Starting phenix.real_space_refine
on Thu Jul 31 11:08:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8twe_41667/07_2025/8twe_41667.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8twe_41667/07_2025/8twe_41667.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8twe_41667/07_2025/8twe_41667.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8twe_41667/07_2025/8twe_41667.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8twe_41667/07_2025/8twe_41667.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8twe_41667/07_2025/8twe_41667.cif"
  }
  resolution = 2.55
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    4210      2.51       5
     N    1154      2.21       5
     O    1283      1.98       5
     H    6636      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13319
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6065
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 387, 6065
          Classifications: {'peptide': 387}
          Link IDs: {'PTRANS': 18, 'TRANS': 368}
    Chain: "B"
      Number of atoms: 6849
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 423, 6849
          Classifications: {'peptide': 423}
          Link IDs: {'PTRANS': 14, 'TRANS': 408}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 201
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 201
          Classifications: {'peptide': 11}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 9}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Planarities with less than four sites: {'MLL%COO:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "D"
      Number of atoms: 204
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 204
          Classifications: {'peptide': 12}
          Link IDs: {'TRANS': 11}
  Time building chain proxies: 9.07, per 1000 atoms: 0.68
  Number of scatterers: 13319
  At special positions: 0
  Unit cell: (100.926, 89.178, 106.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      36     16.00
     O    1283      8.00
     N    1154      7.00
     C    4210      6.00
     H    6636      1.00
    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: 3.60
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1620

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 9 sheets defined
      49.3% alpha, 18.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 20
    Processing helix  chain 'A' and resid 24 through 34
    Processing helix  chain 'A' and resid 34 through 43
    Processing helix  chain 'A' and resid 43 through 50
    Processing helix  chain 'A' and resid 50 through 57
      removed outlier: 3.614A  pdb=" N   PHE A  54 " --> pdb=" O   GLU A  50 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   ASP A  57 " --> pdb=" O   PRO A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 74
      removed outlier: 3.535A  pdb=" N   GLY A  74 " --> pdb=" O   ALA A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 88
      removed outlier: 5.493A  pdb=" N   HIS A  87 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 97
    Processing helix  chain 'A' and resid 101 through 117
      removed outlier: 3.807A  pdb=" N   HIS A 117 " --> pdb=" O   ARG A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 127
    Processing helix  chain 'A' and resid 127 through 137
    Processing helix  chain 'A' and resid 140 through 148
      removed outlier: 3.525A  pdb=" N   CYS A 148 " --> pdb=" O   ARG A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 155
      removed outlier: 3.737A  pdb=" N   CYS A 154 " --> pdb=" O   LEU A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 175
    Processing helix  chain 'A' and resid 178 through 196
      removed outlier: 4.501A  pdb=" N   GLY A 190 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
      removed outlier: 5.123A  pdb=" N   GLU A 191 " --> pdb=" O   SER A 187 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   VAL A 195 " --> pdb=" O   GLU A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 204
    Processing helix  chain 'A' and resid 204 through 214
    Processing helix  chain 'A' and resid 217 through 222
    Processing helix  chain 'A' and resid 223 through 235
      removed outlier: 3.517A  pdb=" N   LEU A 234 " --> pdb=" O   ASN A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 244
      removed outlier: 4.430A  pdb=" N   GLU A 241 " --> pdb=" O   GLN A 237 " (cutoff:3.500A)
      removed outlier: 4.822A  pdb=" N   ALA A 242 " --> pdb=" O   GLU A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 253
    Processing helix  chain 'A' and resid 256 through 266
    Processing helix  chain 'A' and resid 266 through 275
    Processing helix  chain 'A' and resid 275 through 282
    Processing helix  chain 'A' and resid 282 through 292
    Processing helix  chain 'A' and resid 295 through 305
      removed outlier: 3.852A  pdb=" N   LYS A 305 " --> pdb=" O   ALA A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 313
      removed outlier: 3.520A  pdb=" N   LEU A 313 " --> pdb=" O   PHE A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 325
    Processing helix  chain 'A' and resid 325 through 335
      removed outlier: 4.213A  pdb=" N   CYS A 329 " --> pdb=" O   GLN A 325 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLU A 332 " --> pdb=" O   PRO A 328 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   SER A 335 " --> pdb=" O   LYS A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 347
      removed outlier: 3.512A  pdb=" N   SER A 347 " --> pdb=" O   SER A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 351
    Processing helix  chain 'A' and resid 352 through 364
      removed outlier: 6.482A  pdb=" N   LYS A 358 " --> pdb=" O   PRO A 354 " (cutoff:3.500A)
      removed outlier: 8.994A  pdb=" N   ASP A 359 " --> pdb=" O   ILE A 355 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   ASN A 360 " --> pdb=" O   LEU A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 374
      removed outlier: 4.031A  pdb=" N   LEU A 368 " --> pdb=" O   HIS A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 387
    Processing helix  chain 'A' and resid 387 through 395
      removed outlier: 4.658A  pdb=" N   VAL A 391 " --> pdb=" O   ASN A 387 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLU A 393 " --> pdb=" O   ASP A 389 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   VAL A 394 " --> pdb=" O   CYS A 390 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 145 through 149
    Processing helix  chain 'B' and resid 221 through 225
    Processing helix  chain 'B' and resid 281 through 286
    Processing helix  chain 'B' and resid 326 through 330
      removed outlier: 3.577A  pdb=" N   LEU B 329 " --> pdb=" O   HIS B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 339
    Processing helix  chain 'B' and resid 340 through 344
    Processing helix  chain 'B' and resid 382 through 386
      removed outlier: 3.557A  pdb=" N   ASN B 385 " --> pdb=" O   SER B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 413
      No H-bonds generated for 'chain 'B' and resid 411 through 413'
    Processing helix  chain 'D' and resid 83 through 92
    Processing sheet with id=AA1, first strand: chain 'B' and resid 390 through 391
      removed outlier: 4.039A  pdb=" N   THR B 390 " --> pdb=" O   PHE B  14 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   ILE B 441 " --> pdb=" O   SER B  15 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   VAL B  17 " --> pdb=" O   LEU B 439 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   LEU B 439 " --> pdb=" O   VAL B  17 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   HIS B 421 " --> pdb=" O   ALA B 434 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 31 through 36
      removed outlier: 6.147A  pdb=" N   GLY B  46 " --> pdb=" O   SER B  32 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   VAL B  34 " --> pdb=" O   ALA B  44 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ALA B  44 " --> pdb=" O   VAL B  34 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   PHE B  36 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   LEU B  42 " --> pdb=" O   PHE B  36 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   ARG B  51 " --> pdb=" O   ASP B  47 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   VAL B  52 " --> pdb=" O   THR B  76 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   THR B  76 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   ILE B  54 " --> pdb=" O   TYR B  74 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 83 through 85
      removed outlier: 3.565A  pdb=" N   GLU B  83 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 98 through 101
      removed outlier: 3.815A  pdb=" N   LYS B  98 " --> pdb=" O   THR B 114 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ARG B 170 " --> pdb=" O   LEU B 121 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   LYS B 123 " --> pdb=" O   PRO B 168 " (cutoff:3.500A)
      removed outlier: 7.368A  pdb=" N   SER B 125 " --> pdb=" O   ALA B 166 " (cutoff:3.500A)
      removed outlier: 5.293A  pdb=" N   ALA B 166 " --> pdb=" O   SER B 125 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   ARG B 127 " --> pdb=" O   VAL B 164 " (cutoff:3.500A)
      removed outlier: 5.369A  pdb=" N   VAL B 164 " --> pdb=" O   ARG B 127 " (cutoff:3.500A)
      removed outlier: 8.484A  pdb=" N   LYS B 129 " --> pdb=" O   LEU B 162 " (cutoff:3.500A)
      removed outlier: 8.682A  pdb=" N   LEU B 162 " --> pdb=" O   LYS B 129 " (cutoff:3.500A)
      removed outlier: 9.142A  pdb=" N   MET B 160 " --> pdb=" O   PRO B 131 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 182 through 185
      removed outlier: 6.724A  pdb=" N   ILE B 200 " --> pdb=" O   ILE B 214 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.616A  pdb=" N   SER B 245 " --> pdb=" O   THR B 230 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   ALA B 232 " --> pdb=" O   VAL B 243 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   VAL B 243 " --> pdb=" O   ALA B 232 " (cutoff:3.500A)
      removed outlier: 4.987A  pdb=" N   PHE B 234 " --> pdb=" O   THR B 241 " (cutoff:3.500A)
      removed outlier: 7.595A  pdb=" N   THR B 241 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 288 through 293
      removed outlier: 3.652A  pdb=" N   SER B 307 " --> pdb=" O   ASP B 304 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 348 through 350
    Processing sheet with id=AA9, first strand: chain 'B' and resid 397 through 398

    296 hydrogen bonds defined for protein.
    831 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: 4.77

  Time building geometry restraints manager: 4.30 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 6616
        1.03 -     1.23: 31
        1.23 -     1.42: 2812
        1.42 -     1.62: 3930
        1.62 -     1.81: 52
  Bond restraints: 13441
  Sorted by residual:
  bond pdb=" C   MLL C 309 "
       pdb=" OXT MLL C 309 "
    ideal  model  delta    sigma   weight residual
    1.231  1.364 -0.133 2.00e-02 2.50e+03 4.42e+01
  bond pdb=" CA  VAL A 129 "
       pdb=" CB  VAL A 129 "
    ideal  model  delta    sigma   weight residual
    1.534  1.543 -0.009 6.80e-03 2.16e+04 1.58e+00
  bond pdb=" CA  ILE A 206 "
       pdb=" CB  ILE A 206 "
    ideal  model  delta    sigma   weight residual
    1.539  1.533  0.006 5.40e-03 3.43e+04 1.17e+00
  bond pdb=" CB  TRP B 350 "
       pdb=" CG  TRP B 350 "
    ideal  model  delta    sigma   weight residual
    1.498  1.473  0.025 3.10e-02 1.04e+03 6.48e-01
  bond pdb=" CB  GLU B 190 "
       pdb=" CG  GLU B 190 "
    ideal  model  delta    sigma   weight residual
    1.520  1.497  0.023 3.00e-02 1.11e+03 5.70e-01
  ... (remaining 13436 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 23716
        1.37 -     2.73: 522
        2.73 -     4.10: 42
        4.10 -     5.46: 5
        5.46 -     6.83: 2
  Bond angle restraints: 24287
  Sorted by residual:
  angle pdb=" CA  VAL A 348 "
        pdb=" C   VAL A 348 "
        pdb=" N   ILE A 349 "
      ideal   model   delta    sigma   weight residual
     116.60  120.21   -3.61 1.45e+00 4.76e-01 6.21e+00
  angle pdb=" N   MLL C 309 "
        pdb=" CA  MLL C 309 "
        pdb=" CB  MLL C 309 "
      ideal   model   delta    sigma   weight residual
     110.50  114.49   -3.99 1.70e+00 3.46e-01 5.51e+00
  angle pdb=" CA  MLL C 309 "
        pdb=" C   MLL C 309 "
        pdb=" OXT MLL C 309 "
      ideal   model   delta    sigma   weight residual
     121.00  114.17    6.83 3.00e+00 1.11e-01 5.18e+00
  angle pdb=" N   THR B 226 "
        pdb=" CA  THR B 226 "
        pdb=" C   THR B 226 "
      ideal   model   delta    sigma   weight residual
     114.56  111.89    2.67 1.27e+00 6.20e-01 4.43e+00
  angle pdb=" N   VAL A 348 "
        pdb=" CA  VAL A 348 "
        pdb=" C   VAL A 348 "
      ideal   model   delta    sigma   weight residual
     109.34  113.56   -4.22 2.08e+00 2.31e-01 4.11e+00
  ... (remaining 24282 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.73: 5971
       16.73 -    33.46: 221
       33.46 -    50.19: 80
       50.19 -    66.92: 28
       66.92 -    83.65: 18
  Dihedral angle restraints: 6318
    sinusoidal: 3460
      harmonic: 2858
  Sorted by residual:
  dihedral pdb=" CA  TRP B 311 "
           pdb=" C   TRP B 311 "
           pdb=" N   ASP B 312 "
           pdb=" CA  ASP B 312 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.42   19.58     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  TRP B 203 "
           pdb=" C   TRP B 203 "
           pdb=" N   HIS B 204 "
           pdb=" CA  HIS B 204 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.85   18.15     0      5.00e+00 4.00e-02 1.32e+01
  dihedral pdb=" CA  THR B 114 "
           pdb=" C   THR B 114 "
           pdb=" N   ASN B 115 "
           pdb=" CA  ASN B 115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.85   17.15     0      5.00e+00 4.00e-02 1.18e+01
  ... (remaining 6315 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 635
       0.026 -    0.052: 261
       0.052 -    0.078: 80
       0.078 -    0.104: 42
       0.104 -    0.130: 29
  Chirality restraints: 1047
  Sorted by residual:
  chirality pdb=" CA  VAL B 308 "
            pdb=" N   VAL B 308 "
            pdb=" C   VAL B 308 "
            pdb=" CB  VAL B 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.22e-01
  chirality pdb=" CA  VAL B  34 "
            pdb=" N   VAL B  34 "
            pdb=" C   VAL B  34 "
            pdb=" CB  VAL B  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.20e-01
  chirality pdb=" CA  ILE B 171 "
            pdb=" N   ILE B 171 "
            pdb=" C   ILE B 171 "
            pdb=" CB  ILE B 171 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.12e-01
  ... (remaining 1044 not shown)

  Planarity restraints: 1981
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 206 "    0.020 5.00e-02 4.00e+02   3.00e-02 1.44e+00
        pdb=" N   PRO A 207 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 207 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 207 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 129 "   -0.018 5.00e-02 4.00e+02   2.71e-02 1.17e+00
        pdb=" N   PRO A 130 "    0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO A 130 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 130 "   -0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 141 "    0.009 2.00e-02 2.50e+03   5.92e-03 1.05e+00
        pdb=" CG  PHE A 141 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 141 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 141 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 141 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 141 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 141 "    0.000 2.00e-02 2.50e+03
        pdb=" HD1 PHE A 141 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD2 PHE A 141 "   -0.001 2.00e-02 2.50e+03
        pdb=" HE1 PHE A 141 "    0.001 2.00e-02 2.50e+03
        pdb=" HE2 PHE A 141 "    0.001 2.00e-02 2.50e+03
        pdb=" HZ  PHE A 141 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1978 not shown)

  Histogram of nonbonded interaction distances:
        1.42 -     2.06: 217
        2.06 -     2.69: 21222
        2.69 -     3.33: 39580
        3.33 -     3.96: 51805
        3.96 -     4.60: 81111
  Nonbonded interactions: 193935
  Sorted by model distance:
  nonbonded pdb=" OXT MLL C 309 "
            pdb=" C10 MLL C 309 "
     model   vdw
     1.425 3.100
  nonbonded pdb=" OE1 GLU B  94 "
            pdb=" H   GLU B  94 "
     model   vdw
     1.642 2.450
  nonbonded pdb=" O   GLY A 357 "
            pdb=" HG1 THR A 361 "
     model   vdw
     1.645 2.450
  nonbonded pdb=" OD1 ASP B 196 "
            pdb=" H   ARG B 199 "
     model   vdw
     1.648 2.450
  nonbonded pdb=" OE1 GLU A 379 "
            pdb=" H   GLU A 379 "
     model   vdw
     1.659 2.450
  ... (remaining 193930 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             8.380
  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:             0.220
  Extract box with map and model:          0.650
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     34.420
  Find NCS groups from input model:        0.110
  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:11.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   55.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
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      :  0.003   0.133   6805  Z= 0.143
  Angle     :  0.477   6.830   9206  Z= 0.254
  Chirality :  0.038   0.130   1047
  Planarity :  0.003   0.030   1189
  Dihedral  : 10.129  83.646   2557
  Min Nonbonded Distance : 1.425

Molprobity Statistics.
  All-atom Clashscore : 1.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.80 %
    Favored  : 99.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.31), residues: 816
  helix:  1.17 (0.30), residues: 340
  sheet:  0.47 (0.36), residues: 185
  loop :  0.50 (0.39), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 203 
 HIS   0.002   0.001   HIS A 304 
 PHE   0.018   0.001   PHE A 141 
 TYR   0.012   0.001   TYR B 178 
 ARG   0.003   0.000   ARG B 298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.23913 (  296)
  hydrogen bonds       : angle       6.81562 (  831)
  covalent geometry    : bond        0.00307 ( 6805)
  covalent geometry    : angle       0.47736 ( 9206)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 1.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  398 CYS cc_start: 0.7664 (t) cc_final: 0.6951 (p)
  outliers start: 1
  outliers final: 1
  residues processed: 81
  average time/residue: 2.7862
  time to fit residues: 237.3119
Evaluate side-chains
  44 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 43
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  326 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 64 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 200 ASN
** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  87 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.083926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.056623 restraints weight = 36357.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.2744 rms_B_bonded: 2.38
r_work: 0.2615 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2500 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8840
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6805  Z= 0.162
  Angle     :  0.556   5.537   9206  Z= 0.303
  Chirality :  0.041   0.152   1047
  Planarity :  0.004   0.044   1189
  Dihedral  :  5.012  43.652    903
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 1.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  5.98 %
    Favored  : 93.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.30), residues: 816
  helix:  1.09 (0.29), residues: 340
  sheet:  0.34 (0.39), residues: 171
  loop :  0.51 (0.37), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 203 
 HIS   0.004   0.001   HIS A 304 
 PHE   0.020   0.002   PHE A 141 
 TYR   0.011   0.001   TYR B 244 
 ARG   0.003   0.000   ARG B 318 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06097 (  296)
  hydrogen bonds       : angle       5.28890 (  831)
  covalent geometry    : bond        0.00355 ( 6805)
  covalent geometry    : angle       0.55555 ( 9206)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 49
  time to evaluate  : 1.148 
Fit side-chains
   revert: symmetry clash
REVERT: B  393 LYS cc_start: 0.8948 (mttt) cc_final: 0.8736 (mppt)
REVERT: B  398 CYS cc_start: 0.7768 (t) cc_final: 0.7000 (p)
REVERT: D   87 GLN cc_start: 0.7715 (mt0) cc_final: 0.7492 (mt0)
  outliers start: 3
  outliers final: 1
  residues processed: 51
  average time/residue: 2.5921
  time to fit residues: 141.7951
Evaluate side-chains
  45 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 44
  time to evaluate  : 1.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  326 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 80 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 364 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.083488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.056306 restraints weight = 36653.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.2732 rms_B_bonded: 2.40
r_work: 0.2602 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2486 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8854
moved from start:          0.2169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6805  Z= 0.144
  Angle     :  0.493   4.957   9206  Z= 0.266
  Chirality :  0.039   0.143   1047
  Planarity :  0.004   0.046   1189
  Dihedral  :  4.785  36.496    903
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 1.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  6.37 %
    Favored  : 93.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.30), residues: 816
  helix:  1.38 (0.29), residues: 334
  sheet:  0.11 (0.39), residues: 173
  loop :  0.45 (0.36), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 203 
 HIS   0.003   0.001   HIS A 304 
 PHE   0.018   0.001   PHE A 141 
 TYR   0.010   0.001   TYR B 178 
 ARG   0.004   0.000   ARG B 318 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05291 (  296)
  hydrogen bonds       : angle       4.81797 (  831)
  covalent geometry    : bond        0.00325 ( 6805)
  covalent geometry    : angle       0.49311 ( 9206)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 44
  time to evaluate  : 1.732 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  393 LYS cc_start: 0.8977 (mttt) cc_final: 0.8766 (mppt)
REVERT: B  398 CYS cc_start: 0.7880 (t) cc_final: 0.7179 (p)
REVERT: D   90 GLN cc_start: 0.7928 (tm-30) cc_final: 0.7661 (tm-30)
REVERT: D   91 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7516 (mp0)
  outliers start: 3
  outliers final: 1
  residues processed: 45
  average time/residue: 2.4627
  time to fit residues: 119.9281
Evaluate side-chains
  42 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 40
  time to evaluate  : 1.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  326 HIS
Chi-restraints excluded: chain D residue   91 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 76 optimal weight:    4.9990
   chunk 17 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 221 ASN
D  87 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.083500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.056334 restraints weight = 36384.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.2743 rms_B_bonded: 2.39
r_work: 0.2615 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2499 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8841
moved from start:          0.2414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6805  Z= 0.127
  Angle     :  0.474   4.998   9206  Z= 0.254
  Chirality :  0.039   0.145   1047
  Planarity :  0.004   0.047   1189
  Dihedral  :  4.623  35.348    903
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 1.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  6.37 %
    Favored  : 93.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.30), residues: 816
  helix:  1.35 (0.29), residues: 342
  sheet:  0.03 (0.39), residues: 168
  loop :  0.35 (0.37), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 203 
 HIS   0.003   0.001   HIS B 176 
 PHE   0.018   0.001   PHE A 141 
 TYR   0.009   0.001   TYR B 244 
 ARG   0.001   0.000   ARG A  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04478 (  296)
  hydrogen bonds       : angle       4.60147 (  831)
  covalent geometry    : bond        0.00286 ( 6805)
  covalent geometry    : angle       0.47448 ( 9206)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 1.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  393 LYS cc_start: 0.8978 (mttt) cc_final: 0.8771 (mppt)
REVERT: B  398 CYS cc_start: 0.7908 (t) cc_final: 0.7202 (p)
REVERT: D   87 GLN cc_start: 0.7812 (mt0) cc_final: 0.7605 (mt0)
  outliers start: 3
  outliers final: 2
  residues processed: 44
  average time/residue: 2.3026
  time to fit residues: 109.5422
Evaluate side-chains
  41 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 PHE
Chi-restraints excluded: chain B residue  326 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B 221 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.082437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.055115 restraints weight = 36845.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.2712 rms_B_bonded: 2.38
r_work: 0.2583 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2467 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8875
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6805  Z= 0.176
  Angle     :  0.506   5.348   9206  Z= 0.274
  Chirality :  0.040   0.144   1047
  Planarity :  0.004   0.046   1189
  Dihedral  :  4.663  34.241    903
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 1.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  6.64 %
    Favored  : 93.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.30), residues: 816
  helix:  1.39 (0.29), residues: 342
  sheet: -0.06 (0.40), residues: 168
  loop :  0.24 (0.36), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 203 
 HIS   0.003   0.001   HIS B  38 
 PHE   0.053   0.002   PHE A  76 
 TYR   0.011   0.001   TYR B 244 
 ARG   0.002   0.000   ARG B 158 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04837 (  296)
  hydrogen bonds       : angle       4.62682 (  831)
  covalent geometry    : bond        0.00405 ( 6805)
  covalent geometry    : angle       0.50625 ( 9206)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 1.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  393 LYS cc_start: 0.8996 (mttt) cc_final: 0.8791 (mppt)
REVERT: B  398 CYS cc_start: 0.7911 (t) cc_final: 0.7212 (p)
  outliers start: 1
  outliers final: 1
  residues processed: 43
  average time/residue: 2.1537
  time to fit residues: 99.9705
Evaluate side-chains
  42 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 41
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  326 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
D  87 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.081640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.054366 restraints weight = 37036.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.2706 rms_B_bonded: 2.38
r_work: 0.2577 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2462 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8894
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   6805  Z= 0.203
  Angle     :  0.509   4.887   9206  Z= 0.275
  Chirality :  0.040   0.146   1047
  Planarity :  0.004   0.046   1189
  Dihedral  :  4.700  33.472    903
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 1.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  6.77 %
    Favored  : 92.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.30), residues: 816
  helix:  1.35 (0.29), residues: 342
  sheet: -0.10 (0.39), residues: 173
  loop :  0.09 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 203 
 HIS   0.004   0.001   HIS B  38 
 PHE   0.019   0.002   PHE A 141 
 TYR   0.012   0.001   TYR B 244 
 ARG   0.002   0.000   ARG D  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04979 (  296)
  hydrogen bonds       : angle       4.66488 (  831)
  covalent geometry    : bond        0.00470 ( 6805)
  covalent geometry    : angle       0.50900 ( 9206)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 1.174 
Fit side-chains
   revert: symmetry clash
REVERT: B  393 LYS cc_start: 0.9017 (mttt) cc_final: 0.8805 (mppt)
REVERT: B  398 CYS cc_start: 0.7936 (t) cc_final: 0.7226 (p)
  outliers start: 3
  outliers final: 1
  residues processed: 43
  average time/residue: 2.2427
  time to fit residues: 103.7950
Evaluate side-chains
  40 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 39
  time to evaluate  : 1.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  326 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 69 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0020
   chunk 31 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 17 optimal weight:    0.3980
   overall best weight:    0.5588

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

Flipped N/Q/H residues before XYZ refinement:
D  87 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.083319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.056163 restraints weight = 36561.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.2749 rms_B_bonded: 2.40
r_work: 0.2621 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2505 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8858
moved from start:          0.2820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049   6805  Z= 0.102
  Angle     :  0.461   5.279   9206  Z= 0.246
  Chirality :  0.039   0.141   1047
  Planarity :  0.004   0.048   1189
  Dihedral  :  4.463  33.244    903
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 1.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  6.91 %
    Favored  : 92.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.30), residues: 816
  helix:  1.45 (0.30), residues: 344
  sheet: -0.04 (0.39), residues: 173
  loop :  0.16 (0.37), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 203 
 HIS   0.003   0.001   HIS B 176 
 PHE   0.018   0.001   PHE A 141 
 TYR   0.008   0.001   TYR B 244 
 ARG   0.002   0.000   ARG A 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04040 (  296)
  hydrogen bonds       : angle       4.42176 (  831)
  covalent geometry    : bond        0.00228 ( 6805)
  covalent geometry    : angle       0.46084 ( 9206)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 1.081 
Fit side-chains
   revert: symmetry clash
REVERT: B  393 LYS cc_start: 0.9026 (mttt) cc_final: 0.8819 (mppt)
REVERT: B  398 CYS cc_start: 0.7931 (t) cc_final: 0.7254 (p)
  outliers start: 2
  outliers final: 1
  residues processed: 41
  average time/residue: 2.4095
  time to fit residues: 105.6379
Evaluate side-chains
  39 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 1.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  326 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 58 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
D  87 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.083098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.055927 restraints weight = 36966.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.2744 rms_B_bonded: 2.40
r_work: 0.2617 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2502 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8866
moved from start:          0.2874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6805  Z= 0.120
  Angle     :  0.471   5.324   9206  Z= 0.250
  Chirality :  0.038   0.142   1047
  Planarity :  0.004   0.048   1189
  Dihedral  :  4.400  32.950    903
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 1.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  7.17 %
    Favored  : 92.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.30), residues: 816
  helix:  1.53 (0.30), residues: 343
  sheet: -0.04 (0.39), residues: 173
  loop :  0.15 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 203 
 HIS   0.002   0.001   HIS B 176 
 PHE   0.018   0.001   PHE A 141 
 TYR   0.010   0.001   TYR B 244 
 ARG   0.001   0.000   ARG B 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04119 (  296)
  hydrogen bonds       : angle       4.39196 (  831)
  covalent geometry    : bond        0.00277 ( 6805)
  covalent geometry    : angle       0.47105 ( 9206)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 1.116 
Fit side-chains
   revert: symmetry clash
REVERT: B  393 LYS cc_start: 0.9033 (mttt) cc_final: 0.8826 (mppt)
REVERT: B  398 CYS cc_start: 0.7924 (t) cc_final: 0.7238 (p)
  outliers start: 1
  outliers final: 1
  residues processed: 39
  average time/residue: 2.4663
  time to fit residues: 103.3808
Evaluate side-chains
  39 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  326 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
D  87 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.082911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.055727 restraints weight = 36525.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.2741 rms_B_bonded: 2.39
r_work: 0.2615 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2499 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8869
moved from start:          0.2931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6805  Z= 0.128
  Angle     :  0.473   5.704   9206  Z= 0.251
  Chirality :  0.039   0.142   1047
  Planarity :  0.004   0.048   1189
  Dihedral  :  4.382  32.694    903
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 1.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  7.30 %
    Favored  : 92.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.30), residues: 816
  helix:  1.55 (0.30), residues: 343
  sheet: -0.05 (0.40), residues: 168
  loop :  0.12 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 203 
 HIS   0.002   0.001   HIS B 176 
 PHE   0.018   0.001   PHE A 141 
 TYR   0.010   0.001   TYR B 244 
 ARG   0.001   0.000   ARG B 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04128 (  296)
  hydrogen bonds       : angle       4.37745 (  831)
  covalent geometry    : bond        0.00296 ( 6805)
  covalent geometry    : angle       0.47254 ( 9206)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 40
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
REVERT: B  393 LYS cc_start: 0.9036 (mttt) cc_final: 0.8833 (mppt)
REVERT: B  398 CYS cc_start: 0.7952 (t) cc_final: 0.7237 (p)
  outliers start: 1
  outliers final: 1
  residues processed: 41
  average time/residue: 2.9355
  time to fit residues: 131.8312
Evaluate side-chains
  38 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 37
  time to evaluate  : 1.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  326 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 32 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 78 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 70 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
D  87 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.083007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.055930 restraints weight = 36643.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.2735 rms_B_bonded: 2.40
r_work: 0.2607 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2490 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8862
moved from start:          0.2986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6805  Z= 0.118
  Angle     :  0.472   5.651   9206  Z= 0.251
  Chirality :  0.038   0.141   1047
  Planarity :  0.004   0.048   1189
  Dihedral  :  4.340  32.637    903
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 1.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  7.57 %
    Favored  : 92.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.30), residues: 816
  helix:  1.59 (0.30), residues: 343
  sheet: -0.19 (0.39), residues: 174
  loop :  0.12 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 203 
 HIS   0.002   0.001   HIS B 176 
 PHE   0.018   0.001   PHE A 141 
 TYR   0.014   0.001   TYR A  60 
 ARG   0.002   0.000   ARG B 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04015 (  296)
  hydrogen bonds       : angle       4.34957 (  831)
  covalent geometry    : bond        0.00272 ( 6805)
  covalent geometry    : angle       0.47203 ( 9206)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 39
  time to evaluate  : 1.320 
Fit side-chains
   revert: symmetry clash
REVERT: B  393 LYS cc_start: 0.9037 (mttt) cc_final: 0.8794 (mppt)
REVERT: B  398 CYS cc_start: 0.7971 (t) cc_final: 0.7243 (p)
  outliers start: 1
  outliers final: 1
  residues processed: 40
  average time/residue: 2.9311
  time to fit residues: 126.0722
Evaluate side-chains
  40 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 39
  time to evaluate  : 2.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  326 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   chunk 1 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0010
   chunk 3 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0980
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.5386

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

Flipped N/Q/H residues before XYZ refinement:
D  87 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.083640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.056717 restraints weight = 36677.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.2753 rms_B_bonded: 2.38
r_work: 0.2625 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2508 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8849
moved from start:          0.3088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050   6805  Z= 0.099
  Angle     :  0.460   5.902   9206  Z= 0.244
  Chirality :  0.038   0.140   1047
  Planarity :  0.004   0.048   1189
  Dihedral  :  4.256  32.612    903
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 1.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  7.30 %
    Favored  : 92.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.31), residues: 816
  helix:  1.65 (0.30), residues: 344
  sheet: -0.13 (0.39), residues: 174
  loop :  0.15 (0.36), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 203 
 HIS   0.002   0.000   HIS B 176 
 PHE   0.017   0.001   PHE A 141 
 TYR   0.027   0.001   TYR A  60 
 ARG   0.002   0.000   ARG B 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03750 (  296)
  hydrogen bonds       : angle       4.27282 (  831)
  covalent geometry    : bond        0.00226 ( 6805)
  covalent geometry    : angle       0.46046 ( 9206)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 12778.50 seconds
wall clock time: 230 minutes 1.11 seconds (13801.11 seconds total)