Starting phenix.real_space_refine
on Tue Jan 14 23:23:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8x9p_38178/01_2025/8x9p_38178.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8x9p_38178/01_2025/8x9p_38178.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8x9p_38178/01_2025/8x9p_38178.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8x9p_38178/01_2025/8x9p_38178.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8x9p_38178/01_2025/8x9p_38178.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8x9p_38178/01_2025/8x9p_38178.cif"
  }
  resolution = 3.54
  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=  -0.002 sd=   0.043
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      53      5.16       5
     C    4835      2.51       5
     N    1307      2.21       5
     O    1474      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 7669
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3423
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 439, 3423
          Classifications: {'peptide': 439}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 418}
    Chain: "B"
      Number of atoms: 3359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 427, 3359
          Classifications: {'peptide': 427}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406}
    Chain: "C"
      Number of atoms: 887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 887
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 2, 'TRANS': 104}
  Time building chain proxies: 4.88, per 1000 atoms: 0.64
  Number of scatterers: 7669
  At special positions: 0
  Unit cell: (106.24, 79.68, 99.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      53     16.00
     O    1474      8.00
     N    1307      7.00
     C    4835      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.95
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1798

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 5 sheets defined
      57.5% alpha, 12.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 29
    Processing helix  chain 'A' and resid 71 through 80
      removed outlier: 4.261A  pdb=" N   ILE A  75 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   VAL A  78 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 87
      removed outlier: 3.606A  pdb=" N   PHE A  87 " --> pdb=" O   ARG A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 108
    Processing helix  chain 'A' and resid 111 through 128
      removed outlier: 4.638A  pdb=" N   ASP A 116 " --> pdb=" O   LYS A 112 " (cutoff:3.500A)
      removed outlier: 5.571A  pdb=" N   LEU A 117 " --> pdb=" O   GLU A 113 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   GLN A 128 " --> pdb=" O   LYS A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 162
      removed outlier: 4.333A  pdb=" N   THR A 150 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 178
      removed outlier: 3.504A  pdb=" N   SER A 178 " --> pdb=" O   PRO A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 195
    Processing helix  chain 'A' and resid 206 through 216
    Processing helix  chain 'A' and resid 223 through 244
      removed outlier: 3.541A  pdb=" N   LEU A 227 " --> pdb=" O   THR A 223 " (cutoff:3.500A)
      removed outlier: 4.723A  pdb=" N   SER A 241 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 4.912A  pdb=" N   LEU A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 260
      removed outlier: 3.896A  pdb=" N   PHE A 255 " --> pdb=" O   ASP A 251 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   GLN A 256 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 281
    Processing helix  chain 'A' and resid 287 through 297
    Processing helix  chain 'A' and resid 306 through 310
    Processing helix  chain 'A' and resid 324 through 339
    Processing helix  chain 'A' and resid 384 through 400
      removed outlier: 3.726A  pdb=" N   TRP A 388 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   HIS A 393 " --> pdb=" O   ALA A 389 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LYS A 394 " --> pdb=" O   ARG A 390 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   MET A 398 " --> pdb=" O   LYS A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 411
      removed outlier: 4.380A  pdb=" N   TYR A 408 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 438
      removed outlier: 3.975A  pdb=" N   SER A 419 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 28
    Processing helix  chain 'B' and resid 41 through 46
      removed outlier: 4.506A  pdb=" N   ARG B  46 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 49
      No H-bonds generated for 'chain 'B' and resid 47 through 49'
    Processing helix  chain 'B' and resid 70 through 78
      removed outlier: 3.511A  pdb=" N   SER B  78 " --> pdb=" O   ASP B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 90
    Processing helix  chain 'B' and resid 100 through 106
    Processing helix  chain 'B' and resid 109 through 127
      removed outlier: 4.925A  pdb=" N   SER B 115 " --> pdb=" O   GLU B 111 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   SER B 126 " --> pdb=" O   LYS B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 141 through 159
    Processing helix  chain 'B' and resid 180 through 196
      removed outlier: 4.331A  pdb=" N   GLU B 194 " --> pdb=" O   HIS B 190 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   THR B 196 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 214
    Processing helix  chain 'B' and resid 221 through 242
      removed outlier: 4.592A  pdb=" N   CYS B 239 " --> pdb=" O   GLY B 235 " (cutoff:3.500A)
      removed outlier: 5.015A  pdb=" N   LEU B 240 " --> pdb=" O   VAL B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 258
    Processing helix  chain 'B' and resid 285 through 294
    Processing helix  chain 'B' and resid 295 through 299
      removed outlier: 3.853A  pdb=" N   MET B 299 " --> pdb=" O   ALA B 296 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 308
    Processing helix  chain 'B' and resid 322 through 337
      removed outlier: 3.706A  pdb=" N   VAL B 326 " --> pdb=" O   SER B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 341
    Processing helix  chain 'B' and resid 374 through 391
      removed outlier: 3.782A  pdb=" N   PHE B 378 " --> pdb=" O   ILE B 374 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ALA B 387 " --> pdb=" O   GLU B 383 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   ARG B 391 " --> pdb=" O   ALA B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 400
      removed outlier: 3.587A  pdb=" N   GLY B 400 " --> pdb=" O   HIS B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 427
      removed outlier: 4.089A  pdb=" N   PHE B 408 " --> pdb=" O   ASP B 404 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ASP B 427 " --> pdb=" O   GLN B 423 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 230 through 256
    Processing helix  chain 'C' and resid 261 through 281
    Processing helix  chain 'C' and resid 281 through 296
    Processing helix  chain 'C' and resid 303 through 334
      removed outlier: 3.574A  pdb=" N   LEU C 307 " --> pdb=" O   THR C 303 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   GLN C 317 " --> pdb=" O   MET C 313 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94
      removed outlier: 7.804A  pdb=" N   ILE A  93 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   PHE A  67 " --> pdb=" O   ILE A  93 " (cutoff:3.500A)
      removed outlier: 8.639A  pdb=" N   VAL A  66 " --> pdb=" O   CYS A   4 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   SER A   6 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 7.517A  pdb=" N   VAL A  68 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 5.893A  pdb=" N   HIS A   8 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ILE A   5 " --> pdb=" O   GLY A 134 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   SER A 140 " --> pdb=" O   VAL A   9 " (cutoff:3.500A)
      removed outlier: 5.746A  pdb=" N   PHE A 135 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.533A  pdb=" N   PHE A 169 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 6.113A  pdb=" N   VAL A 137 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 7.935A  pdb=" N   ILE A 171 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 7.836A  pdb=" N   HIS A 139 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   CYS A 200 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55
    Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273
      removed outlier: 7.148A  pdb=" N   ALA A 374 " --> pdb=" O   TYR A 319 " (cutoff:3.500A)
      removed outlier: 4.996A  pdb=" N   TYR A 319 " --> pdb=" O   ALA A 374 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   CYS A 376 " --> pdb=" O   LEU A 317 " (cutoff:3.500A)
      removed outlier: 4.983A  pdb=" N   LEU A 317 " --> pdb=" O   CYS A 376 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   LEU A 378 " --> pdb=" O   CYS A 315 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   CYS A 315 " --> pdb=" O   LEU A 378 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   ASN A 380 " --> pdb=" O   MET A 313 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 91 through 92
      removed outlier: 8.386A  pdb=" N   VAL B  91 " --> pdb=" O   ALA B  63 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   LEU B  65 " --> pdb=" O   VAL B  91 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   GLU B   3 " --> pdb=" O   LEU B 130 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   GLY B 132 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   SER B 138 " --> pdb=" O   ALA B   9 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   GLN B 131 " --> pdb=" O   ILE B 163 " (cutoff:3.500A)
      removed outlier: 7.603A  pdb=" N   ASN B 165 " --> pdb=" O   GLN B 131 " (cutoff:3.500A)
      removed outlier: 5.567A  pdb=" N   PHE B 133 " --> pdb=" O   ASN B 165 " (cutoff:3.500A)
      removed outlier: 7.324A  pdb=" N   PHE B 167 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   LEU B 135 " --> pdb=" O   PHE B 167 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   VAL B 169 " --> pdb=" O   LEU B 135 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   HIS B 137 " --> pdb=" O   VAL B 169 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   THR B 166 " --> pdb=" O   GLU B 198 " (cutoff:3.500A)
      removed outlier: 8.489A  pdb=" N   ASP B 203 " --> pdb=" O   PRO B 268 " (cutoff:3.500A)
      removed outlier: 11.860A  pdb=" N   PHE B 270 " --> pdb=" O   ASP B 203 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   PHE B 265 " --> pdb=" O   SER B 371 " (cutoff:3.500A)
      removed outlier: 4.888A  pdb=" N   SER B 371 " --> pdb=" O   PHE B 265 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 53

    421 hydrogen bonds defined for protein.
    1218 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: 2.17

  Time building geometry restraints manager: 2.24 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: 2499
        1.34 -     1.46: 1288
        1.46 -     1.58: 3969
        1.58 -     1.70: 0
        1.70 -     1.82: 83
  Bond restraints: 7839
  Sorted by residual:
  bond pdb=" CB  ILE B  16 "
       pdb=" CG2 ILE B  16 "
    ideal  model  delta    sigma   weight residual
    1.521  1.467  0.054 3.30e-02 9.18e+02 2.65e+00
  bond pdb=" CG1 ILE B  16 "
       pdb=" CD1 ILE B  16 "
    ideal  model  delta    sigma   weight residual
    1.513  1.450  0.063 3.90e-02 6.57e+02 2.62e+00
  bond pdb=" CB  MET B 233 "
       pdb=" CG  MET B 233 "
    ideal  model  delta    sigma   weight residual
    1.520  1.474  0.046 3.00e-02 1.11e+03 2.34e+00
  bond pdb=" C   CYS A   4 "
       pdb=" N   ILE A   5 "
    ideal  model  delta    sigma   weight residual
    1.335  1.314  0.021 1.41e-02 5.03e+03 2.27e+00
  bond pdb=" CG1 ILE A 188 "
       pdb=" CD1 ILE A 188 "
    ideal  model  delta    sigma   weight residual
    1.513  1.460  0.053 3.90e-02 6.57e+02 1.86e+00
  ... (remaining 7834 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.32: 10460
        2.32 -     4.64: 130
        4.64 -     6.96: 21
        6.96 -     9.28: 6
        9.28 -    11.61: 2
  Bond angle restraints: 10619
  Sorted by residual:
  angle pdb=" N   VAL B 180 "
        pdb=" CA  VAL B 180 "
        pdb=" C   VAL B 180 "
      ideal   model   delta    sigma   weight residual
     113.20  109.77    3.43 9.60e-01 1.09e+00 1.28e+01
  angle pdb=" CA  TRP C 311 "
        pdb=" CB  TRP C 311 "
        pdb=" CG  TRP C 311 "
      ideal   model   delta    sigma   weight residual
     113.60  107.01    6.59 1.90e+00 2.77e-01 1.20e+01
  angle pdb=" CA  LEU B 151 "
        pdb=" CB  LEU B 151 "
        pdb=" CG  LEU B 151 "
      ideal   model   delta    sigma   weight residual
     116.30  127.91  -11.61 3.50e+00 8.16e-02 1.10e+01
  angle pdb=" CA  GLN C 285 "
        pdb=" CB  GLN C 285 "
        pdb=" CG  GLN C 285 "
      ideal   model   delta    sigma   weight residual
     114.10  120.67   -6.57 2.00e+00 2.50e-01 1.08e+01
  angle pdb=" CB  MET B 233 "
        pdb=" CG  MET B 233 "
        pdb=" SD  MET B 233 "
      ideal   model   delta    sigma   weight residual
     112.70  102.95    9.75 3.00e+00 1.11e-01 1.06e+01
  ... (remaining 10614 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 4070
       17.99 -    35.99: 487
       35.99 -    53.98: 92
       53.98 -    71.98: 23
       71.98 -    89.97: 6
  Dihedral angle restraints: 4678
    sinusoidal: 1874
      harmonic: 2804
  Sorted by residual:
  dihedral pdb=" CA  MET B   1 "
           pdb=" C   MET B   1 "
           pdb=" N   ARG B   2 "
           pdb=" CA  ARG B   2 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.19   23.81     0      5.00e+00 4.00e-02 2.27e+01
  dihedral pdb=" CA  GLN B 384 "
           pdb=" C   GLN B 384 "
           pdb=" N   PHE B 385 "
           pdb=" CA  PHE B 385 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.24  -17.76     0      5.00e+00 4.00e-02 1.26e+01
  dihedral pdb=" CA  ASN B 195 "
           pdb=" CB  ASN B 195 "
           pdb=" CG  ASN B 195 "
           pdb=" OD1 ASN B 195 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -163.81   73.81     2      2.00e+01 2.50e-03 1.11e+01
  ... (remaining 4675 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 832
       0.045 -    0.089: 255
       0.089 -    0.134: 65
       0.134 -    0.178: 5
       0.178 -    0.223: 1
  Chirality restraints: 1158
  Sorted by residual:
  chirality pdb=" CB  ILE B  16 "
            pdb=" CA  ILE B  16 "
            pdb=" CG1 ILE B  16 "
            pdb=" CG2 ILE B  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" CB  VAL A 363 "
            pdb=" CA  VAL A 363 "
            pdb=" CG1 VAL A 363 "
            pdb=" CG2 VAL A 363 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.56e-01
  chirality pdb=" CA  MET C 313 "
            pdb=" N   MET C 313 "
            pdb=" C   MET C 313 "
            pdb=" CB  MET C 313 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.97e-01
  ... (remaining 1155 not shown)

  Planarity restraints: 1396
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 286 "   -0.025 2.00e-02 2.50e+03   1.85e-02 6.00e+00
        pdb=" CG  PHE C 286 "    0.039 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 286 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 286 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 286 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 286 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 286 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 316 "   -0.018 2.00e-02 2.50e+03   1.83e-02 5.83e+00
        pdb=" CG  PHE C 316 "    0.042 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 316 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 316 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 316 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 316 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 316 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 385 "    0.015 2.00e-02 2.50e+03   1.46e-02 3.71e+00
        pdb=" CG  PHE B 385 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 385 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 385 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 385 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 385 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 385 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1393 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.70: 225
        2.70 -     3.25: 8246
        3.25 -     3.80: 13014
        3.80 -     4.35: 16607
        4.35 -     4.90: 27070
  Nonbonded interactions: 65162
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 285 "
            pdb=" OE1 GLU B 288 "
     model   vdw
     2.145 3.040
  nonbonded pdb=" N   GLU B 407 "
            pdb=" OE1 GLU B 407 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" OG  SER B 145 "
            pdb=" OG  SER B 188 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   GLY B  10 "
            pdb=" ND2 ASN B  14 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" NE2 GLN A 301 "
            pdb=" O   CYS A 305 "
     model   vdw
     2.257 3.120
  ... (remaining 65157 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:             1.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.020
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   7839  Z= 0.262
  Angle     :  0.671  11.605  10619  Z= 0.352
  Chirality :  0.044   0.223   1158
  Planarity :  0.004   0.037   1396
  Dihedral  : 16.057  89.973   2880
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 17.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  : 21.44 %
    Favored  : 78.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  0.51 (0.27), residues: 967
  helix:  0.63 (0.23), residues: 479
  sheet:  0.80 (0.47), residues: 135
  loop : -0.06 (0.34), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP C 311 
 HIS   0.004   0.001   HIS A 406 
 PHE   0.042   0.002   PHE C 316 
 TYR   0.011   0.001   TYR A 399 
 ARG   0.003   0.000   ARG B 391 

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 199
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6177 (tmm) cc_final: 0.5879 (tmm)
REVERT: A  199 ASP cc_start: 0.7970 (t0) cc_final: 0.7658 (t0)
REVERT: A  217 LEU cc_start: 0.8496 (mt) cc_final: 0.7738 (mt)
REVERT: A  272 TYR cc_start: 0.8026 (t80) cc_final: 0.7676 (t80)
REVERT: A  313 MET cc_start: 0.7696 (mmm) cc_final: 0.7325 (tmm)
REVERT: B   65 LEU cc_start: 0.8115 (mm) cc_final: 0.7566 (mm)
REVERT: B  207 LEU cc_start: 0.7547 (mt) cc_final: 0.7154 (mt)
REVERT: B  226 ASN cc_start: 0.8065 (m-40) cc_final: 0.7558 (m110)
REVERT: B  257 MET cc_start: 0.7956 (tpp) cc_final: 0.7233 (mmt)
REVERT: B  364 SER cc_start: 0.8579 (p) cc_final: 0.8342 (m)
REVERT: B  406 MET cc_start: 0.9029 (mmm) cc_final: 0.8805 (mmt)
REVERT: C  231 VAL cc_start: 0.7931 (p) cc_final: 0.7357 (m)
REVERT: C  244 LYS cc_start: 0.8626 (ptmt) cc_final: 0.8295 (pttt)
REVERT: C  267 LEU cc_start: 0.8871 (mm) cc_final: 0.8431 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 200
  average time/residue: 0.1981
  time to fit residues: 53.4028
Evaluate side-chains
  135 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 72 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 28 optimal weight:   10.0000
   chunk 45 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 86 optimal weight:    1.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  37 HIS
B 195 ASN
B 291 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.140076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.106164 restraints weight = 15973.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.110532 restraints weight = 8549.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.113096 restraints weight = 6104.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.1795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7839  Z= 0.273
  Angle     :  0.657  11.805  10619  Z= 0.345
  Chirality :  0.045   0.175   1158
  Planarity :  0.005   0.051   1396
  Dihedral  :  4.154  16.551   1055
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 13.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 20.72 %
    Favored  : 76.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  0.34 (0.27), residues: 967
  helix:  0.52 (0.23), residues: 484
  sheet:  0.60 (0.45), residues: 134
  loop : -0.14 (0.35), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 311 
 HIS   0.009   0.002   HIS A 309 
 PHE   0.034   0.002   PHE C 316 
 TYR   0.014   0.001   TYR A  24 
 ARG   0.005   0.001   ARG C 282 

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 154
  time to evaluate  : 0.937 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 ASP cc_start: 0.8107 (t0) cc_final: 0.7776 (t0)
REVERT: A  213 CYS cc_start: 0.8814 (t) cc_final: 0.8571 (t)
REVERT: A  272 TYR cc_start: 0.8148 (t80) cc_final: 0.7873 (t80)
REVERT: B  209 ASP cc_start: 0.8348 (t0) cc_final: 0.7923 (t0)
REVERT: B  226 ASN cc_start: 0.8139 (m-40) cc_final: 0.7793 (m-40)
REVERT: B  364 SER cc_start: 0.8592 (p) cc_final: 0.8343 (m)
REVERT: C  241 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7447 (mm-30)
REVERT: C  244 LYS cc_start: 0.8734 (ptmt) cc_final: 0.8473 (pttm)
REVERT: C  250 PHE cc_start: 0.8429 (m-80) cc_final: 0.8135 (m-80)
REVERT: C  267 LEU cc_start: 0.8878 (mm) cc_final: 0.8441 (mm)
  outliers start: 23
  outliers final: 16
  residues processed: 173
  average time/residue: 0.1847
  time to fit residues: 44.1506
Evaluate side-chains
  151 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 135
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain B residue    8 GLN
Chi-restraints excluded: chain B residue  159 TYR
Chi-restraints excluded: chain B residue  163 ILE
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  239 CYS
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  371 SER
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain C residue  260 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 47 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 73 optimal weight:    0.0770
   chunk 14 optimal weight:    1.9990
   chunk 46 optimal weight:    7.9990
   chunk 17 optimal weight:    1.9990
   chunk 31 optimal weight:    8.9990
   chunk 65 optimal weight:    0.8980
   chunk 77 optimal weight:    0.4980
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.8940

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

Flipped N/Q/H residues before XYZ refinement:
** A  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  37 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.141206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.107024 restraints weight = 16063.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.111390 restraints weight = 8587.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.114060 restraints weight = 6157.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.2206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7839  Z= 0.207
  Angle     :  0.608   7.925  10619  Z= 0.313
  Chirality :  0.043   0.171   1158
  Planarity :  0.004   0.068   1396
  Dihedral  :  4.064  16.378   1055
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 19.76 %
    Favored  : 76.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.27), residues: 967
  helix:  0.64 (0.23), residues: 490
  sheet:  0.63 (0.45), residues: 127
  loop : -0.22 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 311 
 HIS   0.009   0.001   HIS B 227 
 PHE   0.026   0.002   PHE C 316 
 TYR   0.022   0.001   TYR A  24 
 ARG   0.007   0.000   ARG B 213 

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 150
  time to evaluate  : 0.949 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 ASN cc_start: 0.7978 (p0) cc_final: 0.7586 (p0)
REVERT: A  199 ASP cc_start: 0.8130 (t0) cc_final: 0.7828 (t0)
REVERT: A  213 CYS cc_start: 0.8782 (t) cc_final: 0.8428 (t)
REVERT: A  228 ASN cc_start: 0.7988 (m110) cc_final: 0.7735 (m-40)
REVERT: B   73 MET cc_start: 0.5126 (mpt) cc_final: 0.4617 (mpp)
REVERT: B  207 LEU cc_start: 0.7948 (mt) cc_final: 0.7395 (mt)
REVERT: B  226 ASN cc_start: 0.8158 (m-40) cc_final: 0.7799 (m-40)
REVERT: B  364 SER cc_start: 0.8635 (p) cc_final: 0.8384 (m)
REVERT: B  406 MET cc_start: 0.9047 (mmm) cc_final: 0.8754 (mmm)
REVERT: C  250 PHE cc_start: 0.8457 (m-80) cc_final: 0.8237 (m-10)
REVERT: C  260 ILE cc_start: 0.6208 (OUTLIER) cc_final: 0.5767 (tp)
REVERT: C  267 LEU cc_start: 0.8817 (mm) cc_final: 0.8438 (mm)
REVERT: C  284 LYS cc_start: 0.8365 (mttt) cc_final: 0.8098 (ptpp)
  outliers start: 30
  outliers final: 16
  residues processed: 173
  average time/residue: 0.1929
  time to fit residues: 45.6568
Evaluate side-chains
  149 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain B residue    8 GLN
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue  159 TYR
Chi-restraints excluded: chain B residue  163 ILE
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  239 CYS
Chi-restraints excluded: chain B residue  312 THR
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain C residue  260 ILE
Chi-restraints excluded: chain C residue  306 ASP
Chi-restraints excluded: chain C residue  311 TRP
Chi-restraints excluded: chain C residue  320 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 19 optimal weight:    8.9990
   chunk 84 optimal weight:    0.9990
   chunk 10 optimal weight:    5.9990
   chunk 8 optimal weight:    7.9990
   chunk 28 optimal weight:   10.0000
   chunk 65 optimal weight:    0.8980
   chunk 87 optimal weight:    5.9990
   chunk 64 optimal weight:    4.9990
   chunk 73 optimal weight:    5.9990
   chunk 33 optimal weight:    9.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    2.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  37 HIS
B 245 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.135010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.100326 restraints weight = 16159.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.104504 restraints weight = 8594.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.106942 restraints weight = 6175.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.3015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.078   7839  Z= 0.382
  Angle     :  0.696  11.642  10619  Z= 0.363
  Chirality :  0.045   0.185   1158
  Planarity :  0.005   0.070   1396
  Dihedral  :  4.372  18.872   1055
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 15.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 20.72 %
    Favored  : 74.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  0.17 (0.27), residues: 967
  helix:  0.55 (0.23), residues: 488
  sheet:  0.21 (0.45), residues: 133
  loop : -0.37 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  21 
 HIS   0.008   0.002   HIS A 107 
 PHE   0.017   0.002   PHE B 408 
 TYR   0.018   0.002   TYR A 408 
 ARG   0.006   0.001   ARG C 282 

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 142
  time to evaluate  : 0.905 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 ASP cc_start: 0.8193 (t0) cc_final: 0.7881 (t0)
REVERT: A  213 CYS cc_start: 0.8885 (t) cc_final: 0.8487 (t)
REVERT: A  224 TYR cc_start: 0.3455 (OUTLIER) cc_final: 0.1706 (m-80)
REVERT: B   73 MET cc_start: 0.5342 (mpt) cc_final: 0.4958 (mpp)
REVERT: B  181 GLU cc_start: 0.7376 (mp0) cc_final: 0.7052 (mp0)
REVERT: B  207 LEU cc_start: 0.8023 (mt) cc_final: 0.7445 (mt)
REVERT: B  364 SER cc_start: 0.8881 (p) cc_final: 0.8466 (m)
REVERT: B  406 MET cc_start: 0.9207 (mmm) cc_final: 0.8901 (mmm)
REVERT: C  250 PHE cc_start: 0.8492 (m-10) cc_final: 0.8199 (m-10)
REVERT: C  263 ASP cc_start: 0.8509 (m-30) cc_final: 0.8191 (m-30)
REVERT: C  267 LEU cc_start: 0.9027 (mm) cc_final: 0.8589 (mm)
REVERT: C  281 GLU cc_start: 0.7093 (tt0) cc_final: 0.6610 (tt0)
REVERT: C  284 LYS cc_start: 0.8522 (mttt) cc_final: 0.8124 (ptmt)
  outliers start: 38
  outliers final: 32
  residues processed: 172
  average time/residue: 0.1849
  time to fit residues: 44.0523
Evaluate side-chains
  157 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 124
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  176 GLN
Chi-restraints excluded: chain A residue  186 ASN
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain B residue    8 GLN
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue  135 LEU
Chi-restraints excluded: chain B residue  159 TYR
Chi-restraints excluded: chain B residue  163 ILE
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  239 CYS
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  312 THR
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  335 ASN
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain C residue  260 ILE
Chi-restraints excluded: chain C residue  306 ASP
Chi-restraints excluded: chain C residue  311 TRP
Chi-restraints excluded: chain C residue  320 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 85 optimal weight:    9.9990
   chunk 93 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 78 optimal weight:    9.9990
   chunk 83 optimal weight:    9.9990
   chunk 74 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 33 optimal weight:    0.3980
   chunk 88 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 60 optimal weight:    0.4980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 101 ASN
A 300 ASN
** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  37 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.137755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.103401 restraints weight = 15906.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.107532 restraints weight = 8758.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.110018 restraints weight = 6355.692|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.3220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7839  Z= 0.189
  Angle     :  0.623  10.068  10619  Z= 0.319
  Chirality :  0.042   0.209   1158
  Planarity :  0.004   0.052   1396
  Dihedral  :  4.214  22.296   1055
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 21.08 %
    Favored  : 75.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.27), residues: 967
  helix:  0.59 (0.23), residues: 490
  sheet:  0.27 (0.45), residues: 132
  loop : -0.25 (0.35), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 252 
 HIS   0.005   0.001   HIS A 107 
 PHE   0.022   0.001   PHE B 408 
 TYR   0.047   0.001   TYR A  24 
 ARG   0.003   0.000   ARG C 276 

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 140
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 ASP cc_start: 0.8096 (t0) cc_final: 0.7804 (t0)
REVERT: A  213 CYS cc_start: 0.8826 (t) cc_final: 0.8418 (t)
REVERT: A  224 TYR cc_start: 0.4084 (OUTLIER) cc_final: 0.2168 (m-80)
REVERT: A  228 ASN cc_start: 0.8256 (m110) cc_final: 0.7989 (m110)
REVERT: B   73 MET cc_start: 0.5202 (mpt) cc_final: 0.4858 (mpp)
REVERT: B  207 LEU cc_start: 0.7842 (mt) cc_final: 0.7271 (mt)
REVERT: B  364 SER cc_start: 0.8778 (p) cc_final: 0.8412 (m)
REVERT: B  383 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7319 (mp0)
REVERT: B  406 MET cc_start: 0.9174 (mmm) cc_final: 0.8773 (mmm)
REVERT: C  244 LYS cc_start: 0.8724 (ptmt) cc_final: 0.8462 (ptpt)
REVERT: C  250 PHE cc_start: 0.8559 (m-10) cc_final: 0.8309 (m-10)
REVERT: C  252 TRP cc_start: 0.8013 (m100) cc_final: 0.7621 (m100)
REVERT: C  267 LEU cc_start: 0.8918 (mm) cc_final: 0.8534 (mm)
REVERT: C  284 LYS cc_start: 0.8545 (mttt) cc_final: 0.8189 (ptmt)
  outliers start: 30
  outliers final: 22
  residues processed: 163
  average time/residue: 0.1797
  time to fit residues: 41.0307
Evaluate side-chains
  151 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue    8 GLN
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue  159 TYR
Chi-restraints excluded: chain B residue  163 ILE
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  239 CYS
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain C residue  260 ILE
Chi-restraints excluded: chain C residue  306 ASP
Chi-restraints excluded: chain C residue  311 TRP
Chi-restraints excluded: chain C residue  320 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 63 optimal weight:    0.7980
   chunk 64 optimal weight:    0.2980
   chunk 45 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 92 optimal weight:    9.9990
   chunk 80 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  37 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.137808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.104042 restraints weight = 15846.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.108221 restraints weight = 8706.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.110755 restraints weight = 6268.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.3410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7839  Z= 0.192
  Angle     :  0.618   9.893  10619  Z= 0.315
  Chirality :  0.042   0.231   1158
  Planarity :  0.004   0.053   1396
  Dihedral  :  4.115  23.266   1055
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 21.44 %
    Favored  : 74.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  0.34 (0.27), residues: 967
  helix:  0.67 (0.23), residues: 484
  sheet:  0.30 (0.46), residues: 132
  loop : -0.25 (0.35), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 311 
 HIS   0.006   0.001   HIS A 107 
 PHE   0.018   0.001   PHE B 408 
 TYR   0.044   0.001   TYR A  24 
 ARG   0.003   0.000   ARG C 276 

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 141
  time to evaluate  : 0.860 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 ASP cc_start: 0.8079 (t0) cc_final: 0.7807 (t0)
REVERT: A  207 GLU cc_start: 0.7741 (mp0) cc_final: 0.7518 (mp0)
REVERT: A  213 CYS cc_start: 0.8834 (t) cc_final: 0.8432 (t)
REVERT: A  228 ASN cc_start: 0.8281 (m110) cc_final: 0.7988 (m110)
REVERT: A  351 PHE cc_start: 0.6712 (OUTLIER) cc_final: 0.6501 (p90)
REVERT: B   73 MET cc_start: 0.5197 (mpt) cc_final: 0.4866 (mpp)
REVERT: B  181 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7409 (mp0)
REVERT: B  207 LEU cc_start: 0.7831 (mt) cc_final: 0.7260 (mt)
REVERT: B  226 ASN cc_start: 0.8219 (m-40) cc_final: 0.7801 (m110)
REVERT: B  364 SER cc_start: 0.8744 (p) cc_final: 0.8406 (m)
REVERT: B  383 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7341 (mp0)
REVERT: B  406 MET cc_start: 0.9152 (mmm) cc_final: 0.8818 (mmm)
REVERT: C  250 PHE cc_start: 0.8523 (m-10) cc_final: 0.8238 (m-10)
REVERT: C  267 LEU cc_start: 0.8971 (mm) cc_final: 0.8528 (mm)
REVERT: C  284 LYS cc_start: 0.8558 (mttt) cc_final: 0.8239 (ptmt)
  outliers start: 33
  outliers final: 24
  residues processed: 167
  average time/residue: 0.1807
  time to fit residues: 42.3881
Evaluate side-chains
  153 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 127
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  351 PHE
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue    8 GLN
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue  159 TYR
Chi-restraints excluded: chain B residue  163 ILE
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  181 GLU
Chi-restraints excluded: chain B residue  239 CYS
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  335 ASN
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain C residue  306 ASP
Chi-restraints excluded: chain C residue  311 TRP
Chi-restraints excluded: chain C residue  320 ASP
Chi-restraints excluded: chain C residue  329 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 47 optimal weight:    0.0070
   chunk 29 optimal weight:    0.0270
   chunk 25 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 54 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 93 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.5456

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

Flipped N/Q/H residues before XYZ refinement:
** A  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  37 HIS
B 134 GLN
C 327 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.138524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.104449 restraints weight = 15866.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.108780 restraints weight = 8560.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.111369 restraints weight = 6123.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.3602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7839  Z= 0.186
  Angle     :  0.620  10.222  10619  Z= 0.317
  Chirality :  0.043   0.239   1158
  Planarity :  0.004   0.067   1396
  Dihedral  :  4.003  17.422   1055
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 12.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 22.99 %
    Favored  : 73.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  0.37 (0.27), residues: 967
  helix:  0.69 (0.23), residues: 482
  sheet:  0.51 (0.49), residues: 119
  loop : -0.29 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 311 
 HIS   0.006   0.001   HIS A 107 
 PHE   0.018   0.001   PHE B 408 
 TYR   0.045   0.001   TYR A  24 
 ARG   0.010   0.000   ARG B   2 

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 139
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 ASP cc_start: 0.8057 (t0) cc_final: 0.7784 (t0)
REVERT: A  207 GLU cc_start: 0.7749 (mp0) cc_final: 0.7344 (mp0)
REVERT: A  213 CYS cc_start: 0.8829 (t) cc_final: 0.8420 (t)
REVERT: A  228 ASN cc_start: 0.8293 (m110) cc_final: 0.7991 (m110)
REVERT: A  313 MET cc_start: 0.6831 (OUTLIER) cc_final: 0.6345 (tmm)
REVERT: A  351 PHE cc_start: 0.6698 (OUTLIER) cc_final: 0.6484 (p90)
REVERT: B   73 MET cc_start: 0.5120 (mpt) cc_final: 0.4821 (mpp)
REVERT: B  181 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7245 (mp0)
REVERT: B  207 LEU cc_start: 0.7859 (mt) cc_final: 0.7310 (mt)
REVERT: B  226 ASN cc_start: 0.8181 (m-40) cc_final: 0.7780 (m110)
REVERT: B  364 SER cc_start: 0.8725 (p) cc_final: 0.8368 (m)
REVERT: B  383 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7321 (mp0)
REVERT: B  406 MET cc_start: 0.9185 (mmm) cc_final: 0.8895 (mmm)
REVERT: B  412 GLU cc_start: 0.8226 (pp20) cc_final: 0.7699 (pp20)
REVERT: C  250 PHE cc_start: 0.8592 (m-10) cc_final: 0.8304 (m-10)
REVERT: C  267 LEU cc_start: 0.8955 (mm) cc_final: 0.8511 (mm)
REVERT: C  284 LYS cc_start: 0.8579 (mttt) cc_final: 0.8305 (ptmt)
  outliers start: 30
  outliers final: 23
  residues processed: 160
  average time/residue: 0.1758
  time to fit residues: 40.4263
Evaluate side-chains
  153 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 127
  time to evaluate  : 1.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  351 PHE
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue    8 GLN
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue  159 TYR
Chi-restraints excluded: chain B residue  163 ILE
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  181 GLU
Chi-restraints excluded: chain B residue  239 CYS
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain C residue  263 ASP
Chi-restraints excluded: chain C residue  306 ASP
Chi-restraints excluded: chain C residue  311 TRP
Chi-restraints excluded: chain C residue  320 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 79 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9990
   chunk 29 optimal weight:    4.9990
   chunk 85 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 88 optimal weight:    0.6980
   chunk 75 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  37 HIS
B 134 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.139133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.105713 restraints weight = 15859.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.109815 restraints weight = 8530.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.112318 restraints weight = 6041.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.3765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7839  Z= 0.212
  Angle     :  0.654  11.544  10619  Z= 0.333
  Chirality :  0.043   0.236   1158
  Planarity :  0.004   0.059   1396
  Dihedral  :  4.006  16.607   1055
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 24.31 %
    Favored  : 72.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  0.38 (0.27), residues: 967
  helix:  0.72 (0.23), residues: 481
  sheet:  0.43 (0.48), residues: 119
  loop : -0.28 (0.34), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 311 
 HIS   0.005   0.001   HIS A 107 
 PHE   0.025   0.002   PHE B 270 
 TYR   0.037   0.001   TYR A  24 
 ARG   0.007   0.000   ARG B   2 

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 135
  time to evaluate  : 1.030 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 ASP cc_start: 0.8092 (t0) cc_final: 0.7808 (t0)
REVERT: A  207 GLU cc_start: 0.7762 (mp0) cc_final: 0.7353 (mp0)
REVERT: A  213 CYS cc_start: 0.8824 (t) cc_final: 0.8423 (t)
REVERT: A  228 ASN cc_start: 0.8274 (m110) cc_final: 0.7961 (m110)
REVERT: A  313 MET cc_start: 0.6815 (OUTLIER) cc_final: 0.6346 (tmm)
REVERT: A  351 PHE cc_start: 0.6715 (OUTLIER) cc_final: 0.6506 (p90)
REVERT: B   73 MET cc_start: 0.5232 (mpt) cc_final: 0.4910 (mpp)
REVERT: B  207 LEU cc_start: 0.7866 (mt) cc_final: 0.7324 (mt)
REVERT: B  226 ASN cc_start: 0.8164 (m-40) cc_final: 0.7765 (m110)
REVERT: B  364 SER cc_start: 0.8681 (p) cc_final: 0.8349 (m)
REVERT: B  389 PHE cc_start: 0.8224 (t80) cc_final: 0.8021 (m-80)
REVERT: B  406 MET cc_start: 0.9197 (mmm) cc_final: 0.8935 (mmm)
REVERT: B  412 GLU cc_start: 0.8175 (pp20) cc_final: 0.7728 (pp20)
REVERT: C  243 GLU cc_start: 0.9007 (tp30) cc_final: 0.8736 (tp30)
REVERT: C  250 PHE cc_start: 0.8581 (m-10) cc_final: 0.8327 (m-10)
REVERT: C  267 LEU cc_start: 0.8976 (mm) cc_final: 0.8533 (mm)
REVERT: C  281 GLU cc_start: 0.7363 (tm-30) cc_final: 0.6894 (tt0)
REVERT: C  301 GLU cc_start: 0.5223 (pm20) cc_final: 0.5006 (pm20)
  outliers start: 28
  outliers final: 23
  residues processed: 156
  average time/residue: 0.1847
  time to fit residues: 41.5145
Evaluate side-chains
  156 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 131
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  351 PHE
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue    8 GLN
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue  159 TYR
Chi-restraints excluded: chain B residue  163 ILE
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  239 CYS
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  335 ASN
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain C residue  263 ASP
Chi-restraints excluded: chain C residue  306 ASP
Chi-restraints excluded: chain C residue  311 TRP
Chi-restraints excluded: chain C residue  320 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 57 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0470
   chunk 38 optimal weight:    6.9990
   chunk 33 optimal weight:    6.9990
   chunk 22 optimal weight:    0.4980
   chunk 27 optimal weight:    0.6980
   chunk 35 optimal weight:    0.0470
   chunk 53 optimal weight:    0.9990
   chunk 92 optimal weight:    9.9990
   overall best weight:    0.4576

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

Flipped N/Q/H residues before XYZ refinement:
** A  18 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 = 0.4206 r_free = 0.4206 target = 0.140320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.106973 restraints weight = 15865.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.111172 restraints weight = 8445.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.113710 restraints weight = 5954.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.3883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7839  Z= 0.189
  Angle     :  0.658  12.020  10619  Z= 0.334
  Chirality :  0.043   0.238   1158
  Planarity :  0.004   0.053   1396
  Dihedral  :  3.985  16.482   1055
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 25.03 %
    Favored  : 72.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.27), residues: 967
  helix:  0.66 (0.23), residues: 483
  sheet:  0.41 (0.49), residues: 119
  loop : -0.24 (0.35), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 311 
 HIS   0.005   0.001   HIS A 107 
 PHE   0.024   0.001   PHE B 408 
 TYR   0.039   0.001   TYR A  24 
 ARG   0.005   0.000   ARG B   2 

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 138
  time to evaluate  : 0.887 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 ASP cc_start: 0.8020 (t0) cc_final: 0.7791 (t0)
REVERT: A  207 GLU cc_start: 0.7778 (mp0) cc_final: 0.7355 (mp0)
REVERT: A  213 CYS cc_start: 0.8827 (t) cc_final: 0.8428 (t)
REVERT: A  228 ASN cc_start: 0.8249 (m110) cc_final: 0.7928 (m110)
REVERT: A  313 MET cc_start: 0.6722 (OUTLIER) cc_final: 0.6219 (tmm)
REVERT: A  351 PHE cc_start: 0.6718 (OUTLIER) cc_final: 0.6516 (p90)
REVERT: B   73 MET cc_start: 0.5180 (mpt) cc_final: 0.4875 (mpp)
REVERT: B  207 LEU cc_start: 0.7889 (mt) cc_final: 0.7359 (mt)
REVERT: B  226 ASN cc_start: 0.8167 (m-40) cc_final: 0.7777 (m110)
REVERT: B  364 SER cc_start: 0.8589 (p) cc_final: 0.8291 (m)
REVERT: C  243 GLU cc_start: 0.9013 (tp30) cc_final: 0.8735 (tp30)
REVERT: C  250 PHE cc_start: 0.8624 (m-10) cc_final: 0.8382 (m-10)
REVERT: C  267 LEU cc_start: 0.8969 (mm) cc_final: 0.8541 (mm)
REVERT: C  281 GLU cc_start: 0.7386 (tm-30) cc_final: 0.6985 (tt0)
  outliers start: 24
  outliers final: 20
  residues processed: 154
  average time/residue: 0.1766
  time to fit residues: 38.0761
Evaluate side-chains
  149 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 127
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  351 PHE
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue    8 GLN
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue  159 TYR
Chi-restraints excluded: chain B residue  163 ILE
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  239 CYS
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain C residue  233 TYR
Chi-restraints excluded: chain C residue  311 TRP
Chi-restraints excluded: chain C residue  320 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 67 optimal weight:    0.8980
   chunk 73 optimal weight:    5.9990
   chunk 39 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 24 optimal weight:   10.0000
   chunk 46 optimal weight:    4.9990
   chunk 87 optimal weight:    0.8980
   chunk 85 optimal weight:    6.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  37 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.136552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.101968 restraints weight = 16102.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.106033 restraints weight = 8828.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.108503 restraints weight = 6367.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.4046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7839  Z= 0.220
  Angle     :  0.695  12.002  10619  Z= 0.349
  Chirality :  0.044   0.228   1158
  Planarity :  0.004   0.056   1396
  Dihedral  :  3.957  15.969   1055
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 14.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 25.15 %
    Favored  : 71.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.27), residues: 967
  helix:  0.61 (0.23), residues: 482
  sheet:  0.34 (0.48), residues: 119
  loop : -0.29 (0.35), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 311 
 HIS   0.011   0.001   HIS B 227 
 PHE   0.028   0.002   PHE B 317 
 TYR   0.037   0.001   TYR A  24 
 ARG   0.005   0.000   ARG C 282 

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 126
  time to evaluate  : 1.039 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  207 GLU cc_start: 0.7818 (mp0) cc_final: 0.7381 (mp0)
REVERT: A  213 CYS cc_start: 0.8848 (t) cc_final: 0.8420 (t)
REVERT: A  228 ASN cc_start: 0.8254 (m110) cc_final: 0.7932 (m110)
REVERT: A  313 MET cc_start: 0.6729 (OUTLIER) cc_final: 0.6177 (tmm)
REVERT: A  351 PHE cc_start: 0.6728 (OUTLIER) cc_final: 0.6494 (p90)
REVERT: B   19 LYS cc_start: 0.8971 (tptm) cc_final: 0.8666 (tppt)
REVERT: B   73 MET cc_start: 0.5300 (mpt) cc_final: 0.4796 (mpp)
REVERT: B  207 LEU cc_start: 0.7853 (mt) cc_final: 0.7324 (mt)
REVERT: B  226 ASN cc_start: 0.8121 (m-40) cc_final: 0.7609 (m110)
REVERT: B  364 SER cc_start: 0.8597 (p) cc_final: 0.8360 (m)
REVERT: B  389 PHE cc_start: 0.8214 (t80) cc_final: 0.7944 (m-80)
REVERT: C  243 GLU cc_start: 0.9044 (tp30) cc_final: 0.8766 (tp30)
REVERT: C  250 PHE cc_start: 0.8679 (m-10) cc_final: 0.8436 (m-10)
REVERT: C  267 LEU cc_start: 0.8992 (mm) cc_final: 0.8571 (mm)
  outliers start: 24
  outliers final: 21
  residues processed: 142
  average time/residue: 0.1716
  time to fit residues: 34.5864
Evaluate side-chains
  149 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 126
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  351 PHE
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue    8 GLN
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue  159 TYR
Chi-restraints excluded: chain B residue  163 ILE
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  239 CYS
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  335 ASN
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain C residue  233 TYR
Chi-restraints excluded: chain C residue  311 TRP
Chi-restraints excluded: chain C residue  320 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 88 optimal weight:    0.3980
   chunk 12 optimal weight:    0.0970
   chunk 30 optimal weight:    0.7980
   chunk 3 optimal weight:    0.4980
   chunk 16 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 66 optimal weight:    0.7980
   chunk 73 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
** A  18 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 = 0.4174 r_free = 0.4174 target = 0.137227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.103278 restraints weight = 16017.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.107396 restraints weight = 8682.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.109957 restraints weight = 6214.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.4148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7839  Z= 0.198
  Angle     :  0.690  12.207  10619  Z= 0.346
  Chirality :  0.043   0.227   1158
  Planarity :  0.004   0.053   1396
  Dihedral  :  3.941  15.747   1055
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 24.91 %
    Favored  : 72.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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 (0.27), residues: 967
  helix:  0.54 (0.23), residues: 482
  sheet:  0.33 (0.49), residues: 119
  loop : -0.27 (0.35), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 311 
 HIS   0.013   0.001   HIS B 227 
 PHE   0.021   0.001   PHE B 408 
 TYR   0.039   0.001   TYR A  24 
 ARG   0.006   0.000   ARG C 282 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2688.53 seconds
wall clock time: 49 minutes 7.43 seconds (2947.43 seconds total)