues processed: 57
  average time/residue: 0.1556
  time to fit residues: 12.9039
Evaluate side-chains
  55 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  411 ASN
Chi-restraints excluded: chain B residue    6 ARG
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   25 ASP
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain D residue   48 SER
Chi-restraints excluded: chain D residue  180 VAL
Chi-restraints excluded: chain D residue  228 VAL
Chi-restraints excluded: chain Q residue   30 SER
Chi-restraints excluded: chain Q residue   99 LEU
Chi-restraints excluded: chain Q residue  144 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 0 optimal weight:   50.0000
   chunk 23 optimal weight:   50.0000
   chunk 62 optimal weight:    2.9990
   chunk 17 optimal weight:    8.9990
   chunk 49 optimal weight:    4.9990
   chunk 61 optimal weight:    0.0770
   chunk 40 optimal weight:   20.0000
   chunk 2 optimal weight:   50.0000
   chunk 6 optimal weight:   40.0000
   chunk 83 optimal weight:    1.9990
   overall best weight:    2.2144

-------------------------------------------------------------------------------
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 = 0.4249 r_free = 0.4249 target = 0.183999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.146299 restraints weight = 8873.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3810 rms_B_bonded: 2.16
r_work: 0.3609 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3495 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.1621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   6407  Z= 0.286
  Angle     :  0.638   7.932   8847  Z= 0.341
  Chirality :  0.045   0.139   1105
  Planarity :  0.005   0.053   1193
  Dihedral  :  6.032  79.181   1085
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  5.85 %
    Allowed  : 17.25 %
    Favored  : 76.90 %
  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: -1.02 (0.27), residues: 1018
  helix:  3.39 (0.31), residues: 244
  sheet: -2.16 (0.30), residues: 268
  loop : -1.95 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.004   TRP D  70 
 HIS   0.007   0.002   HIS D  58 
 PHE   0.023   0.002   PHE Q  92 
 TYR   0.019   0.002   TYR Q 112 
 ARG   0.005   0.001   ARG B 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04147 (  325)
  hydrogen bonds       : angle       5.70618 (  900)
  SS BOND              : bond        0.00621 (    2)
  SS BOND              : angle       1.18858 (    4)
  covalent geometry    : bond        0.00645 ( 6405)
  covalent geometry    : angle       0.63765 ( 8843)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 50
  time to evaluate  : 0.755 
Fit side-chains
REVERT: B  112 TYR cc_start: 0.7785 (m-80) cc_final: 0.7409 (m-80)
REVERT: B  142 ASP cc_start: 0.8024 (p0) cc_final: 0.7822 (p0)
  outliers start: 20
  outliers final: 17
  residues processed: 62
  average time/residue: 0.1245
  time to fit residues: 11.8205
Evaluate side-chains
  64 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 47
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  411 ASN
Chi-restraints excluded: chain B residue   25 ASP
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  289 ASP
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   48 SER
Chi-restraints excluded: chain D residue   71 VAL
Chi-restraints excluded: chain D residue  180 VAL
Chi-restraints excluded: chain D residue  228 VAL
Chi-restraints excluded: chain Q residue   30 SER
Chi-restraints excluded: chain Q residue   79 VAL
Chi-restraints excluded: chain Q residue  144 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 73 optimal weight:    6.9990
   chunk 86 optimal weight:    0.0770
   chunk 8 optimal weight:   50.0000
   chunk 59 optimal weight:    0.9980
   chunk 85 optimal weight:    0.8980
   chunk 76 optimal weight:    0.7980
   chunk 63 optimal weight:    0.7980
   chunk 13 optimal weight:   50.0000
   chunk 80 optimal weight:   40.0000
   chunk 40 optimal weight:    0.4980
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.6138

-------------------------------------------------------------------------------
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 = 0.4552 r_free = 0.4552 target = 0.205822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.182203 restraints weight = 8745.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.4316 rms_B_bonded: 1.34
r_work: 0.4073 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3889 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.1745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6407  Z= 0.121
  Angle     :  0.495   6.609   8847  Z= 0.266
  Chirality :  0.042   0.135   1105
  Planarity :  0.004   0.046   1193
  Dihedral  :  5.793  88.391   1085
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 19.30 %
    Favored  : 76.02 %
  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: -0.88 (0.27), residues: 1018
  helix:  3.48 (0.30), residues: 242
  sheet: -2.08 (0.29), residues: 276
  loop : -1.80 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D  70 
 HIS   0.004   0.001   HIS D  58 
 PHE   0.013   0.001   PHE D 176 
 TYR   0.010   0.001   TYR D 127 
 ARG   0.003   0.000   ARG B 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03358 (  325)
  hydrogen bonds       : angle       4.95622 (  900)
  SS BOND              : bond        0.00388 (    2)
  SS BOND              : angle       1.07059 (    4)
  covalent geometry    : bond        0.00260 ( 6405)
  covalent geometry    : angle       0.49480 ( 8843)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 50
  time to evaluate  : 0.704 
Fit side-chains
   revert: symmetry clash
  outliers start: 16
  outliers final: 14
  residues processed: 61
  average time/residue: 0.1678
  time to fit residues: 14.3935
Evaluate side-chains
  63 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  411 ASN
Chi-restraints excluded: chain B residue    6 ARG
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  289 ASP
Chi-restraints excluded: chain D residue   48 SER
Chi-restraints excluded: chain D residue   61 ARG
Chi-restraints excluded: chain D residue   97 THR
Chi-restraints excluded: chain D residue  180 VAL
Chi-restraints excluded: chain D residue  228 VAL
Chi-restraints excluded: chain Q residue   30 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 56 optimal weight:    0.7980
   chunk 93 optimal weight:    7.9990
   chunk 22 optimal weight:   30.0000
   chunk 10 optimal weight:   50.0000
   chunk 68 optimal weight:    0.9990
   chunk 83 optimal weight:    4.9990
   chunk 70 optimal weight:    0.8980
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B  29 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.205370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 95)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.181480 restraints weight = 8780.577|
|-----------------------------------------------------------------------------|
r_work (start): 0.4297 rms_B_bonded: 1.17
r_work: 0.4098 rms_B_bonded: 1.45 restraints_weight: 0.5000
r_work: 0.3913 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.3913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.2040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6407  Z= 0.138
  Angle     :  0.498   6.662   8847  Z= 0.267
  Chirality :  0.042   0.137   1105
  Planarity :  0.004   0.044   1193
  Dihedral  :  5.695  89.390   1085
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.76 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  5.85 %
    Allowed  : 18.42 %
    Favored  : 75.73 %
  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: -0.73 (0.27), residues: 1018
  helix:  3.67 (0.30), residues: 242
  sheet: -2.01 (0.30), residues: 276
  loop : -1.73 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D  70 
 HIS   0.004   0.001   HIS B 352 
 PHE   0.012   0.001   PHE B 267 
 TYR   0.014   0.001   TYR Q  76 
 ARG   0.003   0.000   ARG B 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03237 (  325)
  hydrogen bonds       : angle       4.66002 (  900)
  SS BOND              : bond        0.00314 (    2)
  SS BOND              : angle       0.80380 (    4)
  covalent geometry    : bond        0.00302 ( 6405)
  covalent geometry    : angle       0.49735 ( 8843)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 50
  time to evaluate  : 0.674 
Fit side-chains
   revert: symmetry clash
REVERT: D   44 SER cc_start: 0.8113 (p) cc_final: 0.7826 (p)
  outliers start: 20
  outliers final: 17
  residues processed: 63
  average time/residue: 0.1614
  time to fit residues: 14.3223
Evaluate side-chains
  65 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 48
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  411 ASN
Chi-restraints excluded: chain B residue    6 ARG
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  289 ASP
Chi-restraints excluded: chain D residue   48 SER
Chi-restraints excluded: chain D residue   61 ARG
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  180 VAL
Chi-restraints excluded: chain D residue  228 VAL
Chi-restraints excluded: chain Q residue   30 SER
Chi-restraints excluded: chain Q residue  144 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 16 optimal weight:   50.0000
   chunk 45 optimal weight:    0.5980
   chunk 38 optimal weight:    3.9990
   chunk 98 optimal weight:    8.9990
   chunk 53 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 100 optimal weight:   30.0000
   chunk 83 optimal weight:    1.9990
   chunk 23 optimal weight:   50.0000
   chunk 80 optimal weight:    0.2980
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
Q 145 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4534 r_free = 0.4534 target = 0.203874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.179485 restraints weight = 8672.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.4291 rms_B_bonded: 1.20
r_work: 0.4067 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3904 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.2318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6407  Z= 0.147
  Angle     :  0.502   6.711   8847  Z= 0.269
  Chirality :  0.042   0.133   1105
  Planarity :  0.004   0.042   1193
  Dihedral  :  5.671  88.615   1085
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  6.14 %
    Allowed  : 19.01 %
    Favored  : 74.85 %
  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: -0.64 (0.27), residues: 1018
  helix:  3.85 (0.30), residues: 242
  sheet: -1.94 (0.30), residues: 273
  loop : -1.75 (0.27), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP D  70 
 HIS   0.004   0.001   HIS D  58 
 PHE   0.012   0.001   PHE B 267 
 TYR   0.013   0.001   TYR Q  76 
 ARG   0.004   0.000   ARG B 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03073 (  325)
  hydrogen bonds       : angle       4.51823 (  900)
  SS BOND              : bond        0.00387 (    2)
  SS BOND              : angle       0.90812 (    4)
  covalent geometry    : bond        0.00327 ( 6405)
  covalent geometry    : angle       0.50196 ( 8843)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 51
  time to evaluate  : 0.679 
Fit side-chains
   revert: symmetry clash
REVERT: D   44 SER cc_start: 0.8161 (p) cc_final: 0.7933 (p)
  outliers start: 21
  outliers final: 17
  residues processed: 66
  average time/residue: 0.1770
  time to fit residues: 16.1112
Evaluate side-chains
  65 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 48
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  411 ASN
Chi-restraints excluded: chain B residue    6 ARG
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  289 ASP
Chi-restraints excluded: chain D residue   48 SER
Chi-restraints excluded: chain D residue   61 ARG
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  180 VAL
Chi-restraints excluded: chain D residue  228 VAL
Chi-restraints excluded: chain Q residue   30 SER
Chi-restraints excluded: chain Q residue  144 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 19 optimal weight:   30.0000
   chunk 39 optimal weight:    0.6980
   chunk 47 optimal weight:    0.5980
   chunk 31 optimal weight:    4.9990
   chunk 94 optimal weight:   20.0000
   chunk 71 optimal weight:    1.9990
   chunk 58 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
B  29 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.185098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.149459 restraints weight = 8847.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3858 rms_B_bonded: 1.98
r_work: 0.3640 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3522 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.2589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6407  Z= 0.177
  Angle     :  0.530   6.729   8847  Z= 0.284
  Chirality :  0.042   0.138   1105
  Planarity :  0.004   0.042   1193
  Dihedral  :  5.738  88.875   1085
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  8.45 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  5.85 %
    Allowed  : 19.88 %
    Favored  : 74.27 %
  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: -0.62 (0.28), residues: 1018
  helix:  3.94 (0.30), residues: 242
  sheet: -1.93 (0.31), residues: 269
  loop : -1.79 (0.27), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP D  70 
 HIS   0.004   0.001   HIS D  58 
 PHE   0.013   0.002   PHE Q  92 
 TYR   0.025   0.002   TYR Q  76 
 ARG   0.003   0.000   ARG B 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03122 (  325)
  hydrogen bonds       : angle       4.62038 (  900)
  SS BOND              : bond        0.00412 (    2)
  SS BOND              : angle       0.88468 (    4)
  covalent geometry    : bond        0.00401 ( 6405)
  covalent geometry    : angle       0.53026 ( 8843)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 48
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
REVERT: D   44 SER cc_start: 0.8270 (p) cc_final: 0.7987 (p)
  outliers start: 20
  outliers final: 18
  residues processed: 64
  average time/residue: 0.1502
  time to fit residues: 14.0099
Evaluate side-chains
  64 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 46
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  411 ASN
Chi-restraints excluded: chain B residue    6 ARG
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  289 ASP
Chi-restraints excluded: chain D residue   48 SER
Chi-restraints excluded: chain D residue   61 ARG
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  180 VAL
Chi-restraints excluded: chain D residue  228 VAL
Chi-restraints excluded: chain Q residue   30 SER
Chi-restraints excluded: chain Q residue  144 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 48 optimal weight:    0.5980
   chunk 98 optimal weight:    8.9990
   chunk 72 optimal weight:    0.1980
   chunk 23 optimal weight:    5.9990
   chunk 67 optimal weight:    3.9990
   chunk 19 optimal weight:    9.9990
   chunk 80 optimal weight:    0.0070
   chunk 64 optimal weight:    0.9990
   chunk 16 optimal weight:    8.9990
   chunk 101 optimal weight:    7.9990
   chunk 62 optimal weight:    2.9990
   overall best weight:    0.9602

-------------------------------------------------------------------------------
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 = 0.4266 r_free = 0.4266 target = 0.186002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.150577 restraints weight = 8782.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3871 rms_B_bonded: 1.99
r_work: 0.3657 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3544 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.2692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6407  Z= 0.145
  Angle     :  0.503   6.626   8847  Z= 0.269
  Chirality :  0.042   0.133   1105
  Planarity :  0.004   0.040   1193
  Dihedral  :  5.482  86.266   1085
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.37 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  6.43 %
    Allowed  : 18.13 %
    Favored  : 75.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.27), residues: 1018
  helix:  4.01 (0.29), residues: 242
  sheet: -1.73 (0.31), residues: 266
  loop : -1.77 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D  70 
 HIS   0.003   0.001   HIS B 361 
 PHE   0.011   0.001   PHE D 176 
 TYR   0.023   0.001   TYR Q  76 
 ARG   0.003   0.000   ARG B 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02945 (  325)
  hydrogen bonds       : angle       4.45301 (  900)
  SS BOND              : bond        0.00405 (    2)
  SS BOND              : angle       0.97871 (    4)
  covalent geometry    : bond        0.00324 ( 6405)
  covalent geometry    : angle       0.50258 ( 8843)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 49
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
REVERT: D   44 SER cc_start: 0.8258 (p) cc_final: 0.7986 (p)
  outliers start: 22
  outliers final: 18
  residues processed: 65
  average time/residue: 0.1598
  time to fit residues: 14.7727
Evaluate side-chains
  65 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 47
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  411 ASN
Chi-restraints excluded: chain B residue    6 ARG
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain B residue  289 ASP
Chi-restraints excluded: chain D residue   48 SER
Chi-restraints excluded: chain D residue   61 ARG
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  180 VAL
Chi-restraints excluded: chain D residue  228 VAL
Chi-restraints excluded: chain Q residue   30 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 86 optimal weight:    0.3980
   chunk 88 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0040
   chunk 32 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 74 optimal weight:    0.0070
   chunk 30 optimal weight:    0.5980
   chunk 61 optimal weight:    0.0010
   overall best weight:    0.2016

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

Flipped N/Q/H residues before XYZ refinement:
Q  48 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4570 r_free = 0.4570 target = 0.207864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.185230 restraints weight = 8704.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.4339 rms_B_bonded: 1.25
r_work: 0.4127 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.3954 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.2891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6407  Z= 0.087
  Angle     :  0.467   6.462   8847  Z= 0.249
  Chirality :  0.041   0.126   1105
  Planarity :  0.004   0.040   1193
  Dihedral  :  4.962  82.399   1085
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 20.76 %
    Favored  : 75.15 %
  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 (0.28), residues: 1018
  helix:  4.08 (0.29), residues: 242
  sheet: -1.43 (0.32), residues: 263
  loop : -1.63 (0.27), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP Q  56 
 HIS   0.003   0.001   HIS B 361 
 PHE   0.016   0.001   PHE B 276 
 TYR   0.018   0.001   TYR Q  76 
 ARG   0.006   0.001   ARG B 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02594 (  325)
  hydrogen bonds       : angle       3.94183 (  900)
  SS BOND              : bond        0.00174 (    2)
  SS BOND              : angle       1.01512 (    4)
  covalent geometry    : bond        0.00181 ( 6405)
  covalent geometry    : angle       0.46616 ( 8843)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.689 
Fit side-chains
   revert: symmetry clash
REVERT: D   44 SER cc_start: 0.8120 (p) cc_final: 0.7877 (p)
  outliers start: 14
  outliers final: 12
  residues processed: 59
  average time/residue: 0.1601
  time to fit residues: 13.3327
Evaluate side-chains
  60 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  411 ASN
Chi-restraints excluded: chain B residue    6 ARG
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain B residue  289 ASP
Chi-restraints excluded: chain D residue   48 SER
Chi-restraints excluded: chain D residue   61 ARG
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  180 VAL
Chi-restraints excluded: chain D residue  228 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 64 optimal weight:    0.2980
   chunk 37 optimal weight:    0.9980
   chunk 85 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 14 optimal weight:   50.0000
   chunk 26 optimal weight:    0.7980
   chunk 44 optimal weight:    0.7980
   chunk 10 optimal weight:   50.0000
   chunk 95 optimal weight:    9.9990
   chunk 1 optimal weight:   50.0000
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4537 r_free = 0.4537 target = 0.204444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.178263 restraints weight = 8755.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.4275 rms_B_bonded: 1.51
r_work: 0.3997 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work (final): 0.3997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          0.2925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6407  Z= 0.120
  Angle     :  0.485   6.526   8847  Z= 0.257
  Chirality :  0.041   0.129   1105
  Planarity :  0.004   0.041   1193
  Dihedral  :  5.044  85.095   1085
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.17 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 21.93 %
    Favored  : 74.56 %
  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: -0.13 (0.28), residues: 1018
  helix:  4.20 (0.29), residues: 242
  sheet: -1.35 (0.32), residues: 269
  loop : -1.58 (0.27), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  70 
 HIS   0.003   0.001   HIS D  58 
 PHE   0.011   0.001   PHE B 276 
 TYR   0.017   0.001   TYR Q  76 
 ARG   0.004   0.000   ARG B 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02686 (  325)
  hydrogen bonds       : angle       4.01438 (  900)
  SS BOND              : bond        0.00314 (    2)
  SS BOND              : angle       0.70972 (    4)
  covalent geometry    : bond        0.00265 ( 6405)
  covalent geometry    : angle       0.48504 ( 8843)

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.676 
Fit side-chains
   revert: symmetry clash
REVERT: D   44 SER cc_start: 0.7917 (p) cc_final: 0.7659 (p)
  outliers start: 12
  outliers final: 12
  residues processed: 57
  average time/residue: 0.1701
  time to fit residues: 13.6360
Evaluate side-chains
  60 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  411 ASN
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain B residue  289 ASP
Chi-restraints excluded: chain D residue   48 SER
Chi-restraints excluded: chain D residue   61 ARG
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  180 VAL
Chi-restraints excluded: chain D residue  228 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 12 optimal weight:   50.0000
   chunk 39 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 17 optimal weight:   50.0000
   chunk 20 optimal weight:   20.0000
   chunk 32 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 6 optimal weight:   50.0000
   chunk 23 optimal weight:    6.9990
   chunk 8 optimal weight:    9.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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 = 0.4234 r_free = 0.4234 target = 0.182612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.146698 restraints weight = 9099.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3824 rms_B_bonded: 1.95
r_work: 0.3611 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3498 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.3103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   6407  Z= 0.249
  Angle     :  0.601   6.981   8847  Z= 0.322
  Chirality :  0.044   0.144   1105
  Planarity :  0.004   0.043   1193
  Dihedral  :  5.756  88.963   1085
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  9.53 %
    Favored  : 90.37 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 21.05 %
    Favored  : 74.56 %
  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 (0.28), residues: 1018
  helix:  4.07 (0.30), residues: 248
  sheet: -1.61 (0.32), residues: 271
  loop : -1.75 (0.27), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP D  70 
 HIS   0.006   0.002   HIS D  58 
 PHE   0.017   0.002   PHE Q  92 
 TYR   0.017   0.002   TYR Q 112 
 ARG   0.006   0.001   ARG B 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03215 (  325)
  hydrogen bonds       : angle       4.73536 (  900)
  SS BOND              : bond        0.00610 (    2)
  SS BOND              : angle       1.02814 (    4)
  covalent geometry    : bond        0.00568 ( 6405)
  covalent geometry    : angle       0.60110 ( 8843)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4108.13 seconds
wall clock time: 72 minutes 17.39 seconds (4337.39 seconds total)