Starting phenix.real_space_refine
on Tue Jul 29 20:46:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7b5r_12048/07_2025/7b5r_12048.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7b5r_12048/07_2025/7b5r_12048.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7b5r_12048/07_2025/7b5r_12048.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7b5r_12048/07_2025/7b5r_12048.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7b5r_12048/07_2025/7b5r_12048.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7b5r_12048/07_2025/7b5r_12048.cif"
  }
  resolution = 3.8
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      53      5.16       5
     C    7437      2.51       5
     N    1966      2.21       5
     O    2148      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11606
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "C"
      Number of atoms: 2396
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2396
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 3, 'TRANS': 284}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "T"
      Number of atoms: 2536
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 321, 2536
          Classifications: {'peptide': 321}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 13, 'TRANS': 307}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "K"
      Number of atoms: 598
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 598
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 5, 'TRANS': 63}
    Chain: "S"
      Number of atoms: 1097
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1097
          Classifications: {'peptide': 138}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 7, 'TRANS': 130}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
    Chain: "L"
      Number of atoms: 2279
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2279
          Classifications: {'peptide': 284}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 18, 'TRANS': 265}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'GLU:plan': 1, 'TPO:plan-1': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "Y"
      Number of atoms: 2046
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 2046
          Classifications: {'peptide': 253}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 239}
          Chain breaks: 2
    Chain: "P"
      Number of atoms: 654
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 654
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 6, 'TRANS': 70}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'TPO:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 6.72, per 1000 atoms: 0.58
  Number of scatterers: 11606
  At special positions: 0
  Unit cell: (149.33, 126.44, 103.55, 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      53     16.00
     P       2     15.00
     O    2148      8.00
     N    1966      7.00
     C    7437      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: 2.72
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2740

  Finding SS restraints...
    Secondary structure from input PDB file:
      71 helices and 8 sheets defined
      56.1% alpha, 3.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.06
  Creating SS restraints...
    Processing helix  chain 'C' and resid 18 through 32
      removed outlier: 3.651A  pdb=" N   ASP C  22 " --> pdb=" O   ASP C  18 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   ASP C  23 " --> pdb=" O   GLN C  19 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 38 through 53
    Processing helix  chain 'C' and resid 85 through 106
      removed outlier: 3.552A  pdb=" N   ASP C 106 " --> pdb=" O   ASN C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 114 through 137
      removed outlier: 4.283A  pdb=" N   GLN C 121 " --> pdb=" O   LYS C 117 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 139 through 144
      removed outlier: 3.539A  pdb=" N   HIS C 143 " --> pdb=" O   TYR C 139 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 158 through 172
    Processing helix  chain 'C' and resid 176 through 188
    Processing helix  chain 'C' and resid 189 through 191
      No H-bonds generated for 'chain 'C' and resid 189 through 191'
    Processing helix  chain 'C' and resid 198 through 211
      removed outlier: 3.988A  pdb=" N   GLY C 203 " --> pdb=" O   ARG C 199 " (cutoff:3.500A)
      removed outlier: 4.767A  pdb=" N   VAL C 204 " --> pdb=" O   LEU C 200 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 225 through 232
    Processing helix  chain 'C' and resid 232 through 253
      removed outlier: 3.527A  pdb=" N   THR C 249 " --> pdb=" O   THR C 245 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 256 through 278
      removed outlier: 3.730A  pdb=" N   TYR C 260 " --> pdb=" O   PRO C 256 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   VAL C 275 " --> pdb=" O   GLU C 271 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   GLN C 276 " --> pdb=" O   GLN C 272 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   VAL C 277 " --> pdb=" O   ARG C 273 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 283 through 296
    Processing helix  chain 'C' and resid 299 through 313
    Processing helix  chain 'C' and resid 316 through 329
      removed outlier: 3.892A  pdb=" N   GLY C 320 " --> pdb=" O   ASN C 316 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ILE C 329 " --> pdb=" O   LEU C 325 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 332 through 340
    Processing helix  chain 'T' and resid 96 through 100
    Processing helix  chain 'T' and resid 101 through 110
    Processing helix  chain 'T' and resid 113 through 121
    Processing helix  chain 'T' and resid 124 through 131
    Processing helix  chain 'T' and resid 148 through 158
    Processing helix  chain 'T' and resid 194 through 203
    Processing helix  chain 'T' and resid 219 through 227
    Processing helix  chain 'T' and resid 244 through 255
    Processing helix  chain 'T' and resid 270 through 281
    Processing helix  chain 'T' and resid 298 through 309
    Processing helix  chain 'T' and resid 324 through 334
    Processing helix  chain 'T' and resid 350 through 359
      removed outlier: 3.553A  pdb=" N   GLY T 357 " --> pdb=" O   LEU T 354 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 374 through 383
      removed outlier: 3.763A  pdb=" N   LEU T 378 " --> pdb=" O   GLY T 374 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 25 through 30
    Processing helix  chain 'K' and resid 39 through 47
    Processing helix  chain 'S' and resid 18 through 22
    Processing helix  chain 'S' and resid 24 through 33
      removed outlier: 3.845A  pdb=" N   ASP S  33 " --> pdb=" O   THR S  29 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 45 through 59
      removed outlier: 3.814A  pdb=" N   LYS S  51 " --> pdb=" O   ALA S  47 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 86 through 93
    Processing helix  chain 'S' and resid 96 through 111
    Processing helix  chain 'S' and resid 112 through 128
    Processing helix  chain 'S' and resid 131 through 139
    Processing helix  chain 'S' and resid 149 through 156
    Processing helix  chain 'L' and resid 45 through 56
    Processing helix  chain 'L' and resid 87 through 94
    Processing helix  chain 'L' and resid 100 through 121
    Processing helix  chain 'L' and resid 129 through 132
    Processing helix  chain 'L' and resid 145 through 149
      removed outlier: 4.349A  pdb=" N   LEU L 148 " --> pdb=" O   ASP L 145 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ALA L 149 " --> pdb=" O   PHE L 146 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 145 through 149'
    Processing helix  chain 'L' and resid 170 through 175
    Processing helix  chain 'L' and resid 183 through 199
      removed outlier: 3.688A  pdb=" N   TRP L 187 " --> pdb=" O   ALA L 183 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 207 through 220
    Processing helix  chain 'L' and resid 247 through 252
      removed outlier: 4.039A  pdb=" N   VAL L 251 " --> pdb=" O   ASP L 247 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   VAL L 252 " --> pdb=" O   PHE L 248 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 247 through 252'
    Processing helix  chain 'L' and resid 256 through 265
    Processing helix  chain 'L' and resid 276 through 281
    Processing helix  chain 'L' and resid 283 through 288
    Processing helix  chain 'Y' and resid 178 through 190
    Processing helix  chain 'Y' and resid 198 through 203
      removed outlier: 4.408A  pdb=" N   LYS Y 202 " --> pdb=" O   GLY Y 198 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   GLN Y 203 " --> pdb=" O   TYR Y 199 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'Y' and resid 198 through 203'
    Processing helix  chain 'Y' and resid 207 through 225
    Processing helix  chain 'Y' and resid 228 through 244
      removed outlier: 3.627A  pdb=" N   LEU Y 232 " --> pdb=" O   GLN Y 228 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 249 through 251
      No H-bonds generated for 'chain 'Y' and resid 249 through 251'
    Processing helix  chain 'Y' and resid 252 through 269
    Processing helix  chain 'Y' and resid 274 through 282
      removed outlier: 3.668A  pdb=" N   PHE Y 278 " --> pdb=" O   GLU Y 274 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   THR Y 282 " --> pdb=" O   PHE Y 278 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 287 through 303
      removed outlier: 3.508A  pdb=" N   VAL Y 291 " --> pdb=" O   THR Y 287 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 310 through 320
      removed outlier: 3.977A  pdb=" N   PHE Y 314 " --> pdb=" O   THR Y 310 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   LEU Y 320 " --> pdb=" O   THR Y 316 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 326 through 343
      removed outlier: 3.611A  pdb=" N   GLU Y 330 " --> pdb=" O   ASN Y 326 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   ASP Y 343 " --> pdb=" O   LEU Y 339 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 351 through 369
    Processing helix  chain 'Y' and resid 373 through 381
      removed outlier: 3.718A  pdb=" N   ILE Y 377 " --> pdb=" O   PRO Y 373 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 387 through 401
    Processing helix  chain 'Y' and resid 402 through 404
      No H-bonds generated for 'chain 'Y' and resid 402 through 404'
    Processing helix  chain 'Y' and resid 407 through 413
    Processing helix  chain 'Y' and resid 415 through 419
    Processing helix  chain 'Y' and resid 420 through 424
      removed outlier: 3.771A  pdb=" N   LEU Y 423 " --> pdb=" O   GLY Y 420 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LEU Y 424 " --> pdb=" O   VAL Y 421 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'Y' and resid 420 through 424'
    Processing helix  chain 'P' and resid 38 through 50
    Processing helix  chain 'P' and resid 54 through 61
    Processing helix  chain 'P' and resid 85 through 90
    Processing sheet with id=AA1, first strand: chain 'T' and resid 139 through 141
      removed outlier: 6.727A  pdb=" N   LEU T 140 " --> pdb=" O   ARG T 164 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'T' and resid 260 through 262
      removed outlier: 3.566A  pdb=" N   ASN T 289 " --> pdb=" O   LEU T 261 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'T' and resid 339 through 341
    Processing sheet with id=AA4, first strand: chain 'K' and resid 17 through 23
    Processing sheet with id=AA5, first strand: chain 'S' and resid 14 through 17
      removed outlier: 3.510A  pdb=" N   LEU S   6 " --> pdb=" O   PHE S  14 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 31 through 36
      removed outlier: 3.702A  pdb=" N   ALA L  31 " --> pdb=" O   PHE L  80 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 85 through 86
    Processing sheet with id=AA8, first strand: chain 'L' and resid 123 through 124

    523 hydrogen bonds defined for protein.
    1509 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: 2.78

  Time building geometry restraints manager: 3.23 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: 3735
        1.34 -     1.46: 1868
        1.46 -     1.57: 6170
        1.57 -     1.69: 6
        1.69 -     1.81: 78
  Bond restraints: 11857
  Sorted by residual:
  bond pdb=" OG1 TPO L 160 "
       pdb=" P   TPO L 160 "
    ideal  model  delta    sigma   weight residual
    1.717  1.603  0.114 2.00e-02 2.50e+03 3.24e+01
  bond pdb=" OG1 TPO P 187 "
       pdb=" P   TPO P 187 "
    ideal  model  delta    sigma   weight residual
    1.717  1.615  0.102 2.00e-02 2.50e+03 2.59e+01
  bond pdb=" O1P TPO P 187 "
       pdb=" P   TPO P 187 "
    ideal  model  delta    sigma   weight residual
    1.525  1.609 -0.084 2.00e-02 2.50e+03 1.77e+01
  bond pdb=" O2P TPO P 187 "
       pdb=" P   TPO P 187 "
    ideal  model  delta    sigma   weight residual
    1.528  1.609 -0.081 2.00e-02 2.50e+03 1.63e+01
  bond pdb=" O3P TPO L 160 "
       pdb=" P   TPO L 160 "
    ideal  model  delta    sigma   weight residual
    1.528  1.607 -0.079 2.00e-02 2.50e+03 1.56e+01
  ... (remaining 11852 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.41: 15783
        2.41 -     4.82: 226
        4.82 -     7.23: 39
        7.23 -     9.64: 5
        9.64 -    12.05: 3
  Bond angle restraints: 16056
  Sorted by residual:
  angle pdb=" N   PRO S   2 "
        pdb=" CA  PRO S   2 "
        pdb=" CB  PRO S   2 "
      ideal   model   delta    sigma   weight residual
     103.00  110.53   -7.53 1.10e+00 8.26e-01 4.68e+01
  angle pdb=" CB  TPO P 187 "
        pdb=" OG1 TPO P 187 "
        pdb=" P   TPO P 187 "
      ideal   model   delta    sigma   weight residual
     119.31  107.26   12.05 3.00e+00 1.11e-01 1.61e+01
  angle pdb=" N   VAL L 164 "
        pdb=" CA  VAL L 164 "
        pdb=" C   VAL L 164 "
      ideal   model   delta    sigma   weight residual
     109.34  116.61   -7.27 2.08e+00 2.31e-01 1.22e+01
  angle pdb=" N   GLY P  72 "
        pdb=" CA  GLY P  72 "
        pdb=" C   GLY P  72 "
      ideal   model   delta    sigma   weight residual
     110.29  114.61   -4.32 1.28e+00 6.10e-01 1.14e+01
  angle pdb=" CB  TPO L 160 "
        pdb=" OG1 TPO L 160 "
        pdb=" P   TPO L 160 "
      ideal   model   delta    sigma   weight residual
     119.31  109.24   10.07 3.00e+00 1.11e-01 1.13e+01
  ... (remaining 16051 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 6410
       17.91 -    35.81: 639
       35.81 -    53.72: 85
       53.72 -    71.63: 23
       71.63 -    89.54: 10
  Dihedral angle restraints: 7167
    sinusoidal: 2956
      harmonic: 4211
  Sorted by residual:
  dihedral pdb=" CA  LEU K  37 "
           pdb=" C   LEU K  37 "
           pdb=" N   MET K  38 "
           pdb=" CA  MET K  38 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.07  -27.93     0      5.00e+00 4.00e-02 3.12e+01
  dihedral pdb=" CA  VAL L 163 "
           pdb=" C   VAL L 163 "
           pdb=" N   VAL L 164 "
           pdb=" CA  VAL L 164 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.43  -24.57     0      5.00e+00 4.00e-02 2.41e+01
  dihedral pdb=" CA  ARG P  50 "
           pdb=" C   ARG P  50 "
           pdb=" N   ASP P  51 "
           pdb=" CA  ASP P  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.47   22.53     0      5.00e+00 4.00e-02 2.03e+01
  ... (remaining 7164 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1317
       0.047 -    0.094: 400
       0.094 -    0.141: 80
       0.141 -    0.188: 9
       0.188 -    0.235: 1
  Chirality restraints: 1807
  Sorted by residual:
  chirality pdb=" CA  PRO S   2 "
            pdb=" N   PRO S   2 "
            pdb=" C   PRO S   2 "
            pdb=" CB  PRO S   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.48    0.24 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" CA  VAL L 163 "
            pdb=" N   VAL L 163 "
            pdb=" C   VAL L 163 "
            pdb=" CB  VAL L 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.26    0.18 2.00e-01 2.50e+01 8.14e-01
  chirality pdb=" CA  PRO L 238 "
            pdb=" N   PRO L 238 "
            pdb=" C   PRO L 238 "
            pdb=" CB  PRO L 238 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.18 2.00e-01 2.50e+01 8.07e-01
  ... (remaining 1804 not shown)

  Planarity restraints: 2034
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL K  32 "   -0.042 5.00e-02 4.00e+02   6.36e-02 6.46e+00
        pdb=" N   PRO K  33 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO K  33 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO K  33 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP Y 217 "    0.015 2.00e-02 2.50e+03   1.53e-02 5.88e+00
        pdb=" CG  TRP Y 217 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 TRP Y 217 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 TRP Y 217 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP Y 217 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP Y 217 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP Y 217 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP Y 217 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP Y 217 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP Y 217 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR S 131 "   -0.037 5.00e-02 4.00e+02   5.56e-02 4.94e+00
        pdb=" N   PRO S 132 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO S 132 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO S 132 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 2031 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 143
        2.58 -     3.16: 10701
        3.16 -     3.74: 18110
        3.74 -     4.32: 24069
        4.32 -     4.90: 38814
  Nonbonded interactions: 91837
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP Y 216 "
            pdb=" OG  SER Y 408 "
     model   vdw
     2.001 3.040
  nonbonded pdb=" O   GLY Y 337 "
            pdb=" OG  SER Y 340 "
     model   vdw
     2.109 3.040
  nonbonded pdb=" OE2 GLU L  57 "
            pdb=" OH  TYR Y 185 "
     model   vdw
     2.147 3.040
  nonbonded pdb=" OH  TYR Y 350 "
            pdb=" OD2 ASP Y 393 "
     model   vdw
     2.171 3.040
  nonbonded pdb=" NH1 ARG L 157 "
            pdb=" OE2 GLU Y 268 "
     model   vdw
     2.171 3.120
  ... (remaining 91832 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 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:             1.860
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.490
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     26.130
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
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      :  0.006   0.114  11857  Z= 0.272
  Angle     :  0.806  12.049  16056  Z= 0.440
  Chirality :  0.046   0.235   1807
  Planarity :  0.005   0.064   2034
  Dihedral  : 14.425  89.536   4427
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 16.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.34 %
    Favored  : 90.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.23), residues: 1392
  helix:  0.48 (0.19), residues: 734
  sheet: -3.59 (0.53), residues: 80
  loop : -2.45 (0.25), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP Y 217 
 HIS   0.008   0.002   HIS K  56 
 PHE   0.020   0.002   PHE S 101 
 TYR   0.021   0.002   TYR Y 225 
 ARG   0.012   0.001   ARG P  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14152 (  523)
  hydrogen bonds       : angle       6.41445 ( 1509)
  covalent geometry    : bond        0.00591 (11857)
  covalent geometry    : angle       0.80627 (16056)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 1.468 
Fit side-chains
   revert: symmetry clash
REVERT: C  301 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8734 (pm20)
REVERT: K   14 ASP cc_start: 0.7886 (p0) cc_final: 0.7486 (p0)
REVERT: K   54 TRP cc_start: 0.8759 (m100) cc_final: 0.7721 (m100)
REVERT: Y  211 ARG cc_start: 0.8459 (ptm-80) cc_final: 0.7890 (ttp80)
REVERT: Y  250 ARG cc_start: 0.6697 (tpt170) cc_final: 0.6456 (tpt170)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.2344
  time to fit residues: 41.9850
Evaluate side-chains
  86 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 1.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 117 optimal weight:    0.5980
   chunk 105 optimal weight:    2.9990
   chunk 58 optimal weight:    0.4980
   chunk 35 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 56 optimal weight:    0.6980
   chunk 108 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 66 optimal weight:    9.9990
   chunk 81 optimal weight:    0.8980
   chunk 126 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
T 177 HIS
** T 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 268 HIS
Y 179 HIS
Y 208 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.085707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.066197 restraints weight = 41978.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.068413 restraints weight = 22541.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.069850 restraints weight = 15255.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.1217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11857  Z= 0.132
  Angle     :  0.633  10.172  16056  Z= 0.327
  Chirality :  0.042   0.139   1807
  Planarity :  0.005   0.057   2034
  Dihedral  :  5.190  40.537   1545
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  7.45 %
    Favored  : 92.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.23), residues: 1392
  helix:  0.89 (0.20), residues: 730
  sheet: -2.71 (0.52), residues: 96
  loop : -2.30 (0.26), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP K  43 
 HIS   0.010   0.001   HIS T 177 
 PHE   0.026   0.001   PHE T 328 
 TYR   0.023   0.001   TYR L 180 
 ARG   0.005   0.000   ARG P  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04332 (  523)
  hydrogen bonds       : angle       5.10360 ( 1509)
  covalent geometry    : bond        0.00294 (11857)
  covalent geometry    : angle       0.63267 (16056)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 112
  time to evaluate  : 1.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   37 MET cc_start: 0.7488 (mmm) cc_final: 0.6761 (mmm)
REVERT: K   54 TRP cc_start: 0.8495 (m100) cc_final: 0.7851 (m100)
REVERT: L   91 MET cc_start: 0.8329 (mtm) cc_final: 0.7895 (mtm)
REVERT: Y  211 ARG cc_start: 0.8495 (ptm-80) cc_final: 0.8034 (ttp80)
  outliers start: 7
  outliers final: 6
  residues processed: 115
  average time/residue: 0.2265
  time to fit residues: 38.4910
Evaluate side-chains
  98 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 1.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain T residue  104 LEU
Chi-restraints excluded: chain T residue  106 LEU
Chi-restraints excluded: chain K residue   34 LYS
Chi-restraints excluded: chain S residue  122 THR
Chi-restraints excluded: chain L residue  164 VAL
Chi-restraints excluded: chain Y residue  341 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 100 optimal weight:    0.6980
   chunk 45 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 20 optimal weight:    6.9990
   chunk 13 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 6 optimal weight:    6.9990
   chunk 101 optimal weight:    0.0870
   chunk 130 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 158 GLN
L 268 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.086369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.066556 restraints weight = 42783.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.068812 restraints weight = 22811.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.070268 restraints weight = 15413.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.1681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11857  Z= 0.114
  Angle     :  0.576  10.590  16056  Z= 0.297
  Chirality :  0.040   0.135   1807
  Planarity :  0.004   0.055   2034
  Dihedral  :  4.838  40.764   1545
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 10.63 %
    Favored  : 87.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.23), residues: 1392
  helix:  1.16 (0.20), residues: 723
  sheet: -2.38 (0.53), residues: 97
  loop : -2.15 (0.26), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP K  43 
 HIS   0.004   0.001   HIS Y 395 
 PHE   0.031   0.001   PHE T 328 
 TYR   0.020   0.001   TYR L 180 
 ARG   0.005   0.000   ARG P  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03781 (  523)
  hydrogen bonds       : angle       4.71201 ( 1509)
  covalent geometry    : bond        0.00254 (11857)
  covalent geometry    : angle       0.57633 (16056)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 1.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  261 MET cc_start: 0.7756 (tmm) cc_final: 0.7466 (tmm)
REVERT: T  316 ASP cc_start: 0.7751 (m-30) cc_final: 0.7267 (m-30)
REVERT: K   14 ASP cc_start: 0.7883 (p0) cc_final: 0.7369 (p0)
REVERT: K   18 GLU cc_start: 0.8011 (pt0) cc_final: 0.7644 (pt0)
REVERT: K   54 TRP cc_start: 0.8394 (m100) cc_final: 0.8053 (m100)
REVERT: L  286 PHE cc_start: 0.5618 (t80) cc_final: 0.5095 (t80)
REVERT: Y  211 ARG cc_start: 0.8553 (ptm-80) cc_final: 0.8018 (ttp80)
REVERT: P   68 LYS cc_start: 0.8907 (tppt) cc_final: 0.8515 (ptmt)
  outliers start: 20
  outliers final: 13
  residues processed: 128
  average time/residue: 0.2272
  time to fit residues: 43.0001
Evaluate side-chains
  105 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 1.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  296 ILE
Chi-restraints excluded: chain C residue  319 LEU
Chi-restraints excluded: chain T residue  104 LEU
Chi-restraints excluded: chain T residue  106 LEU
Chi-restraints excluded: chain T residue  284 THR
Chi-restraints excluded: chain T residue  409 ILE
Chi-restraints excluded: chain K residue   34 LYS
Chi-restraints excluded: chain S residue  122 THR
Chi-restraints excluded: chain L residue  164 VAL
Chi-restraints excluded: chain L residue  248 PHE
Chi-restraints excluded: chain Y residue  231 THR
Chi-restraints excluded: chain Y residue  315 LEU
Chi-restraints excluded: chain Y residue  341 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 101 optimal weight:    0.6980
   chunk 112 optimal weight:    0.9990
   chunk 64 optimal weight:    0.7980
   chunk 125 optimal weight:    3.9990
   chunk 119 optimal weight:    4.9990
   chunk 73 optimal weight:    0.0980
   chunk 95 optimal weight:    0.0980
   chunk 47 optimal weight:    3.9990
   chunk 97 optimal weight:    3.9990
   chunk 102 optimal weight:    6.9990
   overall best weight:    0.5382

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

Flipped N/Q/H residues before XYZ refinement:
** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T 229 ASN ** 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 = 0.3722 r_free = 0.3722 target = 0.086721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.066895 restraints weight = 42223.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.069159 restraints weight = 22590.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.070588 restraints weight = 15239.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.2008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  11857  Z= 0.106
  Angle     :  0.565  11.036  16056  Z= 0.285
  Chirality :  0.040   0.142   1807
  Planarity :  0.004   0.053   2034
  Dihedral  :  4.658  40.654   1545
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 13.34 %
    Favored  : 85.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.24), residues: 1392
  helix:  1.31 (0.20), residues: 725
  sheet: -2.22 (0.54), residues: 97
  loop : -2.04 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP K  43 
 HIS   0.006   0.001   HIS T 177 
 PHE   0.034   0.001   PHE T 328 
 TYR   0.018   0.001   TYR L 180 
 ARG   0.010   0.000   ARG P  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03433 (  523)
  hydrogen bonds       : angle       4.53173 ( 1509)
  covalent geometry    : bond        0.00236 (11857)
  covalent geometry    : angle       0.56474 (16056)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 1.598 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: T  316 ASP cc_start: 0.7809 (m-30) cc_final: 0.7515 (m-30)
REVERT: K   14 ASP cc_start: 0.7635 (p0) cc_final: 0.7226 (p0)
REVERT: L   91 MET cc_start: 0.8395 (mtm) cc_final: 0.7948 (mtm)
REVERT: L  286 PHE cc_start: 0.5489 (t80) cc_final: 0.5066 (t80)
REVERT: Y  211 ARG cc_start: 0.8567 (ptm-80) cc_final: 0.8253 (ttp80)
REVERT: Y  293 ARG cc_start: 0.8638 (mmm160) cc_final: 0.8211 (mmm160)
REVERT: P   59 LYS cc_start: 0.8680 (ptmm) cc_final: 0.8451 (tttp)
REVERT: P   68 LYS cc_start: 0.8925 (tppt) cc_final: 0.8719 (tppt)
  outliers start: 20
  outliers final: 10
  residues processed: 121
  average time/residue: 0.2567
  time to fit residues: 45.6314
Evaluate side-chains
  109 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 1.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  319 LEU
Chi-restraints excluded: chain T residue  106 LEU
Chi-restraints excluded: chain T residue  222 ILE
Chi-restraints excluded: chain T residue  284 THR
Chi-restraints excluded: chain T residue  409 ILE
Chi-restraints excluded: chain K residue   34 LYS
Chi-restraints excluded: chain S residue  122 THR
Chi-restraints excluded: chain L residue  164 VAL
Chi-restraints excluded: chain L residue  248 PHE
Chi-restraints excluded: chain Y residue  341 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 136 optimal weight:    7.9990
   chunk 9 optimal weight:    2.9990
   chunk 131 optimal weight:    0.5980
   chunk 108 optimal weight:    4.9990
   chunk 138 optimal weight:    0.2980
   chunk 5 optimal weight:    3.9990
   chunk 132 optimal weight:    0.0070
   chunk 86 optimal weight:    0.7980
   chunk 92 optimal weight:    4.9990
   chunk 98 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.5400

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

Flipped N/Q/H residues before XYZ refinement:
** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T 229 ASN ** 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 = 0.3730 r_free = 0.3730 target = 0.087095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.067334 restraints weight = 41719.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.069591 restraints weight = 22398.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.071020 restraints weight = 15147.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.051  11857  Z= 0.105
  Angle     :  0.564  11.263  16056  Z= 0.282
  Chirality :  0.040   0.239   1807
  Planarity :  0.004   0.052   2034
  Dihedral  :  4.523  40.837   1545
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 14.20 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.24), residues: 1392
  helix:  1.41 (0.20), residues: 725
  sheet: -2.08 (0.55), residues: 97
  loop : -1.92 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP K  54 
 HIS   0.005   0.001   HIS T 177 
 PHE   0.036   0.001   PHE T 328 
 TYR   0.017   0.001   TYR Y 178 
 ARG   0.007   0.000   ARG P  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03275 (  523)
  hydrogen bonds       : angle       4.42200 ( 1509)
  covalent geometry    : bond        0.00237 (11857)
  covalent geometry    : angle       0.56400 (16056)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 104
  time to evaluate  : 1.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  261 MET cc_start: 0.7810 (tmm) cc_final: 0.7523 (tmm)
REVERT: T  316 ASP cc_start: 0.7796 (m-30) cc_final: 0.7547 (m-30)
REVERT: K   14 ASP cc_start: 0.7579 (p0) cc_final: 0.7195 (p0)
REVERT: Y  211 ARG cc_start: 0.8549 (ptm-80) cc_final: 0.8289 (ttp80)
REVERT: Y  261 MET cc_start: 0.8590 (mmm) cc_final: 0.8276 (tpt)
REVERT: Y  293 ARG cc_start: 0.8672 (mmm160) cc_final: 0.8303 (mmm160)
  outliers start: 27
  outliers final: 12
  residues processed: 125
  average time/residue: 0.3505
  time to fit residues: 62.4222
Evaluate side-chains
  108 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 2.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   20 ILE
Chi-restraints excluded: chain C residue  172 PHE
Chi-restraints excluded: chain C residue  319 LEU
Chi-restraints excluded: chain T residue  106 LEU
Chi-restraints excluded: chain T residue  220 ASP
Chi-restraints excluded: chain T residue  284 THR
Chi-restraints excluded: chain T residue  409 ILE
Chi-restraints excluded: chain K residue   34 LYS
Chi-restraints excluded: chain S residue  122 THR
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue  164 VAL
Chi-restraints excluded: chain Y residue  341 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 2 optimal weight:    0.0980
   chunk 83 optimal weight:    4.9990
   chunk 26 optimal weight:    0.5980
   chunk 49 optimal weight:    0.0040
   chunk 64 optimal weight:    0.0670
   chunk 52 optimal weight:    4.9990
   chunk 101 optimal weight:    0.9990
   chunk 127 optimal weight:    0.1980
   chunk 58 optimal weight:    0.0570
   chunk 113 optimal weight:    5.9990
   chunk 81 optimal weight:    7.9990
   overall best weight:    0.0848

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

Flipped N/Q/H residues before XYZ refinement:
T 229 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.089163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.069456 restraints weight = 41517.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.071778 restraints weight = 21874.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.073280 restraints weight = 14644.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.2739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  11857  Z= 0.100
  Angle     :  0.572  11.306  16056  Z= 0.281
  Chirality :  0.039   0.156   1807
  Planarity :  0.004   0.051   2034
  Dihedral  :  4.355  44.315   1545
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 15.67 %
    Favored  : 82.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.24), residues: 1392
  helix:  1.47 (0.20), residues: 726
  sheet: -2.11 (0.53), residues: 102
  loop : -1.67 (0.27), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP K  43 
 HIS   0.004   0.001   HIS T 177 
 PHE   0.032   0.001   PHE T 328 
 TYR   0.015   0.001   TYR L 180 
 ARG   0.005   0.000   ARG P  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02982 (  523)
  hydrogen bonds       : angle       4.33993 ( 1509)
  covalent geometry    : bond        0.00214 (11857)
  covalent geometry    : angle       0.57242 (16056)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 122
  time to evaluate  : 2.161 
Fit side-chains
   revert: symmetry clash
REVERT: C   43 MET cc_start: 0.8882 (mmm) cc_final: 0.8583 (mmt)
REVERT: C  261 MET cc_start: 0.7853 (tmm) cc_final: 0.7580 (tmm)
REVERT: K   13 ASP cc_start: 0.8379 (p0) cc_final: 0.8130 (p0)
REVERT: S  110 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8403 (tp)
REVERT: L   91 MET cc_start: 0.8385 (mtm) cc_final: 0.7927 (mtm)
REVERT: L  123 VAL cc_start: 0.8173 (t) cc_final: 0.7935 (t)
REVERT: Y  211 ARG cc_start: 0.8622 (ptm-80) cc_final: 0.8086 (ttp80)
REVERT: P   44 ASP cc_start: 0.6331 (t0) cc_final: 0.5498 (t0)
REVERT: P   68 LYS cc_start: 0.8897 (tppt) cc_final: 0.8518 (ptmt)
  outliers start: 18
  outliers final: 9
  residues processed: 137
  average time/residue: 0.3010
  time to fit residues: 61.9742
Evaluate side-chains
  112 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 2.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  338 LYS
Chi-restraints excluded: chain T residue  106 LEU
Chi-restraints excluded: chain T residue  284 THR
Chi-restraints excluded: chain T residue  332 PHE
Chi-restraints excluded: chain K residue   34 LYS
Chi-restraints excluded: chain S residue  110 LEU
Chi-restraints excluded: chain S residue  122 THR
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue  164 VAL
Chi-restraints excluded: chain Y residue  341 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 101 optimal weight:    0.0170
   chunk 41 optimal weight:    5.9990
   chunk 117 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 14 optimal weight:    9.9990
   chunk 49 optimal weight:    0.2980
   chunk 45 optimal weight:    2.9990
   chunk 72 optimal weight:    5.9990
   chunk 99 optimal weight:    1.9990
   chunk 110 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.6018

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

Flipped N/Q/H residues before XYZ refinement:
Y 254 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.087678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.068105 restraints weight = 42232.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.070362 restraints weight = 22376.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.071811 restraints weight = 15065.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.2796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  11857  Z= 0.112
  Angle     :  0.584  11.482  16056  Z= 0.289
  Chirality :  0.041   0.266   1807
  Planarity :  0.004   0.050   2034
  Dihedral  :  4.397  43.519   1545
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 16.21 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.24), residues: 1392
  helix:  1.46 (0.20), residues: 725
  sheet: -1.97 (0.55), residues: 97
  loop : -1.66 (0.27), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP K  43 
 HIS   0.005   0.001   HIS P  48 
 PHE   0.041   0.001   PHE T 328 
 TYR   0.014   0.001   TYR L 180 
 ARG   0.004   0.000   ARG P  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03184 (  523)
  hydrogen bonds       : angle       4.36788 ( 1509)
  covalent geometry    : bond        0.00258 (11857)
  covalent geometry    : angle       0.58441 (16056)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 102
  time to evaluate  : 1.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  261 MET cc_start: 0.7840 (tmm) cc_final: 0.7556 (tmm)
REVERT: T  334 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8093 (mm)
REVERT: K   13 ASP cc_start: 0.8371 (p0) cc_final: 0.8072 (p0)
REVERT: L   91 MET cc_start: 0.8586 (mtm) cc_final: 0.8150 (mtm)
REVERT: Y  211 ARG cc_start: 0.8627 (ptm-80) cc_final: 0.8079 (ttp80)
REVERT: Y  371 SER cc_start: 0.7292 (m) cc_final: 0.7078 (t)
REVERT: P   68 LYS cc_start: 0.8932 (tppt) cc_final: 0.8555 (ptmt)
  outliers start: 25
  outliers final: 13
  residues processed: 123
  average time/residue: 0.2355
  time to fit residues: 43.7210
Evaluate side-chains
  110 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 1.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  319 LEU
Chi-restraints excluded: chain C residue  338 LYS
Chi-restraints excluded: chain T residue  106 LEU
Chi-restraints excluded: chain T residue  143 THR
Chi-restraints excluded: chain T residue  284 THR
Chi-restraints excluded: chain T residue  334 LEU
Chi-restraints excluded: chain T residue  409 ILE
Chi-restraints excluded: chain K residue   34 LYS
Chi-restraints excluded: chain S residue  122 THR
Chi-restraints excluded: chain L residue   28 GLU
Chi-restraints excluded: chain L residue   87 LEU
Chi-restraints excluded: chain L residue  164 VAL
Chi-restraints excluded: chain L residue  285 PHE
Chi-restraints excluded: chain Y residue  341 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 116 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 110 optimal weight:    4.9990
   chunk 14 optimal weight:    7.9990
   chunk 59 optimal weight:    0.0870
   chunk 131 optimal weight:    0.0970
   chunk 55 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.5156

-------------------------------------------------------------------------------
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 = 0.3747 r_free = 0.3747 target = 0.087828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.068233 restraints weight = 41878.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.070494 restraints weight = 22282.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.071951 restraints weight = 15000.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.2909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  11857  Z= 0.107
  Angle     :  0.580  11.853  16056  Z= 0.287
  Chirality :  0.041   0.280   1807
  Planarity :  0.004   0.050   2034
  Dihedral  :  4.376  42.606   1545
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 16.83 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.24), residues: 1392
  helix:  1.47 (0.20), residues: 725
  sheet: -1.81 (0.55), residues: 102
  loop : -1.61 (0.27), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP K  43 
 HIS   0.004   0.001   HIS T 177 
 PHE   0.040   0.001   PHE T 328 
 TYR   0.014   0.001   TYR L 180 
 ARG   0.004   0.000   ARG P  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03092 (  523)
  hydrogen bonds       : angle       4.35991 ( 1509)
  covalent geometry    : bond        0.00244 (11857)
  covalent geometry    : angle       0.58026 (16056)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 1.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  261 MET cc_start: 0.7865 (tmm) cc_final: 0.7586 (tmm)
REVERT: T  334 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8075 (mm)
REVERT: K   13 ASP cc_start: 0.8407 (p0) cc_final: 0.8127 (p0)
REVERT: Y  211 ARG cc_start: 0.8586 (ptm-80) cc_final: 0.8188 (ttp80)
REVERT: Y  293 ARG cc_start: 0.8639 (mmm160) cc_final: 0.8239 (mmm160)
REVERT: Y  371 SER cc_start: 0.7278 (m) cc_final: 0.7034 (t)
REVERT: Y  392 MET cc_start: 0.8018 (ppp) cc_final: 0.7576 (mmt)
REVERT: P   68 LYS cc_start: 0.8963 (tppt) cc_final: 0.8541 (ptmt)
  outliers start: 23
  outliers final: 18
  residues processed: 115
  average time/residue: 0.2425
  time to fit residues: 41.1067
Evaluate side-chains
  112 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 1.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  172 PHE
Chi-restraints excluded: chain C residue  319 LEU
Chi-restraints excluded: chain C residue  338 LYS
Chi-restraints excluded: chain T residue  106 LEU
Chi-restraints excluded: chain T residue  143 THR
Chi-restraints excluded: chain T residue  222 ILE
Chi-restraints excluded: chain T residue  284 THR
Chi-restraints excluded: chain T residue  334 LEU
Chi-restraints excluded: chain T residue  409 ILE
Chi-restraints excluded: chain K residue   31 LEU
Chi-restraints excluded: chain K residue   34 LYS
Chi-restraints excluded: chain S residue   39 VAL
Chi-restraints excluded: chain S residue  122 THR
Chi-restraints excluded: chain L residue   28 GLU
Chi-restraints excluded: chain L residue   87 LEU
Chi-restraints excluded: chain L residue  164 VAL
Chi-restraints excluded: chain L residue  281 LEU
Chi-restraints excluded: chain L residue  285 PHE
Chi-restraints excluded: chain Y residue  341 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 80 optimal weight:    4.9990
   chunk 85 optimal weight:    0.1980
   chunk 25 optimal weight:    0.8980
   chunk 41 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   chunk 95 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 100 optimal weight:    0.0870
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.9960

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

Flipped N/Q/H residues before XYZ refinement:
S  59 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.086215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.066619 restraints weight = 42247.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.068779 restraints weight = 23033.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.070170 restraints weight = 15739.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.2821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11857  Z= 0.135
  Angle     :  0.609  12.859  16056  Z= 0.301
  Chirality :  0.042   0.279   1807
  Planarity :  0.004   0.049   2034
  Dihedral  :  4.474  39.145   1545
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 16.91 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.24), residues: 1392
  helix:  1.44 (0.20), residues: 726
  sheet: -1.71 (0.57), residues: 97
  loop : -1.70 (0.27), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP K  43 
 HIS   0.009   0.001   HIS P  48 
 PHE   0.044   0.002   PHE T 328 
 TYR   0.014   0.001   TYR L 180 
 ARG   0.004   0.000   ARG P  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03363 (  523)
  hydrogen bonds       : angle       4.45909 ( 1509)
  covalent geometry    : bond        0.00313 (11857)
  covalent geometry    : angle       0.60944 (16056)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 88
  time to evaluate  : 2.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   43 MET cc_start: 0.8859 (mmm) cc_final: 0.8466 (mmt)
REVERT: C  261 MET cc_start: 0.7900 (tmm) cc_final: 0.7617 (tmm)
REVERT: C  338 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8085 (ptmm)
REVERT: T  334 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8127 (mm)
REVERT: L   91 MET cc_start: 0.8431 (mtm) cc_final: 0.7930 (mtm)
REVERT: Y  211 ARG cc_start: 0.8730 (ptm-80) cc_final: 0.8422 (ttp80)
REVERT: Y  293 ARG cc_start: 0.8621 (mmm160) cc_final: 0.8284 (mmm160)
REVERT: Y  371 SER cc_start: 0.7275 (m) cc_final: 0.7055 (t)
REVERT: Y  392 MET cc_start: 0.8050 (ppp) cc_final: 0.7585 (mmt)
REVERT: P   68 LYS cc_start: 0.8988 (tppt) cc_final: 0.8590 (ptmt)
  outliers start: 22
  outliers final: 17
  residues processed: 106
  average time/residue: 0.2519
  time to fit residues: 39.5287
Evaluate side-chains
  106 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 1.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  172 PHE
Chi-restraints excluded: chain C residue  319 LEU
Chi-restraints excluded: chain C residue  338 LYS
Chi-restraints excluded: chain T residue  106 LEU
Chi-restraints excluded: chain T residue  143 THR
Chi-restraints excluded: chain T residue  220 ASP
Chi-restraints excluded: chain T residue  222 ILE
Chi-restraints excluded: chain T residue  284 THR
Chi-restraints excluded: chain T residue  334 LEU
Chi-restraints excluded: chain T residue  409 ILE
Chi-restraints excluded: chain K residue   31 LEU
Chi-restraints excluded: chain K residue   34 LYS
Chi-restraints excluded: chain S residue   39 VAL
Chi-restraints excluded: chain S residue  122 THR
Chi-restraints excluded: chain L residue   28 GLU
Chi-restraints excluded: chain L residue   87 LEU
Chi-restraints excluded: chain L residue  164 VAL
Chi-restraints excluded: chain L residue  285 PHE
Chi-restraints excluded: chain Y residue  341 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 105 optimal weight:    3.9990
   chunk 118 optimal weight:    5.9990
   chunk 76 optimal weight:    1.9990
   chunk 75 optimal weight:    0.5980
   chunk 116 optimal weight:    3.9990
   chunk 110 optimal weight:    0.7980
   chunk 128 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3711 r_free = 0.3711 target = 0.086062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.066747 restraints weight = 41949.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.068783 restraints weight = 23552.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.070137 restraints weight = 16376.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11857  Z= 0.138
  Angle     :  0.613  12.271  16056  Z= 0.304
  Chirality :  0.042   0.267   1807
  Planarity :  0.004   0.049   2034
  Dihedral  :  4.558  34.211   1545
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 17.15 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.24), residues: 1392
  helix:  1.41 (0.20), residues: 720
  sheet: -1.75 (0.57), residues: 97
  loop : -1.72 (0.26), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP K  43 
 HIS   0.009   0.001   HIS P  48 
 PHE   0.043   0.001   PHE T 328 
 TYR   0.015   0.001   TYR C  42 
 ARG   0.003   0.000   ARG P  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03467 (  523)
  hydrogen bonds       : angle       4.49933 ( 1509)
  covalent geometry    : bond        0.00319 (11857)
  covalent geometry    : angle       0.61331 (16056)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 84
  time to evaluate  : 2.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   43 MET cc_start: 0.8854 (mmm) cc_final: 0.8542 (mmt)
REVERT: C  261 MET cc_start: 0.7907 (tmm) cc_final: 0.7635 (tmm)
REVERT: T  334 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8095 (mm)
REVERT: L   91 MET cc_start: 0.8550 (mtm) cc_final: 0.8084 (mtm)
REVERT: Y  293 ARG cc_start: 0.8651 (mmm160) cc_final: 0.8323 (mmm160)
REVERT: Y  392 MET cc_start: 0.8031 (ppp) cc_final: 0.7574 (mmt)
REVERT: P   68 LYS cc_start: 0.8996 (tppt) cc_final: 0.8611 (ptpt)
  outliers start: 20
  outliers final: 17
  residues processed: 100
  average time/residue: 0.3261
  time to fit residues: 47.7920
Evaluate side-chains
  99 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 3.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  172 PHE
Chi-restraints excluded: chain C residue  319 LEU
Chi-restraints excluded: chain C residue  338 LYS
Chi-restraints excluded: chain T residue  106 LEU
Chi-restraints excluded: chain T residue  143 THR
Chi-restraints excluded: chain T residue  220 ASP
Chi-restraints excluded: chain T residue  222 ILE
Chi-restraints excluded: chain T residue  284 THR
Chi-restraints excluded: chain T residue  334 LEU
Chi-restraints excluded: chain T residue  409 ILE
Chi-restraints excluded: chain K residue   31 LEU
Chi-restraints excluded: chain K residue   34 LYS
Chi-restraints excluded: chain S residue  122 THR
Chi-restraints excluded: chain L residue   28 GLU
Chi-restraints excluded: chain L residue   87 LEU
Chi-restraints excluded: chain L residue  164 VAL
Chi-restraints excluded: chain L residue  285 PHE
Chi-restraints excluded: chain Y residue  341 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 58 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0020
   chunk 118 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0000
   chunk 34 optimal weight:    0.0970
   chunk 122 optimal weight:    7.9990
   chunk 105 optimal weight:    7.9990
   chunk 100 optimal weight:    0.3980
   chunk 86 optimal weight:    0.8980
   overall best weight:    0.2790

-------------------------------------------------------------------------------
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 = 0.3751 r_free = 0.3751 target = 0.088118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.068547 restraints weight = 41683.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.070793 restraints weight = 22250.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.072215 restraints weight = 15014.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.3113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  11857  Z= 0.105
  Angle     :  0.593  11.811  16056  Z= 0.292
  Chirality :  0.040   0.262   1807
  Planarity :  0.004   0.051   2034
  Dihedral  :  4.368  36.994   1545
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 17.92 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.24), residues: 1392
  helix:  1.43 (0.20), residues: 720
  sheet: -1.82 (0.54), residues: 105
  loop : -1.55 (0.27), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP K  43 
 HIS   0.005   0.001   HIS P  48 
 PHE   0.043   0.001   PHE T 328 
 TYR   0.014   0.001   TYR L 180 
 ARG   0.004   0.000   ARG P  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03036 (  523)
  hydrogen bonds       : angle       4.37638 ( 1509)
  covalent geometry    : bond        0.00229 (11857)
  covalent geometry    : angle       0.59273 (16056)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4007.76 seconds
wall clock time: 74 minutes 31.42 seconds (4471.42 seconds total)