Starting phenix.real_space_refine
on Sat Aug 23 16:46:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8twe_41667/08_2025/8twe_41667.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8twe_41667/08_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_41667/08_2025/8twe_41667.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8twe_41667/08_2025/8twe_41667.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8twe_41667/08_2025/8twe_41667.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8twe_41667/08_2025/8twe_41667.cif"
  }
  resolution = 2.55
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.01, per 1000 atoms: 0.23
  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: 1.16
  Conformation dependent library (CDL) restraints added in 565.2 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  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: 0.46
  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: 3.41

  Time building geometry restraints manager: 1.72 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:             15.820
  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:             0.090
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     15.920
  Find NCS groups from input model:        0.060
  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:9.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.830
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.003   0.000   ARG B 298 
 TYR   0.012   0.001   TYR B 178 
 PHE   0.018   0.001   PHE A 141 
 TRP   0.011   0.002   TRP B 203 
 HIS   0.002   0.001   HIS A 304 

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

*********************** 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  : 0.402 
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: 1.5360
  time to fit residues: 130.0018
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  : 0.386 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.0030
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.7392

-------------------------------------------------------------------------------
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 = 0.3309 r_free = 0.3309 target = 0.084497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.057222 restraints weight = 36488.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.2757 rms_B_bonded: 2.38
r_work: 0.2628 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2513 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8827
moved from start:          0.1765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6805  Z= 0.141
  Angle     :  0.543   5.538   9206  Z= 0.296
  Chirality :  0.040   0.152   1047
  Planarity :  0.004   0.044   1189
  Dihedral  :  4.978  45.327    903
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 1.65
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.02 (0.30), residues: 816
  helix:  1.15 (0.29), residues: 340
  sheet:  0.38 (0.38), residues: 171
  loop :  0.53 (0.37), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 318 
 TYR   0.010   0.001   TYR B 244 
 PHE   0.019   0.001   PHE A 141 
 TRP   0.011   0.001   TRP B 203 
 HIS   0.004   0.001   HIS A 304 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 6805)
  covalent geometry    : angle       0.54312 ( 9206)
  hydrogen bonds       : bond        0.06272 (  296)
  hydrogen bonds       : angle       5.28983 (  831)

*********************** 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
  50 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 47
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  393 LYS cc_start: 0.8938 (mttt) cc_final: 0.8733 (mppt)
REVERT: B  398 CYS cc_start: 0.7743 (t) cc_final: 0.7005 (p)
REVERT: D   87 GLN cc_start: 0.7735 (mt0) cc_final: 0.7450 (mt0)
REVERT: D   91 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7756 (mp0)
  outliers start: 3
  outliers final: 1
  residues processed: 49
  average time/residue: 1.1943
  time to fit residues: 62.1337
Evaluate side-chains
  47 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 45
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  326 HIS
Chi-restraints excluded: chain D residue   91 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0270
   chunk 48 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   overall best weight:    0.9242

-------------------------------------------------------------------------------
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 = 0.3301 r_free = 0.3301 target = 0.083818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.056673 restraints weight = 36880.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.2743 rms_B_bonded: 2.38
r_work: 0.2614 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2497 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8848
moved from start:          0.2204

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= 0.137
  Angle     :  0.487   4.885   9206  Z= 0.262
  Chirality :  0.039   0.143   1047
  Planarity :  0.004   0.047   1189
  Dihedral  :  4.729  36.462    903
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 1.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  6.11 %
    Favored  : 93.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.11 (0.30), residues: 816
  helix:  1.42 (0.29), residues: 334
  sheet:  0.26 (0.39), residues: 166
  loop :  0.45 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  46 
 TYR   0.010   0.001   TYR B 178 
 PHE   0.018   0.001   PHE A 141 
 TRP   0.012   0.001   TRP B 203 
 HIS   0.002   0.001   HIS A 304 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6805)
  covalent geometry    : angle       0.48669 ( 9206)
  hydrogen bonds       : bond        0.05027 (  296)
  hydrogen bonds       : angle       4.75524 (  831)

*********************** 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
  49 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
REVERT: B  393 LYS cc_start: 0.8971 (mttt) cc_final: 0.8763 (mppt)
REVERT: B  398 CYS cc_start: 0.7876 (t) cc_final: 0.7178 (p)
REVERT: B  408 ILE cc_start: 0.8903 (mm) cc_final: 0.8647 (mm)
  outliers start: 3
  outliers final: 2
  residues processed: 47
  average time/residue: 1.0845
  time to fit residues: 54.8300
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  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 ASP
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 77 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 50 optimal weight:    5.9990
   chunk 68 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 11 optimal weight:    2.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.3272 r_free = 0.3272 target = 0.082117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2740 r_free = 0.2740 target = 0.054739 restraints weight = 36695.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.2709 rms_B_bonded: 2.40
r_work: 0.2580 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2462 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8871
moved from start:          0.2387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6805  Z= 0.194
  Angle     :  0.508   4.889   9206  Z= 0.275
  Chirality :  0.040   0.145   1047
  Planarity :  0.004   0.046   1189
  Dihedral  :  4.768  34.941    903
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 1.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.86 (0.30), residues: 816
  helix:  1.25 (0.29), residues: 342
  sheet:  0.08 (0.39), residues: 166
  loop :  0.27 (0.36), residues: 308

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 6805)
  covalent geometry    : angle       0.50794 ( 9206)
  hydrogen bonds       : bond        0.05133 (  296)
  hydrogen bonds       : angle       4.75926 (  831)

*********************** 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  : 0.410 
Fit side-chains
   revert: symmetry clash
REVERT: B  393 LYS cc_start: 0.8993 (mttt) cc_final: 0.8777 (mppt)
REVERT: B  398 CYS cc_start: 0.7937 (t) cc_final: 0.7197 (p)
  outliers start: 3
  outliers final: 2
  residues processed: 44
  average time/residue: 1.1326
  time to fit residues: 53.2082
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  : 0.417 
-------------------------------------------------------------------------------
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 81 optimal weight:    2.9990
   chunk 74 optimal weight:    5.9990
   chunk 13 optimal weight:    0.0070
   chunk 18 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 34 optimal weight:    0.4980
   chunk 54 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 17 optimal weight:    0.2980
   overall best weight:    0.5398

-------------------------------------------------------------------------------
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 = 0.3300 r_free = 0.3300 target = 0.083601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.056551 restraints weight = 36863.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.2718 rms_B_bonded: 2.39
r_work: 0.2584 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2467 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8843
moved from start:          0.2574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   6805  Z= 0.100
  Angle     :  0.460   5.038   9206  Z= 0.246
  Chirality :  0.038   0.141   1047
  Planarity :  0.004   0.047   1189
  Dihedral  :  4.541  34.425    903
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 1.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  6.64 %
    Favored  : 93.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.30), residues: 816
  helix:  1.39 (0.30), residues: 343
  sheet: -0.01 (0.38), residues: 173
  loop :  0.30 (0.37), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 183 
 TYR   0.008   0.001   TYR B 244 
 PHE   0.017   0.001   PHE A 141 
 TRP   0.011   0.001   TRP B 203 
 HIS   0.002   0.001   HIS B 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 6805)
  covalent geometry    : angle       0.45973 ( 9206)
  hydrogen bonds       : bond        0.04203 (  296)
  hydrogen bonds       : angle       4.49663 (  831)

*********************** 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  : 0.397 
Fit side-chains
   revert: symmetry clash
REVERT: B  393 LYS cc_start: 0.8994 (mttt) cc_final: 0.8792 (mppt)
REVERT: B  398 CYS cc_start: 0.7895 (t) cc_final: 0.7218 (p)
  outliers start: 2
  outliers final: 1
  residues processed: 43
  average time/residue: 1.2158
  time to fit residues: 55.7141
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  : 0.352 
-------------------------------------------------------------------------------
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 34 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0770
   chunk 12 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 30 optimal weight:    0.4980
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.6140

-------------------------------------------------------------------------------
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 = 0.083778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.056700 restraints weight = 36765.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.2760 rms_B_bonded: 2.39
r_work: 0.2633 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2519 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8850
moved from start:          0.2730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   6805  Z= 0.109
  Angle     :  0.457   4.819   9206  Z= 0.243
  Chirality :  0.038   0.141   1047
  Planarity :  0.004   0.047   1189
  Dihedral  :  4.391  33.660    903
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 1.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  6.64 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.02 (0.30), residues: 816
  helix:  1.52 (0.30), residues: 343
  sheet: -0.01 (0.39), residues: 173
  loop :  0.29 (0.37), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 183 
 TYR   0.009   0.001   TYR B 244 
 PHE   0.017   0.001   PHE A 141 
 TRP   0.011   0.001   TRP B 203 
 HIS   0.002   0.001   HIS B 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 6805)
  covalent geometry    : angle       0.45718 ( 9206)
  hydrogen bonds       : bond        0.04005 (  296)
  hydrogen bonds       : angle       4.36767 (  831)

*********************** 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  : 0.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  398 CYS cc_start: 0.7888 (t) cc_final: 0.7240 (p)
  outliers start: 3
  outliers final: 1
  residues processed: 43
  average time/residue: 1.2223
  time to fit residues: 55.8966
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  : 0.404 
-------------------------------------------------------------------------------
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 46 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 75 optimal weight:    0.0040
   chunk 8 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   overall best weight:    0.8996

-------------------------------------------------------------------------------
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 = 0.3295 r_free = 0.3295 target = 0.083262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.056037 restraints weight = 36634.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.2736 rms_B_bonded: 2.39
r_work: 0.2608 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2491 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8863
moved from start:          0.2812

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= 0.130
  Angle     :  0.471   5.444   9206  Z= 0.250
  Chirality :  0.039   0.141   1047
  Planarity :  0.004   0.048   1189
  Dihedral  :  4.390  33.266    903
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 1.73
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.02 (0.30), residues: 816
  helix:  1.54 (0.30), residues: 343
  sheet:  0.01 (0.39), residues: 173
  loop :  0.25 (0.37), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 127 
 TYR   0.010   0.001   TYR B 244 
 PHE   0.018   0.001   PHE A 141 
 TRP   0.010   0.001   TRP B 203 
 HIS   0.002   0.001   HIS B 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 6805)
  covalent geometry    : angle       0.47110 ( 9206)
  hydrogen bonds       : bond        0.04185 (  296)
  hydrogen bonds       : angle       4.38241 (  831)

*********************** 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
  39 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  398 CYS cc_start: 0.7904 (t) cc_final: 0.7225 (p)
  outliers start: 1
  outliers final: 1
  residues processed: 39
  average time/residue: 1.1050
  time to fit residues: 46.0275
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  : 0.359 
-------------------------------------------------------------------------------
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 52 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 30 optimal weight:    0.2980
   chunk 59 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.3298 r_free = 0.3298 target = 0.083404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.056366 restraints weight = 36281.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.2752 rms_B_bonded: 2.39
r_work: 0.2626 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2511 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8857
moved from start:          0.2892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6805  Z= 0.117
  Angle     :  0.460   4.856   9206  Z= 0.245
  Chirality :  0.038   0.141   1047
  Planarity :  0.004   0.048   1189
  Dihedral  :  4.335  33.032    903
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 1.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  6.64 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.30), residues: 816
  helix:  1.57 (0.30), residues: 343
  sheet: -0.02 (0.39), residues: 173
  loop :  0.24 (0.37), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 127 
 TYR   0.009   0.001   TYR B 244 
 PHE   0.018   0.001   PHE A 141 
 TRP   0.011   0.001   TRP B 203 
 HIS   0.002   0.001   HIS B 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 6805)
  covalent geometry    : angle       0.46023 ( 9206)
  hydrogen bonds       : bond        0.04019 (  296)
  hydrogen bonds       : angle       4.34461 (  831)

*********************** 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
  43 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  398 CYS cc_start: 0.7877 (t) cc_final: 0.7244 (p)
  outliers start: 3
  outliers final: 2
  residues processed: 43
  average time/residue: 1.1030
  time to fit residues: 50.6976
Evaluate side-chains
  40 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 PHE
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 43 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   overall best weight:    1.2786

-------------------------------------------------------------------------------
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 = 0.3281 r_free = 0.3281 target = 0.082375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.055070 restraints weight = 37079.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.2716 rms_B_bonded: 2.42
r_work: 0.2589 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2473 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8879
moved from start:          0.2924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6805  Z= 0.170
  Angle     :  0.488   5.709   9206  Z= 0.261
  Chirality :  0.039   0.143   1047
  Planarity :  0.004   0.048   1189
  Dihedral  :  4.424  32.850    903
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 1.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  6.77 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.30), residues: 816
  helix:  1.53 (0.30), residues: 343
  sheet: -0.07 (0.40), residues: 168
  loop :  0.16 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 303 
 TYR   0.011   0.001   TYR B 244 
 PHE   0.018   0.001   PHE A 141 
 TRP   0.011   0.001   TRP B 203 
 HIS   0.003   0.001   HIS B  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 6805)
  covalent geometry    : angle       0.48784 ( 9206)
  hydrogen bonds       : bond        0.04448 (  296)
  hydrogen bonds       : angle       4.44354 (  831)

*********************** 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
  44 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  398 CYS cc_start: 0.7884 (t) cc_final: 0.7196 (p)
  outliers start: 5
  outliers final: 2
  residues processed: 44
  average time/residue: 1.2037
  time to fit residues: 56.5509
Evaluate side-chains
  39 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 37
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 PHE
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 50 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 81 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 18 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 67 optimal weight:    0.8980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.083094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.056019 restraints weight = 36603.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.2735 rms_B_bonded: 2.38
r_work: 0.2608 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2492 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8862
moved from start:          0.2992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6805  Z= 0.120
  Angle     :  0.470   5.604   9206  Z= 0.250
  Chirality :  0.038   0.141   1047
  Planarity :  0.004   0.048   1189
  Dihedral  :  4.349  32.761    903
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 1.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  7.04 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.30), residues: 816
  helix:  1.60 (0.30), residues: 343
  sheet: -0.07 (0.40), residues: 168
  loop :  0.20 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 127 
 TYR   0.010   0.001   TYR B 244 
 PHE   0.018   0.001   PHE A 141 
 TRP   0.012   0.001   TRP B 203 
 HIS   0.002   0.001   HIS B 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 6805)
  covalent geometry    : angle       0.47001 ( 9206)
  hydrogen bonds       : bond        0.04063 (  296)
  hydrogen bonds       : angle       4.36228 (  831)

********************** 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
  42 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  398 CYS cc_start: 0.7875 (t) cc_final: 0.7207 (p)
  outliers start: 3
  outliers final: 2
  residues processed: 42
  average time/residue: 1.1193
  time to fit residues: 50.3882
Evaluate side-chains
  40 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 PHE
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 30 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 68 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 23 optimal weight:    0.2980
   chunk 78 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.083203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.056209 restraints weight = 36494.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.2741 rms_B_bonded: 2.37
r_work: 0.2612 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2496 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8859
moved from start:          0.3044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6805  Z= 0.121
  Angle     :  0.493   7.823   9206  Z= 0.266
  Chirality :  0.039   0.141   1047
  Planarity :  0.004   0.048   1189
  Dihedral  :  4.427  32.727    903
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 1.80
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.30), residues: 816
  helix:  1.62 (0.30), residues: 343
  sheet: -0.23 (0.39), residues: 174
  loop :  0.16 (0.37), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 169 
 TYR   0.015   0.001   TYR A  60 
 PHE   0.106   0.002   PHE A  76 
 TRP   0.011   0.001   TRP B 203 
 HIS   0.002   0.001   HIS B 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 6805)
  covalent geometry    : angle       0.49262 ( 9206)
  hydrogen bonds       : bond        0.03990 (  296)
  hydrogen bonds       : angle       4.33593 (  831)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5864.97 seconds
wall clock time: 100 minutes 10.05 seconds (6010.05 seconds total)