Starting phenix.real_space_refine
on Wed Sep 17 06:44:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9m0d_63543/09_2025/9m0d_63543.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9m0d_63543/09_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_63543/09_2025/9m0d_63543.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9m0d_63543/09_2025/9m0d_63543.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9m0d_63543/09_2025/9m0d_63543.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9m0d_63543/09_2025/9m0d_63543.cif"
  }
  resolution = 3.41
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.039
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'TYR:plan': 16, 'PHE:plan': 17, 'ASN:plan1': 11, 'ARG:plan': 11, 'HIS:plan': 7, 'ASP:plan': 4, 'GLU:plan': 4, 'TRP:plan': 4, 'GLN:plan1': 3, 'TPO:plan-1': 1}
          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: {'ASP:plan': 11, 'GLU:plan': 21, 'TYR:plan': 2, 'ARG:plan': 13, 'PHE:plan': 4, 'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 7}
          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, 'PHE:plan': 2, 'TYR:plan': 5, 'ASP:plan': 6, 'ASN:plan1': 5, 'ARG:plan': 1, 'GLU:plan': 3, 'TRP: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, 'ASP:plan': 8, 'ARG:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'ASN:plan1': 5, 'TYR:plan': 3, 'TRP:plan': 1, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 179
  Time building chain proxies: 1.90, per 1000 atoms: 0.30
  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: 0.49
  Conformation dependent library (CDL) restraints added in 457.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.26
  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: 0.91

  Time building geometry restraints manager: 0.69 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:             2.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.820
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.260
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.004   0.001   ARG D  42 
 TYR   0.009   0.001   TYR D 127 
 PHE   0.010   0.001   PHE B 267 
 TRP   0.010   0.001   TRP D  70 
 HIS   0.004   0.001   HIS B 352 

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

*********************** 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  : 0.238 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 55
  average time/residue: 0.0700
  time to fit residues: 5.5407
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  : 0.230 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.0470
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:   30.0000
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.4980
   overall best weight:    0.9480

-------------------------------------------------------------------------------
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 = 0.4304 r_free = 0.4304 target = 0.189367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.156011 restraints weight = 8873.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3941 rms_B_bonded: 2.07
r_work: 0.3682 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3562 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.1044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6407  Z= 0.151
  Angle     :  0.530   6.876   8847  Z= 0.287
  Chirality :  0.043   0.140   1105
  Planarity :  0.004   0.055   1193
  Dihedral  :  5.879  81.302   1087
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 17.25 %
    Favored  : 78.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.99 (0.27), residues: 1018
  helix:  3.04 (0.30), residues: 243
  sheet: -1.99 (0.31), residues: 278
  loop : -1.78 (0.27), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B   6 
 TYR   0.014   0.001   TYR B 143 
 PHE   0.014   0.002   PHE B 267 
 TRP   0.014   0.002   TRP D  70 
 HIS   0.006   0.001   HIS D  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 6405)
  covalent geometry    : angle       0.52997 ( 8843)
  SS BOND              : bond        0.00338 (    2)
  SS BOND              : angle       0.99147 (    4)
  hydrogen bonds       : bond        0.04056 (  325)
  hydrogen bonds       : angle       5.79295 (  900)

*********************** 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
  66 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 51
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
  outliers start: 15
  outliers final: 13
  residues processed: 61
  average time/residue: 0.0573
  time to fit residues: 5.1012
Evaluate side-chains
  61 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
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   25 ASP
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  289 ASP
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 52 optimal weight:    2.9990
   chunk 35 optimal weight:    0.2980
   chunk 12 optimal weight:   50.0000
   chunk 13 optimal weight:   50.0000
   chunk 23 optimal weight:   50.0000
   chunk 15 optimal weight:   50.0000
   chunk 19 optimal weight:   20.0000
   chunk 70 optimal weight:    1.9990
   chunk 30 optimal weight:    0.1980
   chunk 29 optimal weight:    3.9990
   chunk 61 optimal weight:    0.0470
   overall best weight:    1.1082

-------------------------------------------------------------------------------
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 = 0.4281 r_free = 0.4281 target = 0.187209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.152429 restraints weight = 8780.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3894 rms_B_bonded: 2.11
r_work: 0.3655 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3537 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6407  Z= 0.163
  Angle     :  0.532   6.602   8847  Z= 0.284
  Chirality :  0.043   0.144   1105
  Planarity :  0.004   0.049   1193
  Dihedral  :  6.027  83.070   1087
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  5.85 %
    Allowed  : 17.54 %
    Favored  : 76.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.90 (0.27), residues: 1018
  helix:  3.36 (0.30), residues: 242
  sheet: -2.01 (0.31), residues: 267
  loop : -1.83 (0.27), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 102 
 TYR   0.011   0.001   TYR Q 112 
 PHE   0.015   0.002   PHE B 267 
 TRP   0.013   0.002   TRP D  70 
 HIS   0.005   0.001   HIS D  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 6405)
  covalent geometry    : angle       0.53067 ( 8843)
  SS BOND              : bond        0.00547 (    2)
  SS BOND              : angle       1.49647 (    4)
  hydrogen bonds       : bond        0.03801 (  325)
  hydrogen bonds       : angle       5.20294 (  900)

*********************** 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
  69 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 49
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
  outliers start: 20
  outliers final: 14
  residues processed: 62
  average time/residue: 0.0688
  time to fit residues: 6.0639
Evaluate side-chains
  59 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 45
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
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  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   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 28 optimal weight:    0.7980
   chunk 79 optimal weight:    4.9990
   chunk 69 optimal weight:    0.7980
   chunk 91 optimal weight:    0.6980
   chunk 82 optimal weight:    0.7980
   chunk 97 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 89 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 0 optimal weight:   50.0000
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.4549 r_free = 0.4549 target = 0.205564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.183354 restraints weight = 8733.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.4330 rms_B_bonded: 1.28
r_work: 0.4092 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.3894 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.1883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6407  Z= 0.125
  Angle     :  0.491   6.676   8847  Z= 0.263
  Chirality :  0.042   0.133   1105
  Planarity :  0.004   0.045   1193
  Dihedral  :  5.979  89.899   1087
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 18.13 %
    Favored  : 76.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.71 (0.27), residues: 1018
  helix:  3.58 (0.30), residues: 242
  sheet: -1.87 (0.31), residues: 268
  loop : -1.77 (0.27), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 102 
 TYR   0.014   0.001   TYR Q  76 
 PHE   0.011   0.001   PHE B 267 
 TRP   0.008   0.002   TRP Q  56 
 HIS   0.003   0.001   HIS B 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 6405)
  covalent geometry    : angle       0.49019 ( 8843)
  SS BOND              : bond        0.00317 (    2)
  SS BOND              : angle       1.15211 (    4)
  hydrogen bonds       : bond        0.03278 (  325)
  hydrogen bonds       : angle       4.71200 (  900)

*********************** 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
  64 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 46
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
REVERT: B  352 HIS cc_start: 0.8270 (OUTLIER) cc_final: 0.7238 (m-70)
  outliers start: 18
  outliers final: 13
  residues processed: 59
  average time/residue: 0.0583
  time to fit residues: 5.0690
Evaluate side-chains
  58 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 44
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
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  166 VAL
Chi-restraints excluded: chain B residue  289 ASP
Chi-restraints excluded: chain B residue  352 HIS
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 90 optimal weight:    0.2980
   chunk 67 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 10 optimal weight:   50.0000
   chunk 25 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 95 optimal weight:    6.9990
   chunk 78 optimal weight:    0.4980
   chunk 18 optimal weight:   50.0000
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.4265 r_free = 0.4265 target = 0.185872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.152613 restraints weight = 8911.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.3899 rms_B_bonded: 1.94
r_work: 0.3654 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3531 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.2150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6407  Z= 0.165
  Angle     :  0.522   6.598   8847  Z= 0.279
  Chirality :  0.042   0.141   1105
  Planarity :  0.004   0.044   1193
  Dihedral  :  6.029  87.947   1087
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  6.14 %
    Allowed  : 18.42 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.71 (0.27), residues: 1018
  helix:  3.78 (0.30), residues: 242
  sheet: -1.96 (0.31), residues: 268
  loop : -1.82 (0.27), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 102 
 TYR   0.015   0.001   TYR Q  76 
 PHE   0.013   0.002   PHE B 267 
 TRP   0.011   0.002   TRP D  70 
 HIS   0.005   0.001   HIS D  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 6405)
  covalent geometry    : angle       0.52164 ( 8843)
  SS BOND              : bond        0.00459 (    2)
  SS BOND              : angle       0.97902 (    4)
  hydrogen bonds       : bond        0.03259 (  325)
  hydrogen bonds       : angle       4.74564 (  900)

*********************** 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
  68 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 47
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
REVERT: B   50 ARG cc_start: 0.5131 (mtm180) cc_final: 0.4856 (mmp-170)
REVERT: B  352 HIS cc_start: 0.8372 (OUTLIER) cc_final: 0.7248 (m-70)
REVERT: D   44 SER cc_start: 0.8377 (p) cc_final: 0.8098 (p)
  outliers start: 21
  outliers final: 17
  residues processed: 62
  average time/residue: 0.0739
  time to fit residues: 6.3895
Evaluate side-chains
  63 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 45
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
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   25 ASP
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 B residue  352 HIS
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 20 optimal weight:   20.0000
   chunk 65 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0170
   chunk 99 optimal weight:    0.9980
   chunk 13 optimal weight:   50.0000
   chunk 76 optimal weight:    4.9990
   chunk 77 optimal weight:   20.0000
   chunk 56 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.7422

-------------------------------------------------------------------------------
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 = 0.204188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.169172 restraints weight = 8678.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.4117 rms_B_bonded: 2.45
r_work: 0.3863 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.2314

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= 0.121
  Angle     :  0.487   6.462   8847  Z= 0.260
  Chirality :  0.042   0.133   1105
  Planarity :  0.004   0.042   1193
  Dihedral  :  5.904  88.588   1087
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 19.30 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.58 (0.27), residues: 1018
  helix:  3.86 (0.29), residues: 242
  sheet: -1.78 (0.32), residues: 259
  loop : -1.79 (0.26), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 102 
 TYR   0.022   0.001   TYR Q  76 
 PHE   0.010   0.001   PHE D 176 
 TRP   0.009   0.002   TRP D  70 
 HIS   0.003   0.001   HIS B 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 6405)
  covalent geometry    : angle       0.48624 ( 8843)
  SS BOND              : bond        0.00288 (    2)
  SS BOND              : angle       0.95409 (    4)
  hydrogen bonds       : bond        0.03019 (  325)
  hydrogen bonds       : angle       4.49024 (  900)

*********************** 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
  64 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 46
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
REVERT: B   50 ARG cc_start: 0.5065 (mtm180) cc_final: 0.4848 (mmp-170)
REVERT: D   44 SER cc_start: 0.8274 (p) cc_final: 0.7985 (p)
  outliers start: 18
  outliers final: 16
  residues processed: 59
  average time/residue: 0.0786
  time to fit residues: 6.4748
Evaluate side-chains
  62 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 46
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
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  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
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 91 optimal weight:    0.9980
   chunk 50 optimal weight:   10.0000
   chunk 71 optimal weight:    1.9990
   chunk 73 optimal weight:    8.9990
   chunk 79 optimal weight:    6.9990
   chunk 87 optimal weight:    0.0670
   chunk 99 optimal weight:    0.9990
   chunk 16 optimal weight:   50.0000
   chunk 39 optimal weight:    2.9990
   chunk 10 optimal weight:   50.0000
   overall best weight:    1.4124

-------------------------------------------------------------------------------
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 = 0.4251 r_free = 0.4251 target = 0.184330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.149493 restraints weight = 8854.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3861 rms_B_bonded: 1.90
r_work: 0.3642 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3527 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.2547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6407  Z= 0.188
  Angle     :  0.540   6.660   8847  Z= 0.289
  Chirality :  0.043   0.142   1105
  Planarity :  0.004   0.042   1193
  Dihedral  :  6.113  89.481   1087
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  8.74 %
    Favored  : 91.16 %
  Rotamer:
    Outliers :  5.85 %
    Allowed  : 19.30 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.67 (0.28), residues: 1018
  helix:  3.81 (0.30), residues: 248
  sheet: -1.91 (0.31), residues: 261
  loop : -1.89 (0.26), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 102 
 TYR   0.025   0.002   TYR Q  76 
 PHE   0.013   0.002   PHE Q  92 
 TRP   0.013   0.002   TRP D  70 
 HIS   0.004   0.001   HIS D  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 6405)
  covalent geometry    : angle       0.54002 ( 8843)
  SS BOND              : bond        0.00507 (    2)
  SS BOND              : angle       0.96965 (    4)
  hydrogen bonds       : bond        0.03173 (  325)
  hydrogen bonds       : angle       4.75818 (  900)

*********************** 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
  66 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 46
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
REVERT: B   50 ARG cc_start: 0.5206 (mtm180) cc_final: 0.4909 (mmp-170)
REVERT: B  352 HIS cc_start: 0.8407 (OUTLIER) cc_final: 0.7298 (m-70)
REVERT: D   44 SER cc_start: 0.8287 (p) cc_final: 0.7989 (p)
  outliers start: 20
  outliers final: 17
  residues processed: 62
  average time/residue: 0.0767
  time to fit residues: 6.6367
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  : 0.235 
-------------------------------------------------------------------------------
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   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 B residue  352 HIS
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   52 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 38 optimal weight:    0.3980
   chunk 23 optimal weight:    7.9990
   chunk 28 optimal weight:    0.8980
   chunk 75 optimal weight:    0.2980
   chunk 100 optimal weight:    6.9990
   chunk 57 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 101 optimal weight:   20.0000
   chunk 0 optimal weight:   70.0000
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.4525 r_free = 0.4525 target = 0.202841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.179884 restraints weight = 8776.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.4288 rms_B_bonded: 1.35
r_work: 0.4039 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3843 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.2672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6407  Z= 0.137
  Angle     :  0.497   6.498   8847  Z= 0.266
  Chirality :  0.042   0.132   1105
  Planarity :  0.004   0.040   1193
  Dihedral  :  5.842  86.717   1087
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.07 %
    Favored  : 92.83 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.55 (0.28), residues: 1018
  helix:  3.88 (0.30), residues: 248
  sheet: -1.73 (0.31), residues: 262
  loop : -1.86 (0.27), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 102 
 TYR   0.022   0.001   TYR Q  76 
 PHE   0.011   0.001   PHE D 176 
 TRP   0.011   0.002   TRP D  70 
 HIS   0.003   0.001   HIS B 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6405)
  covalent geometry    : angle       0.49683 ( 8843)
  SS BOND              : bond        0.00384 (    2)
  SS BOND              : angle       1.01614 (    4)
  hydrogen bonds       : bond        0.02894 (  325)
  hydrogen bonds       : angle       4.45760 (  900)

*********************** 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
  67 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 47
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
REVERT: D   44 SER cc_start: 0.8213 (p) cc_final: 0.7942 (p)
  outliers start: 20
  outliers final: 18
  residues processed: 63
  average time/residue: 0.0736
  time to fit residues: 6.5302
Evaluate side-chains
  61 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 43
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
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 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   52 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 96 optimal weight:    7.9990
   chunk 0 optimal weight:   70.0000
   chunk 8 optimal weight:    9.9990
   chunk 64 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 45 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9990
   chunk 67 optimal weight:    0.6980
   chunk 80 optimal weight:    2.9990
   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 = 0.4265 r_free = 0.4265 target = 0.185840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.152477 restraints weight = 8958.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3900 rms_B_bonded: 1.98
r_work: 0.3660 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3532 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.2837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6407  Z= 0.134
  Angle     :  0.496   6.541   8847  Z= 0.264
  Chirality :  0.042   0.133   1105
  Planarity :  0.004   0.040   1193
  Dihedral  :  5.367  86.115   1085
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.76 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  6.14 %
    Allowed  : 19.30 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.45 (0.28), residues: 1018
  helix:  3.93 (0.30), residues: 248
  sheet: -1.69 (0.32), residues: 262
  loop : -1.77 (0.27), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 102 
 TYR   0.021   0.001   TYR Q  76 
 PHE   0.013   0.001   PHE B 276 
 TRP   0.010   0.002   TRP D  70 
 HIS   0.003   0.001   HIS B  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6405)
  covalent geometry    : angle       0.49569 ( 8843)
  SS BOND              : bond        0.00361 (    2)
  SS BOND              : angle       0.93575 (    4)
  hydrogen bonds       : bond        0.02821 (  325)
  hydrogen bonds       : angle       4.37201 (  900)

*********************** 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
  66 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 45
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
REVERT: D   44 SER cc_start: 0.8280 (p) cc_final: 0.7993 (p)
  outliers start: 21
  outliers final: 18
  residues processed: 61
  average time/residue: 0.0680
  time to fit residues: 5.9795
Evaluate side-chains
  60 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 42
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
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   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
Chi-restraints excluded: chain Q residue   52 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 58 optimal weight:    6.9990
   chunk 12 optimal weight:   40.0000
   chunk 88 optimal weight:    3.9990
   chunk 91 optimal weight:    0.2980
   chunk 33 optimal weight:    5.9990
   chunk 10 optimal weight:   50.0000
   chunk 2 optimal weight:   50.0000
   chunk 73 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   chunk 84 optimal weight:    0.3980
   chunk 50 optimal weight:    0.0370
   overall best weight:    1.1260

-------------------------------------------------------------------------------
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 = 0.4255 r_free = 0.4255 target = 0.184816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.150503 restraints weight = 8809.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3875 rms_B_bonded: 2.01
r_work: 0.3640 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3511 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.2929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6407  Z= 0.162
  Angle     :  0.522   6.605   8847  Z= 0.277
  Chirality :  0.042   0.137   1105
  Planarity :  0.004   0.040   1193
  Dihedral  :  5.406  86.294   1085
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  8.25 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 20.18 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.40 (0.28), residues: 1018
  helix:  4.01 (0.30), residues: 248
  sheet: -1.62 (0.33), residues: 261
  loop : -1.79 (0.27), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 102 
 TYR   0.022   0.002   TYR Q  76 
 PHE   0.012   0.001   PHE D 176 
 TRP   0.010   0.002   TRP D  70 
 HIS   0.004   0.001   HIS D  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 6405)
  covalent geometry    : angle       0.52134 ( 8843)
  SS BOND              : bond        0.00414 (    2)
  SS BOND              : angle       0.96690 (    4)
  hydrogen bonds       : bond        0.02864 (  325)
  hydrogen bonds       : angle       4.45160 (  900)

********************** 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
  62 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 44
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
REVERT: D   44 SER cc_start: 0.8312 (p) cc_final: 0.8027 (p)
  outliers start: 18
  outliers final: 18
  residues processed: 58
  average time/residue: 0.0721
  time to fit residues: 6.0366
Evaluate side-chains
  61 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 43
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
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   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
Chi-restraints excluded: chain Q residue   52 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 81 optimal weight:    0.5980
   chunk 22 optimal weight:    8.9990
   chunk 58 optimal weight:    0.0670
   chunk 9 optimal weight:   50.0000
   chunk 88 optimal weight:    2.9990
   chunk 92 optimal weight:    7.9990
   chunk 50 optimal weight:    5.9990
   chunk 79 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9980
   chunk 15 optimal weight:   50.0000
   chunk 29 optimal weight:    5.9990
   overall best weight:    1.9322

-------------------------------------------------------------------------------
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 = 0.4228 r_free = 0.4228 target = 0.181916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.145840 restraints weight = 8952.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3815 rms_B_bonded: 2.00
r_work: 0.3602 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3491 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.3188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   6407  Z= 0.249
  Angle     :  0.603   6.900   8847  Z= 0.322
  Chirality :  0.044   0.145   1105
  Planarity :  0.004   0.042   1193
  Dihedral  :  5.911  88.922   1085
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  9.72 %
    Favored  : 90.18 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 20.18 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.55 (0.28), residues: 1018
  helix:  4.02 (0.30), residues: 248
  sheet: -1.77 (0.32), residues: 262
  loop : -1.93 (0.27), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 102 
 TYR   0.026   0.002   TYR Q  76 
 PHE   0.016   0.002   PHE Q  92 
 TRP   0.016   0.003   TRP D  70 
 HIS   0.005   0.002   HIS D  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00571 ( 6405)
  covalent geometry    : angle       0.60246 ( 8843)
  SS BOND              : bond        0.00606 (    2)
  SS BOND              : angle       1.10905 (    4)
  hydrogen bonds       : bond        0.03210 (  325)
  hydrogen bonds       : angle       4.95866 (  900)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1985.43 seconds
wall clock time: 34 minutes 31.49 seconds (2071.49 seconds total)