Starting phenix.real_space_refine
on Thu May 15 17:28:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8twe_41667/05_2025/8twe_41667.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8twe_41667/05_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_41667/05_2025/8twe_41667.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8twe_41667/05_2025/8twe_41667.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8twe_41667/05_2025/8twe_41667.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8twe_41667/05_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-5687/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: 8.03, per 1000 atoms: 0.60
  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: 3.55
  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: 1.29
  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: 4.64

  Time building geometry restraints manager: 4.18 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:             10.670
  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:             0.230
  Extract box with map and model:          0.600
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     32.250
  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:             0.010
  Load rotamer database and sin/cos tables:10.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   54.590
-------------------------------------------------------------------------------
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  : 1.109 
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: 2.8052
  time to fit residues: 238.6777
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  : 1.069 
-------------------------------------------------------------------------------
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 = 0.056624 restraints weight = 36357.219|
|-----------------------------------------------------------------------------|
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: 0.2499 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2499
-------------------------------------------------------------------------------
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  43.654    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        0.06098 (  296)
  hydrogen bonds       : angle       5.28893 (  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  : 0.970 
Fit side-chains
   revert: symmetry clash
REVERT: B  393 LYS cc_start: 0.8949 (mttt) cc_final: 0.8737 (mppt)
REVERT: B  398 CYS cc_start: 0.7768 (t) cc_final: 0.6999 (p)
REVERT: D   87 GLN cc_start: 0.7713 (mt0) cc_final: 0.7490 (mt0)
  outliers start: 3
  outliers final: 1
  residues processed: 51
  average time/residue: 2.2160
  time to fit residues: 120.9219
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  : 1.078 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   overall best weight:    1.2386

-------------------------------------------------------------------------------
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 = 0.3288 r_free = 0.3288 target = 0.083034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2759 r_free = 0.2759 target = 0.055787 restraints weight = 36620.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.2722 rms_B_bonded: 2.38
r_work: 0.2593 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2475 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8865
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6805  Z= 0.167
  Angle     :  0.506   4.932   9206  Z= 0.274
  Chirality :  0.040   0.145   1047
  Planarity :  0.004   0.046   1189
  Dihedral  :  4.848  36.398    903
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 1.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  6.24 %
    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:  0.97 (0.30), residues: 816
  helix:  1.33 (0.29), residues: 334
  sheet:  0.08 (0.39), residues: 173
  loop :  0.42 (0.36), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 203 
 HIS   0.003   0.001   HIS B 425 
 PHE   0.018   0.001   PHE A 141 
 TYR   0.011   0.001   TYR B 178 
 ARG   0.003   0.000   ARG B 318 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05514 (  296)
  hydrogen bonds       : angle       4.89106 (  831)
  covalent geometry    : bond        0.00379 ( 6805)
  covalent geometry    : angle       0.50585 ( 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
  48 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 1.068 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  393 LYS cc_start: 0.8979 (mttt) cc_final: 0.8769 (mppt)
REVERT: B  398 CYS cc_start: 0.7889 (t) cc_final: 0.7158 (p)
  outliers start: 4
  outliers final: 2
  residues processed: 45
  average time/residue: 2.0709
  time to fit residues: 100.5892
Evaluate side-chains
  43 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 41
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  280 PHE
Chi-restraints excluded: chain B residue  326 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 35 optimal weight:    0.2980
   chunk 79 optimal weight:    1.9990
   chunk 58 optimal weight:    0.1980
   chunk 26 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 76 optimal weight:    4.9990
   chunk 17 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.3312 r_free = 0.3312 target = 0.084271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.057251 restraints weight = 36331.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.2751 rms_B_bonded: 2.37
r_work: 0.2621 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2504 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8835
moved from start:          0.2396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6805  Z= 0.103
  Angle     :  0.466   5.156   9206  Z= 0.249
  Chirality :  0.039   0.143   1047
  Planarity :  0.004   0.047   1189
  Dihedral  :  4.596  35.704    903
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 1.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  6.51 %
    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:  1.34 (0.29), residues: 342
  sheet:  0.04 (0.39), residues: 168
  loop :  0.36 (0.37), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 311 
 HIS   0.002   0.001   HIS B 176 
 PHE   0.017   0.001   PHE A 141 
 TYR   0.008   0.001   TYR B 244 
 ARG   0.002   0.000   ARG A  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04289 (  296)
  hydrogen bonds       : angle       4.58840 (  831)
  covalent geometry    : bond        0.00224 ( 6805)
  covalent geometry    : angle       0.46564 ( 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
  45 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 43
  time to evaluate  : 1.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  393 LYS cc_start: 0.8977 (mttt) cc_final: 0.8774 (mppt)
REVERT: B  398 CYS cc_start: 0.7906 (t) cc_final: 0.7211 (p)
  outliers start: 2
  outliers final: 2
  residues processed: 45
  average time/residue: 2.1591
  time to fit residues: 104.3493
Evaluate side-chains
  43 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 41
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  280 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:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9980
   overall best weight:    1.3986

-------------------------------------------------------------------------------
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 = 0.3281 r_free = 0.3281 target = 0.082505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.055224 restraints weight = 36793.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.2719 rms_B_bonded: 2.41
r_work: 0.2592 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2475 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8859
moved from start:          0.2516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6805  Z= 0.184
  Angle     :  0.496   4.890   9206  Z= 0.268
  Chirality :  0.040   0.144   1047
  Planarity :  0.004   0.046   1189
  Dihedral  :  4.650  34.409    903
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 1.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  6.77 %
    Favored  : 92.96 %
  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:  0.85 (0.30), residues: 816
  helix:  1.33 (0.29), residues: 343
  sheet: -0.07 (0.39), residues: 168
  loop :  0.24 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 203 
 HIS   0.003   0.001   HIS B  38 
 PHE   0.019   0.001   PHE A 141 
 TYR   0.011   0.001   TYR B 244 
 ARG   0.002   0.000   ARG D  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04934 (  296)
  hydrogen bonds       : angle       4.65509 (  831)
  covalent geometry    : bond        0.00423 ( 6805)
  covalent geometry    : angle       0.49636 ( 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: 2
    poor density    : 41
  time to evaluate  : 1.049 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  393 LYS cc_start: 0.8988 (mttt) cc_final: 0.8771 (mppt)
REVERT: B  398 CYS cc_start: 0.7936 (t) cc_final: 0.7192 (p)
  outliers start: 2
  outliers final: 3
  residues processed: 43
  average time/residue: 2.1917
  time to fit residues: 101.0544
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  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 PHE
Chi-restraints excluded: chain B residue  280 PHE
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:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 13 optimal weight:    0.4980
   chunk 16 optimal weight:    1.9990
   overall best weight:    1.4786

-------------------------------------------------------------------------------
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 = 0.3274 r_free = 0.3274 target = 0.082099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.054885 restraints weight = 36992.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.2682 rms_B_bonded: 2.40
r_work: 0.2551 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2432 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8872
moved from start:          0.2660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   6805  Z= 0.186
  Angle     :  0.501   5.019   9206  Z= 0.270
  Chirality :  0.040   0.146   1047
  Planarity :  0.004   0.047   1189
  Dihedral  :  4.662  33.466    903
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 1.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  6.64 %
    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:  0.76 (0.30), residues: 816
  helix:  1.30 (0.29), residues: 343
  sheet: -0.11 (0.39), residues: 173
  loop :  0.14 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 203 
 HIS   0.003   0.001   HIS B  38 
 PHE   0.019   0.001   PHE A 141 
 TYR   0.011   0.001   TYR B 244 
 ARG   0.002   0.000   ARG D  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04830 (  296)
  hydrogen bonds       : angle       4.63609 (  831)
  covalent geometry    : bond        0.00430 ( 6805)
  covalent geometry    : angle       0.50098 ( 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
  45 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 41
  time to evaluate  : 1.200 
Fit side-chains
   revert: symmetry clash
REVERT: B  393 LYS cc_start: 0.9018 (mttt) cc_final: 0.8796 (mppt)
REVERT: B  398 CYS cc_start: 0.7940 (t) cc_final: 0.7198 (p)
  outliers start: 4
  outliers final: 2
  residues processed: 45
  average time/residue: 2.2313
  time to fit residues: 107.5658
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  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 PHE
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:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 17 optimal weight:    0.1980
   overall best weight:    0.7384

-------------------------------------------------------------------------------
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 = 0.3288 r_free = 0.3288 target = 0.082885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.055869 restraints weight = 36621.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.2740 rms_B_bonded: 2.38
r_work: 0.2614 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2498 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8865
moved from start:          0.2780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6805  Z= 0.114
  Angle     :  0.465   5.002   9206  Z= 0.248
  Chirality :  0.039   0.141   1047
  Planarity :  0.004   0.048   1189
  Dihedral  :  4.476  33.107    903
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 1.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  6.91 %
    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:  0.90 (0.30), residues: 816
  helix:  1.44 (0.30), residues: 343
  sheet: -0.08 (0.39), residues: 173
  loop :  0.20 (0.37), residues: 300

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   0.009   0.001   TYR B 244 
 ARG   0.002   0.000   ARG A 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04175 (  296)
  hydrogen bonds       : angle       4.45085 (  831)
  covalent geometry    : bond        0.00256 ( 6805)
  covalent geometry    : angle       0.46474 ( 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
  43 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
REVERT: B  393 LYS cc_start: 0.9017 (mttt) cc_final: 0.8812 (mppt)
REVERT: B  398 CYS cc_start: 0.7939 (t) cc_final: 0.7261 (p)
  outliers start: 3
  outliers final: 1
  residues processed: 43
  average time/residue: 2.1954
  time to fit residues: 101.1423
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  : 0.962 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 27 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3288 r_free = 0.3288 target = 0.082848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2766 r_free = 0.2766 target = 0.055667 restraints weight = 36971.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.2739 rms_B_bonded: 2.39
r_work: 0.2614 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2498 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8868
moved from start:          0.2867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6805  Z= 0.124
  Angle     :  0.474   5.407   9206  Z= 0.252
  Chirality :  0.039   0.142   1047
  Planarity :  0.004   0.048   1189
  Dihedral  :  4.419  33.065    903
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 1.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  7.44 %
    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:  0.94 (0.30), residues: 816
  helix:  1.49 (0.30), residues: 343
  sheet: -0.05 (0.39), residues: 173
  loop :  0.19 (0.37), 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   0.003   0.000   ARG B 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04158 (  296)
  hydrogen bonds       : angle       4.41015 (  831)
  covalent geometry    : bond        0.00285 ( 6805)
  covalent geometry    : angle       0.47439 ( 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
  41 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 40
  time to evaluate  : 1.064 
Fit side-chains
   revert: symmetry clash
REVERT: B  393 LYS cc_start: 0.9026 (mttt) cc_final: 0.8821 (mppt)
REVERT: B  398 CYS cc_start: 0.7958 (t) cc_final: 0.7244 (p)
  outliers start: 1
  outliers final: 1
  residues processed: 41
  average time/residue: 2.2141
  time to fit residues: 97.3183
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  : 0.986 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   chunk 50 optimal weight:    0.8980
   chunk 27 optimal weight:    0.2980
   chunk 64 optimal weight:    0.1980
   chunk 11 optimal weight:    0.9980
   chunk 70 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3299 r_free = 0.3299 target = 0.083458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.056373 restraints weight = 36557.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.2747 rms_B_bonded: 2.39
r_work: 0.2621 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2505 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8852
moved from start:          0.2975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048   6805  Z= 0.103
  Angle     :  0.461   5.576   9206  Z= 0.244
  Chirality :  0.038   0.140   1047
  Planarity :  0.004   0.048   1189
  Dihedral  :  4.316  32.755    903
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 1.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  7.57 %
    Favored  : 92.16 %
  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:  0.97 (0.31), residues: 816
  helix:  1.57 (0.30), residues: 344
  sheet: -0.18 (0.39), residues: 179
  loop :  0.25 (0.37), residues: 293

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   0.017   0.001   PHE A 141 
 TYR   0.009   0.001   TYR B 244 
 ARG   0.002   0.000   ARG A 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03856 (  296)
  hydrogen bonds       : angle       4.30522 (  831)
  covalent geometry    : bond        0.00234 ( 6805)
  covalent geometry    : angle       0.46107 ( 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: 2
    poor density    : 39
  time to evaluate  : 1.138 
Fit side-chains
   revert: symmetry clash
REVERT: B  398 CYS cc_start: 0.7939 (t) cc_final: 0.7245 (p)
  outliers start: 2
  outliers final: 1
  residues processed: 41
  average time/residue: 2.3911
  time to fit residues: 105.7843
Evaluate side-chains
  37 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 36
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
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:    0.2980
   chunk 43 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 68 optimal weight:    0.4980
   chunk 53 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 70 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.6780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.083502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.056592 restraints weight = 36661.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.2735 rms_B_bonded: 2.39
r_work: 0.2608 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2491 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8844
moved from start:          0.3026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6805  Z= 0.114
  Angle     :  0.470   5.750   9206  Z= 0.249
  Chirality :  0.038   0.140   1047
  Planarity :  0.004   0.048   1189
  Dihedral  :  4.289  32.947    903
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 1.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  7.97 %
    Favored  : 91.90 %
  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:  1.64 (0.30), residues: 343
  sheet: -0.18 (0.40), residues: 174
  loop :  0.20 (0.37), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 203 
 HIS   0.002   0.001   HIS B 176 
 PHE   0.017   0.001   PHE A 141 
 TYR   0.016   0.001   TYR A  60 
 ARG   0.001   0.000   ARG B 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03908 (  296)
  hydrogen bonds       : angle       4.29682 (  831)
  covalent geometry    : bond        0.00261 ( 6805)
  covalent geometry    : angle       0.46962 ( 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  : 1.047 
Fit side-chains
   revert: symmetry clash
REVERT: B  398 CYS cc_start: 0.7948 (t) cc_final: 0.7215 (p)
  outliers start: 1
  outliers final: 1
  residues processed: 40
  average time/residue: 2.3409
  time to fit residues: 100.2231
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  : 1.000 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 8 optimal weight:    0.3980
   chunk 1 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 19 optimal weight:    0.1980
   chunk 3 optimal weight:    0.6980
   chunk 49 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.4980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.083791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.056956 restraints weight = 36773.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.2758 rms_B_bonded: 2.38
r_work: 0.2631 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2514 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8845
moved from start:          0.3151

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= 0.096
  Angle     :  0.459   5.772   9206  Z= 0.242
  Chirality :  0.038   0.139   1047
  Planarity :  0.004   0.048   1189
  Dihedral  :  4.199  32.711    903
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 1.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  8.10 %
    Favored  : 91.77 %
  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:  1.07 (0.31), residues: 816
  helix:  1.70 (0.30), residues: 344
  sheet: -0.14 (0.40), residues: 174
  loop :  0.24 (0.37), 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        0.03628 (  296)
  hydrogen bonds       : angle       4.21191 (  831)
  covalent geometry    : bond        0.00221 ( 6805)
  covalent geometry    : angle       0.45895 ( 9206)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10326.17 seconds
wall clock time: 177 minutes 48.11 seconds (10668.11 seconds total)