Starting phenix.real_space_refine
on Thu Jul 24 09:45:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7til_25913/07_2025/7til_25913.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7til_25913/07_2025/7til_25913.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7til_25913/07_2025/7til_25913.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7til_25913/07_2025/7til_25913.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7til_25913/07_2025/7til_25913.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7til_25913/07_2025/7til_25913.cif"
  }
  resolution = 3.7
  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=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      12      5.16       5
     C    3707      2.51       5
     N    1037      2.21       5
     O    1059      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 5815
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2876
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 365, 2876
          Classifications: {'peptide': 365}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 341}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 28
    Chain: "B"
      Number of atoms: 2939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 374, 2939
          Classifications: {'peptide': 374}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 349}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 28
  Time building chain proxies: 4.67, per 1000 atoms: 0.80
  Number of scatterers: 5815
  At special positions: 0
  Unit cell: (65.65, 107.25, 112.45, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      12     16.00
     O    1059      8.00
     N    1037      7.00
     C    3707      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.40
  Conformation dependent library (CDL) restraints added in 917.7 milliseconds
  

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1400

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 4 sheets defined
      55.6% alpha, 7.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 16
      removed outlier: 3.616A  pdb=" N   GLN A  16 " --> pdb=" O   ALA A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 17 through 26
    Processing helix  chain 'A' and resid 27 through 31
      removed outlier: 3.847A  pdb=" N   TRP A  31 " --> pdb=" O   PRO A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 48
    Processing helix  chain 'A' and resid 48 through 59
      removed outlier: 3.676A  pdb=" N   VAL A  52 " --> pdb=" O   ASN A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 100
    Processing helix  chain 'A' and resid 101 through 118
      removed outlier: 3.516A  pdb=" N   GLN A 117 " --> pdb=" O   TYR A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 121
      No H-bonds generated for 'chain 'A' and resid 119 through 121'
    Processing helix  chain 'A' and resid 122 through 129
    Processing helix  chain 'A' and resid 129 through 136
      removed outlier: 4.328A  pdb=" N   TRP A 133 " --> pdb=" O   GLN A 129 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   THR A 135 " --> pdb=" O   SER A 131 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   ARG A 136 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 150
    Processing helix  chain 'A' and resid 160 through 165
      removed outlier: 3.625A  pdb=" N   ALA A 165 " --> pdb=" O   LEU A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 189
      removed outlier: 3.561A  pdb=" N   ARG A 188 " --> pdb=" O   LEU A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 197
      removed outlier: 3.994A  pdb=" N   GLU A 195 " --> pdb=" O   GLY A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 202
    Processing helix  chain 'A' and resid 231 through 235
    Processing helix  chain 'A' and resid 252 through 256
    Processing helix  chain 'A' and resid 273 through 277
      removed outlier: 3.639A  pdb=" N   ALA A 277 " --> pdb=" O   HIS A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 307
    Processing helix  chain 'A' and resid 316 through 323
    Processing helix  chain 'A' and resid 344 through 356
      removed outlier: 3.970A  pdb=" N   VAL A 356 " --> pdb=" O   ARG A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 367
      removed outlier: 3.593A  pdb=" N   TYR A 366 " --> pdb=" O   GLU A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 380
      removed outlier: 3.626A  pdb=" N   VAL A 372 " --> pdb=" O   PRO A 368 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   LEU A 374 " --> pdb=" O   ALA A 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 16
      removed outlier: 3.582A  pdb=" N   GLN B  16 " --> pdb=" O   ALA B  12 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 26
    Processing helix  chain 'B' and resid 41 through 48
    Processing helix  chain 'B' and resid 48 through 61
      removed outlier: 4.028A  pdb=" N   VAL B  52 " --> pdb=" O   ASN B  48 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   SER B  61 " --> pdb=" O   GLU B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 91 through 100
      removed outlier: 3.615A  pdb=" N   ASP B 100 " --> pdb=" O   ILE B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 118
      removed outlier: 3.552A  pdb=" N   GLU B 116 " --> pdb=" O   GLU B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 121
      No H-bonds generated for 'chain 'B' and resid 119 through 121'
    Processing helix  chain 'B' and resid 122 through 129
    Processing helix  chain 'B' and resid 129 through 135
      removed outlier: 4.273A  pdb=" N   TRP B 133 " --> pdb=" O   GLN B 129 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   THR B 135 " --> pdb=" O   SER B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 150
      removed outlier: 3.567A  pdb=" N   GLN B 150 " --> pdb=" O   GLN B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 165
      removed outlier: 3.727A  pdb=" N   LEU B 164 " --> pdb=" O   PRO B 160 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   ALA B 165 " --> pdb=" O   LEU B 161 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 160 through 165'
    Processing helix  chain 'B' and resid 177 through 189
      removed outlier: 3.567A  pdb=" N   GLU B 187 " --> pdb=" O   LYS B 183 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ARG B 188 " --> pdb=" O   LEU B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 197
      removed outlier: 3.828A  pdb=" N   GLU B 195 " --> pdb=" O   GLY B 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 202
    Processing helix  chain 'B' and resid 230 through 235
    Processing helix  chain 'B' and resid 252 through 256
    Processing helix  chain 'B' and resid 293 through 307
    Processing helix  chain 'B' and resid 316 through 323
      removed outlier: 3.551A  pdb=" N   PHE B 320 " --> pdb=" O   GLU B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 344 through 357
      removed outlier: 3.565A  pdb=" N   VAL B 356 " --> pdb=" O   ARG B 352 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   GLN B 357 " --> pdb=" O   TYR B 353 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 368 through 381
    Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 36
      removed outlier: 3.578A  pdb=" N   GLN A  33 " --> pdb=" O   LEU A  89 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LEU A  89 " --> pdb=" O   GLN A  33 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LYS A  66 " --> pdb=" O   HIS A  88 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 227 through 230
      removed outlier: 3.595A  pdb=" N   VAL A 214 " --> pdb=" O   LEU A 227 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   LEU A 244 " --> pdb=" O   GLY A 287 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   TRP A 289 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   VAL A 246 " --> pdb=" O   TRP A 289 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   ILE A 286 " --> pdb=" O   GLU A 311 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 33 through 36
      removed outlier: 3.597A  pdb=" N   GLN B  33 " --> pdb=" O   LEU B  89 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   ARG B  86 " --> pdb=" O   ASP B  68 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 227 through 229
      removed outlier: 6.829A  pdb=" N   ARG B 243 " --> pdb=" O   LEU B 264 " (cutoff:3.500A)
      removed outlier: 8.211A  pdb=" N   VAL B 266 " --> pdb=" O   ARG B 243 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   LEU B 245 " --> pdb=" O   VAL B 266 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   ILE B 286 " --> pdb=" O   GLU B 311 " (cutoff:3.500A)

    247 hydrogen bonds defined for protein.
    708 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: 1.42

  Time building geometry restraints manager: 1.65 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1956
        1.34 -     1.46: 1205
        1.46 -     1.58: 2774
        1.58 -     1.69: 0
        1.69 -     1.81: 20
  Bond restraints: 5955
  Sorted by residual:
  bond pdb=" CA  PRO A  32 "
       pdb=" CB  PRO A  32 "
    ideal  model  delta    sigma   weight residual
    1.533  1.517  0.016 1.80e-02 3.09e+03 7.61e-01
  bond pdb=" C   ASP B 101 "
       pdb=" O   ASP B 101 "
    ideal  model  delta    sigma   weight residual
    1.248  1.238  0.011 1.26e-02 6.30e+03 7.28e-01
  bond pdb=" CA  ASP B 262 "
       pdb=" CB  ASP B 262 "
    ideal  model  delta    sigma   weight residual
    1.530  1.544 -0.014 1.69e-02 3.50e+03 6.47e-01
  bond pdb=" CB  LYS B 334 "
       pdb=" CG  LYS B 334 "
    ideal  model  delta    sigma   weight residual
    1.520  1.543 -0.023 3.00e-02 1.11e+03 5.77e-01
  bond pdb=" C   ILE B  37 "
       pdb=" N   GLY B  38 "
    ideal  model  delta    sigma   weight residual
    1.322  1.331 -0.009 1.20e-02 6.94e+03 5.61e-01
  ... (remaining 5950 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 7961
        1.75 -     3.51: 146
        3.51 -     5.26: 8
        5.26 -     7.01: 3
        7.01 -     8.77: 1
  Bond angle restraints: 8119
  Sorted by residual:
  angle pdb=" C   PRO B 261 "
        pdb=" N   ASP B 262 "
        pdb=" CA  ASP B 262 "
      ideal   model   delta    sigma   weight residual
     121.54  127.04   -5.50 1.91e+00 2.74e-01 8.29e+00
  angle pdb=" CA  LYS B 172 "
        pdb=" CB  LYS B 172 "
        pdb=" CG  LYS B 172 "
      ideal   model   delta    sigma   weight residual
     114.10  119.61   -5.51 2.00e+00 2.50e-01 7.58e+00
  angle pdb=" CA  LYS A 172 "
        pdb=" CB  LYS A 172 "
        pdb=" CG  LYS A 172 "
      ideal   model   delta    sigma   weight residual
     114.10  119.55   -5.45 2.00e+00 2.50e-01 7.43e+00
  angle pdb=" N   LYS A 172 "
        pdb=" CA  LYS A 172 "
        pdb=" C   LYS A 172 "
      ideal   model   delta    sigma   weight residual
     113.19  109.39    3.80 1.58e+00 4.01e-01 5.79e+00
  angle pdb=" CA  LYS A 172 "
        pdb=" C   LYS A 172 "
        pdb=" O   LYS A 172 "
      ideal   model   delta    sigma   weight residual
     119.08  121.36   -2.28 1.03e+00 9.43e-01 4.91e+00
  ... (remaining 8114 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.53: 3223
       17.53 -    35.06: 289
       35.06 -    52.58: 54
       52.58 -    70.11: 9
       70.11 -    87.64: 6
  Dihedral angle restraints: 3581
    sinusoidal: 1435
      harmonic: 2146
  Sorted by residual:
  dihedral pdb=" CA  GLU A  57 "
           pdb=" C   GLU A  57 "
           pdb=" N   ASN A  58 "
           pdb=" CA  ASN A  58 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.33   20.67     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" CA  ARG B 359 "
           pdb=" C   ARG B 359 "
           pdb=" N   GLY B 360 "
           pdb=" CA  GLY B 360 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.77   16.23     0      5.00e+00 4.00e-02 1.05e+01
  dihedral pdb=" CG  ARG B  86 "
           pdb=" CD  ARG B  86 "
           pdb=" NE  ARG B  86 "
           pdb=" CZ  ARG B  86 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  130.55  -40.55     2      1.50e+01 4.44e-03 9.02e+00
  ... (remaining 3578 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 654
       0.033 -    0.066: 199
       0.066 -    0.099: 49
       0.099 -    0.132: 11
       0.132 -    0.165: 2
  Chirality restraints: 915
  Sorted by residual:
  chirality pdb=" CA  GLU A  57 "
            pdb=" N   GLU A  57 "
            pdb=" C   GLU A  57 "
            pdb=" CB  GLU A  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.17 2.00e-01 2.50e+01 6.82e-01
  chirality pdb=" CA  ASP B 262 "
            pdb=" N   ASP B 262 "
            pdb=" C   ASP B 262 "
            pdb=" CB  ASP B 262 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.15 2.00e-01 2.50e+01 5.28e-01
  chirality pdb=" CA  ILE B  81 "
            pdb=" N   ILE B  81 "
            pdb=" C   ILE B  81 "
            pdb=" CB  ILE B  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.44e-01
  ... (remaining 912 not shown)

  Planarity restraints: 1049
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B  27 "   -0.026 5.00e-02 4.00e+02   3.96e-02 2.51e+00
        pdb=" N   PRO B  28 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO B  28 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B  28 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B   3 "   -0.022 5.00e-02 4.00e+02   3.39e-02 1.84e+00
        pdb=" N   PRO B   4 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO B   4 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B   4 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A  53 "    0.006 2.00e-02 2.50e+03   1.29e-02 1.67e+00
        pdb=" C   LEU A  53 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   LEU A  53 "    0.008 2.00e-02 2.50e+03
        pdb=" N   ARG A  54 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1046 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1214
        2.78 -     3.31: 5637
        3.31 -     3.84: 9424
        3.84 -     4.37: 10546
        4.37 -     4.90: 18185
  Nonbonded interactions: 45006
  Sorted by model distance:
  nonbonded pdb=" O   GLU B 318 "
            pdb=" NE2 GLN B 322 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" OE1 GLU B 331 "
            pdb=" NZ  LYS B 334 "
     model   vdw
     2.258 3.120
  nonbonded pdb=" OD2 ASP A 186 "
            pdb=" OG  SER A 194 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" O   GLU B 233 "
            pdb=" OG1 THR B 237 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" OD2 ASP B 186 "
            pdb=" OG  SER B 194 "
     model   vdw
     2.284 3.040
  ... (remaining 45001 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 1 through 325 or resid 335 through 381))
}

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 group one per residue
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:             3.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.930
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   5955  Z= 0.105
  Angle     :  0.536   8.768   8119  Z= 0.280
  Chirality :  0.035   0.165    915
  Planarity :  0.004   0.040   1049
  Dihedral  : 13.783  87.638   2181
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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:  0.14 (0.31), residues: 729
  helix:  1.50 (0.30), residues: 342
  sheet: -0.39 (0.62), residues: 65
  loop : -1.38 (0.32), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 289 
 HIS   0.002   0.000   HIS A 280 
 PHE   0.009   0.001   PHE B 205 
 TYR   0.005   0.001   TYR B 288 
 ARG   0.006   0.000   ARG A 130 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22853 (  247)
  hydrogen bonds       : angle       6.66390 (  708)
  covalent geometry    : bond        0.00227 ( 5955)
  covalent geometry    : angle       0.53595 ( 8119)

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

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

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 LEU cc_start: 0.9104 (mm) cc_final: 0.8739 (mm)
REVERT: A  205 PHE cc_start: 0.6997 (m-80) cc_final: 0.6681 (m-10)
REVERT: B   85 MET cc_start: 0.7782 (ppp) cc_final: 0.7262 (ppp)
REVERT: B  249 ASN cc_start: 0.7516 (t0) cc_final: 0.6903 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.2632
  time to fit residues: 45.3813
Evaluate side-chains
  73 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 61 optimal weight:    0.2980
   chunk 55 optimal weight:    0.2980
   chunk 30 optimal weight:    0.4980
   chunk 18 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 34 optimal weight:    9.9990
   chunk 42 optimal weight:    0.4980
   chunk 66 optimal weight:    0.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 322 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.079141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.057823 restraints weight = 23203.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.059792 restraints weight = 13332.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.061086 restraints weight = 9565.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.2770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5955  Z= 0.129
  Angle     :  0.657  13.431   8119  Z= 0.321
  Chirality :  0.040   0.163    915
  Planarity :  0.005   0.064   1049
  Dihedral  :  3.783  19.738    798
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 11.20 %
    Favored  : 88.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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 (0.32), residues: 729
  helix:  1.18 (0.29), residues: 359
  sheet: -0.29 (0.61), residues: 66
  loop : -1.13 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 289 
 HIS   0.004   0.001   HIS A  55 
 PHE   0.018   0.002   PHE B 350 
 TYR   0.019   0.003   TYR B 351 
 ARG   0.008   0.001   ARG B  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04653 (  247)
  hydrogen bonds       : angle       4.88611 (  708)
  covalent geometry    : bond        0.00278 ( 5955)
  covalent geometry    : angle       0.65729 ( 8119)

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

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

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 84
  time to evaluate  : 0.645 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 GLU cc_start: 0.9240 (mp0) cc_final: 0.8822 (tp30)
REVERT: A  205 PHE cc_start: 0.7387 (m-80) cc_final: 0.7168 (m-10)
REVERT: A  374 LEU cc_start: 0.9468 (mt) cc_final: 0.9267 (pp)
REVERT: B  249 ASN cc_start: 0.7407 (t0) cc_final: 0.6627 (t0)
  outliers start: 4
  outliers final: 2
  residues processed: 86
  average time/residue: 0.2110
  time to fit residues: 23.2380
Evaluate side-chains
  71 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 69
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain B residue  271 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 44 optimal weight:    0.0670
   chunk 70 optimal weight:    2.9990
   chunk 66 optimal weight:   10.0000
   chunk 37 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 34 optimal weight:    8.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    1.5924

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

Flipped N/Q/H residues before XYZ refinement:
A 129 GLN
A 274 HIS
A 306 HIS
** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.075406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.054112 restraints weight = 23719.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.055845 restraints weight = 14363.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.056984 restraints weight = 10552.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.3607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   5955  Z= 0.194
  Angle     :  0.658   9.605   8119  Z= 0.325
  Chirality :  0.041   0.186    915
  Planarity :  0.005   0.038   1049
  Dihedral  :  4.054  19.808    798
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 13.01 %
    Favored  : 84.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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:  0.05 (0.31), residues: 729
  helix:  1.13 (0.29), residues: 354
  sheet: -0.63 (0.58), residues: 66
  loop : -1.08 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 289 
 HIS   0.003   0.001   HIS A 280 
 PHE   0.013   0.002   PHE B 224 
 TYR   0.010   0.002   TYR B 108 
 ARG   0.009   0.001   ARG B  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04112 (  247)
  hydrogen bonds       : angle       4.59648 (  708)
  covalent geometry    : bond        0.00438 ( 5955)
  covalent geometry    : angle       0.65764 ( 8119)

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

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

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.684 
Fit side-chains
REVERT: A  366 TYR cc_start: 0.7774 (m-80) cc_final: 0.7090 (m-80)
REVERT: B  172 LYS cc_start: 0.8177 (mmtp) cc_final: 0.7715 (mmmt)
REVERT: B  249 ASN cc_start: 0.7711 (t0) cc_final: 0.7018 (t0)
  outliers start: 13
  outliers final: 10
  residues processed: 82
  average time/residue: 0.1803
  time to fit residues: 19.5841
Evaluate side-chains
  73 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LYS
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  167 HIS
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain B residue   61 SER
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  163 LEU
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  366 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 65 optimal weight:    8.9990
   chunk 1 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 69 optimal weight:    0.3980
   chunk 62 optimal weight:    6.9990
   chunk 49 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 274 HIS
** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.076487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.055253 restraints weight = 23796.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.057066 restraints weight = 14210.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.058254 restraints weight = 10385.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.4036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5955  Z= 0.115
  Angle     :  0.636  13.277   8119  Z= 0.302
  Chirality :  0.039   0.166    915
  Planarity :  0.004   0.032   1049
  Dihedral  :  3.858  19.143    798
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 14.83 %
    Favored  : 83.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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:  0.19 (0.32), residues: 729
  helix:  1.22 (0.29), residues: 355
  sheet: -0.41 (0.61), residues: 66
  loop : -1.03 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 289 
 HIS   0.003   0.001   HIS A  55 
 PHE   0.015   0.002   PHE B 224 
 TYR   0.013   0.002   TYR B 108 
 ARG   0.003   0.000   ARG B  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03376 (  247)
  hydrogen bonds       : angle       4.29004 (  708)
  covalent geometry    : bond        0.00254 ( 5955)
  covalent geometry    : angle       0.63603 ( 8119)

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

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

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.654 
Fit side-chains
REVERT: A   57 GLU cc_start: 0.8990 (pt0) cc_final: 0.8560 (tp30)
REVERT: B   39 LYS cc_start: 0.8608 (tptt) cc_final: 0.8405 (tptt)
REVERT: B  172 LYS cc_start: 0.8098 (mmtp) cc_final: 0.7634 (mmmt)
REVERT: B  249 ASN cc_start: 0.7676 (t0) cc_final: 0.6929 (t0)
REVERT: B  318 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8761 (pm20)
  outliers start: 9
  outliers final: 7
  residues processed: 77
  average time/residue: 0.1748
  time to fit residues: 18.0391
Evaluate side-chains
  72 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LYS
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  318 GLU
Chi-restraints excluded: chain B residue  366 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 70 optimal weight:    7.9990
   chunk 8 optimal weight:    0.0970
   chunk 9 optimal weight:    0.9990
   chunk 50 optimal weight:    0.3980
   chunk 40 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 63 optimal weight:    6.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.075184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.053601 restraints weight = 23537.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.055381 restraints weight = 14121.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.056555 restraints weight = 10323.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.4259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   5955  Z= 0.108
  Angle     :  0.611   9.422   8119  Z= 0.291
  Chirality :  0.038   0.161    915
  Planarity :  0.004   0.031   1049
  Dihedral  :  3.792  19.086    798
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 15.82 %
    Favored  : 83.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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:  0.19 (0.32), residues: 729
  helix:  1.19 (0.29), residues: 360
  sheet: -0.30 (0.63), residues: 66
  loop : -1.04 (0.35), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 289 
 HIS   0.003   0.001   HIS A  55 
 PHE   0.009   0.001   PHE B 350 
 TYR   0.014   0.002   TYR B 108 
 ARG   0.004   0.000   ARG B  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03197 (  247)
  hydrogen bonds       : angle       4.10880 (  708)
  covalent geometry    : bond        0.00240 ( 5955)
  covalent geometry    : angle       0.61108 ( 8119)

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

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

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.637 
Fit side-chains
REVERT: A   39 LYS cc_start: 0.8488 (tptp) cc_final: 0.8274 (tptp)
REVERT: B  172 LYS cc_start: 0.8266 (mmtp) cc_final: 0.7732 (mmmt)
REVERT: B  249 ASN cc_start: 0.7554 (t0) cc_final: 0.6719 (t0)
REVERT: B  318 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8796 (pm20)
  outliers start: 7
  outliers final: 4
  residues processed: 75
  average time/residue: 0.1724
  time to fit residues: 17.3064
Evaluate side-chains
  71 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  318 GLU
Chi-restraints excluded: chain B residue  366 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 28 optimal weight:    5.9990
   chunk 48 optimal weight:    0.1980
   chunk 53 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0060
   chunk 33 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0060
   chunk 54 optimal weight:    0.2980
   chunk 7 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.2412

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

Flipped N/Q/H residues before XYZ refinement:
A 274 HIS
** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.076092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.054410 restraints weight = 23450.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.056190 restraints weight = 14001.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.057426 restraints weight = 10233.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.4393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5955  Z= 0.096
  Angle     :  0.632  11.297   8119  Z= 0.295
  Chirality :  0.039   0.164    915
  Planarity :  0.004   0.030   1049
  Dihedral  :  3.644  18.983    798
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 17.46 %
    Favored  : 81.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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:  0.23 (0.32), residues: 729
  helix:  1.21 (0.29), residues: 364
  sheet: -0.21 (0.63), residues: 66
  loop : -1.07 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 289 
 HIS   0.004   0.001   HIS A  55 
 PHE   0.018   0.001   PHE B 224 
 TYR   0.014   0.001   TYR B 108 
 ARG   0.003   0.000   ARG A  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02963 (  247)
  hydrogen bonds       : angle       4.03137 (  708)
  covalent geometry    : bond        0.00211 ( 5955)
  covalent geometry    : angle       0.63180 ( 8119)

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

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

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.755 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.8459 (tptp) cc_final: 0.8186 (tptp)
REVERT: A  315 MET cc_start: 0.7485 (mmt) cc_final: 0.6977 (mmm)
REVERT: B  172 LYS cc_start: 0.8262 (mmtp) cc_final: 0.7726 (mmmt)
REVERT: B  249 ASN cc_start: 0.7447 (t0) cc_final: 0.6567 (t0)
REVERT: B  256 LEU cc_start: 0.9446 (mp) cc_final: 0.9236 (mp)
REVERT: B  318 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8761 (pm20)
  outliers start: 5
  outliers final: 2
  residues processed: 79
  average time/residue: 0.2056
  time to fit residues: 21.0552
Evaluate side-chains
  72 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 69
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain B residue  318 GLU
Chi-restraints excluded: chain B residue  366 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 66 optimal weight:    9.9990
   chunk 19 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 7 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:
A 210 HIS
A 274 HIS
** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.074403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.052751 restraints weight = 23793.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.054492 restraints weight = 14254.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.055665 restraints weight = 10428.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.4612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5955  Z= 0.131
  Angle     :  0.635   9.882   8119  Z= 0.300
  Chirality :  0.038   0.157    915
  Planarity :  0.004   0.036   1049
  Dihedral  :  3.711  18.839    798
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 17.63 %
    Favored  : 81.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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:  0.33 (0.32), residues: 729
  helix:  1.28 (0.29), residues: 361
  sheet: -0.20 (0.62), residues: 66
  loop : -0.98 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 289 
 HIS   0.002   0.001   HIS A 123 
 PHE   0.017   0.001   PHE B 224 
 TYR   0.014   0.002   TYR A 113 
 ARG   0.007   0.000   ARG A  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03127 (  247)
  hydrogen bonds       : angle       4.03315 (  708)
  covalent geometry    : bond        0.00299 ( 5955)
  covalent geometry    : angle       0.63456 ( 8119)

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

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

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.640 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.8467 (tptp) cc_final: 0.8190 (tptp)
REVERT: A   85 MET cc_start: 0.7758 (mmp) cc_final: 0.7536 (mmp)
REVERT: A  315 MET cc_start: 0.7592 (mmt) cc_final: 0.7146 (mmm)
REVERT: B  172 LYS cc_start: 0.8243 (mmtp) cc_final: 0.7709 (mmmt)
REVERT: B  249 ASN cc_start: 0.7556 (t0) cc_final: 0.6775 (t0)
REVERT: B  292 MET cc_start: 0.5126 (mmm) cc_final: 0.4903 (mmm)
REVERT: B  318 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8726 (pm20)
  outliers start: 5
  outliers final: 4
  residues processed: 72
  average time/residue: 0.1794
  time to fit residues: 17.1996
Evaluate side-chains
  69 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  167 HIS
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  318 GLU
Chi-restraints excluded: chain B residue  366 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0030
   chunk 53 optimal weight:    0.6980
   chunk 60 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.8794

-------------------------------------------------------------------------------
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 = 0.3596 r_free = 0.3596 target = 0.074249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.052661 restraints weight = 23510.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.054393 restraints weight = 14117.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.055573 restraints weight = 10322.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.4805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5955  Z= 0.122
  Angle     :  0.634  10.780   8119  Z= 0.299
  Chirality :  0.039   0.175    915
  Planarity :  0.004   0.033   1049
  Dihedral  :  3.691  18.184    798
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 17.13 %
    Favored  : 81.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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:  0.39 (0.32), residues: 729
  helix:  1.36 (0.29), residues: 355
  sheet: -0.19 (0.62), residues: 66
  loop : -0.93 (0.36), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 289 
 HIS   0.002   0.001   HIS A  55 
 PHE   0.018   0.001   PHE B 224 
 TYR   0.012   0.002   TYR B 108 
 ARG   0.004   0.000   ARG A  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03057 (  247)
  hydrogen bonds       : angle       4.03783 (  708)
  covalent geometry    : bond        0.00282 ( 5955)
  covalent geometry    : angle       0.63446 ( 8119)

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

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

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.645 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.8499 (tptp) cc_final: 0.8203 (tptp)
REVERT: A   85 MET cc_start: 0.7811 (mmp) cc_final: 0.7559 (mmp)
REVERT: A  315 MET cc_start: 0.7636 (mmt) cc_final: 0.7149 (mmm)
REVERT: B  172 LYS cc_start: 0.8256 (mmtp) cc_final: 0.7719 (mmmt)
REVERT: B  249 ASN cc_start: 0.7530 (t0) cc_final: 0.6745 (t0)
REVERT: B  318 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8680 (pm20)
  outliers start: 8
  outliers final: 5
  residues processed: 74
  average time/residue: 0.1722
  time to fit residues: 17.1786
Evaluate side-chains
  71 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  318 GLU
Chi-restraints excluded: chain B residue  366 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 43 optimal weight:    7.9990
   chunk 60 optimal weight:    0.7980
   chunk 70 optimal weight:   10.0000
   chunk 1 optimal weight:    2.9990
   chunk 8 optimal weight:    8.9990
   chunk 22 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3592 r_free = 0.3592 target = 0.074058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.052492 restraints weight = 23883.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.054205 restraints weight = 14291.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.055391 restraints weight = 10461.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.4955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5955  Z= 0.124
  Angle     :  0.671  12.835   8119  Z= 0.308
  Chirality :  0.039   0.193    915
  Planarity :  0.004   0.031   1049
  Dihedral  :  3.703  20.961    798
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 17.79 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.32), residues: 729
  helix:  1.29 (0.29), residues: 360
  sheet: -0.22 (0.61), residues: 66
  loop : -1.00 (0.36), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 289 
 HIS   0.002   0.001   HIS A  55 
 PHE   0.018   0.001   PHE B 224 
 TYR   0.012   0.002   TYR B 108 
 ARG   0.003   0.000   ARG A  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03156 (  247)
  hydrogen bonds       : angle       4.07765 (  708)
  covalent geometry    : bond        0.00286 ( 5955)
  covalent geometry    : angle       0.67139 ( 8119)

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

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

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.8562 (tptp) cc_final: 0.8284 (tptp)
REVERT: A   85 MET cc_start: 0.7847 (mmp) cc_final: 0.7609 (mmm)
REVERT: A  315 MET cc_start: 0.7643 (mmt) cc_final: 0.7180 (mmm)
REVERT: B   85 MET cc_start: 0.7945 (ppp) cc_final: 0.7609 (ppp)
REVERT: B  172 LYS cc_start: 0.8259 (mmtp) cc_final: 0.7708 (mmmt)
REVERT: B  249 ASN cc_start: 0.7573 (t0) cc_final: 0.6796 (t0)
  outliers start: 8
  outliers final: 7
  residues processed: 73
  average time/residue: 0.1956
  time to fit residues: 19.3015
Evaluate side-chains
  72 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  366 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 21 optimal weight:    0.0170
   chunk 10 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 72 optimal weight:    0.5980
   chunk 31 optimal weight:    9.9990
   chunk 9 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 4 optimal weight:    6.9990
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.5618

-------------------------------------------------------------------------------
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 = 0.3601 r_free = 0.3601 target = 0.074481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.052929 restraints weight = 23941.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.054682 restraints weight = 14254.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.055873 restraints weight = 10369.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.5105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5955  Z= 0.110
  Angle     :  0.681  11.558   8119  Z= 0.313
  Chirality :  0.039   0.192    915
  Planarity :  0.004   0.031   1049
  Dihedral  :  3.667  20.237    798
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 18.78 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.32), residues: 729
  helix:  1.31 (0.29), residues: 360
  sheet: -0.19 (0.61), residues: 66
  loop : -1.02 (0.35), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 289 
 HIS   0.007   0.001   HIS A 210 
 PHE   0.019   0.002   PHE B 224 
 TYR   0.014   0.002   TYR B 108 
 ARG   0.003   0.000   ARG A  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03029 (  247)
  hydrogen bonds       : angle       4.02565 (  708)
  covalent geometry    : bond        0.00255 ( 5955)
  covalent geometry    : angle       0.68074 ( 8119)

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

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

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 1.036 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.8603 (tptp) cc_final: 0.8339 (tptp)
REVERT: A   53 LEU cc_start: 0.9685 (mt) cc_final: 0.9345 (pp)
REVERT: A   85 MET cc_start: 0.7911 (mmp) cc_final: 0.7662 (mmm)
REVERT: A  315 MET cc_start: 0.7598 (mmt) cc_final: 0.7122 (mmm)
REVERT: B   85 MET cc_start: 0.7990 (ppp) cc_final: 0.7692 (ppp)
REVERT: B  172 LYS cc_start: 0.8329 (mmtp) cc_final: 0.7761 (mmmt)
REVERT: B  249 ASN cc_start: 0.7516 (t0) cc_final: 0.6728 (t0)
  outliers start: 7
  outliers final: 6
  residues processed: 71
  average time/residue: 0.1853
  time to fit residues: 17.9030
Evaluate side-chains
  73 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  366 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 29 optimal weight:    7.9990
   chunk 0 optimal weight:    4.9990
   chunk 9 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0670
   chunk 37 optimal weight:    3.9990
   overall best weight:    1.5324

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

Flipped N/Q/H residues before XYZ refinement:
** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.072319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.050653 restraints weight = 24218.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.052303 restraints weight = 14615.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.053428 restraints weight = 10772.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.5384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5955  Z= 0.183
  Angle     :  0.716  10.914   8119  Z= 0.336
  Chirality :  0.040   0.201    915
  Planarity :  0.004   0.033   1049
  Dihedral  :  3.885  18.929    798
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 18.78 %
    Favored  : 79.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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:  0.19 (0.32), residues: 729
  helix:  1.17 (0.29), residues: 359
  sheet: -0.44 (0.60), residues: 66
  loop : -0.98 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 289 
 HIS   0.013   0.001   HIS A 210 
 PHE   0.017   0.002   PHE B 224 
 TYR   0.011   0.002   TYR B 108 
 ARG   0.004   0.000   ARG A  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03566 (  247)
  hydrogen bonds       : angle       4.25567 (  708)
  covalent geometry    : bond        0.00421 ( 5955)
  covalent geometry    : angle       0.71552 ( 8119)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3035.54 seconds
wall clock time: 53 minutes 52.16 seconds (3232.16 seconds total)