Starting phenix.real_space_refine
on Thu Jun  5 10:14:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xit_38389/06_2025/8xit_38389.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xit_38389/06_2025/8xit_38389.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xit_38389/06_2025/8xit_38389.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xit_38389/06_2025/8xit_38389.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xit_38389/06_2025/8xit_38389.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xit_38389/06_2025/8xit_38389.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C    3968      2.51       5
     N     950      2.21       5
     O    1024      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6002
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3001
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 392, 3001
          Classifications: {'peptide': 392}
          Link IDs: {'PTRANS': 16, 'TRANS': 375}
          Chain breaks: 6
    Chain: "B"
      Number of atoms: 3001
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 392, 3001
          Classifications: {'peptide': 392}
          Link IDs: {'PTRANS': 16, 'TRANS': 375}
          Chain breaks: 6
  Time building chain proxies: 4.67, per 1000 atoms: 0.78
  Number of scatterers: 6002
  At special positions: 0
  Unit cell: (90.1, 92.65, 95.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      60     16.00
     O    1024      8.00
     N     950      7.00
     C    3968      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.44
  Conformation dependent library (CDL) restraints added in 864.0 milliseconds
  

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1428

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 0 sheets defined
      92.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 39
    Processing helix  chain 'A' and resid 40 through 42
      No H-bonds generated for 'chain 'A' and resid 40 through 42'
    Processing helix  chain 'A' and resid 43 through 49
    Processing helix  chain 'A' and resid 134 through 159
      removed outlier: 5.087A  pdb=" N   LYS A 141 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
      removed outlier: 4.884A  pdb=" N   ALA A 142 " --> pdb=" O   PHE A 138 " (cutoff:3.500A)
      Proline residue:  A 150  - end of helix
    Processing helix  chain 'A' and resid 161 through 182
      removed outlier: 3.834A  pdb=" N   MET A 165 " --> pdb=" O   TYR A 161 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   PHE A 166 " --> pdb=" O   PRO A 162 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   THR A 167 " --> pdb=" O   ILE A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 214
      removed outlier: 3.586A  pdb=" N   TYR A 214 " --> pdb=" O   LEU A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 249
      removed outlier: 4.271A  pdb=" N   VAL A 235 " --> pdb=" O   LEU A 231 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   LEU A 236 " --> pdb=" O   ALA A 232 " (cutoff:3.500A)
      Proline residue:  A 239  - end of helix
    Processing helix  chain 'A' and resid 252 through 272
    Processing helix  chain 'A' and resid 297 through 314
      removed outlier: 3.594A  pdb=" N   ALA A 312 " --> pdb=" O   ASN A 308 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LEU A 314 " --> pdb=" O   GLY A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 328
      removed outlier: 3.516A  pdb=" N   THR A 325 " --> pdb=" O   TRP A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 338
    Processing helix  chain 'A' and resid 338 through 348
      removed outlier: 4.183A  pdb=" N   ILE A 342 " --> pdb=" O   LEU A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 371
      removed outlier: 3.622A  pdb=" N   ASN A 365 " --> pdb=" O   ASP A 361 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   TRP A 366 " --> pdb=" O   LEU A 362 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   THR A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   LEU A 369 " --> pdb=" O   ASN A 365 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ASP A 371 " --> pdb=" O   GLU A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 394
      removed outlier: 3.987A  pdb=" N   ALA A 394 " --> pdb=" O   THR A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 433
      removed outlier: 3.573A  pdb=" N   ASP A 433 " --> pdb=" O   GLY A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 491
    Processing helix  chain 'A' and resid 492 through 494
      No H-bonds generated for 'chain 'A' and resid 492 through 494'
    Processing helix  chain 'A' and resid 497 through 499
      No H-bonds generated for 'chain 'A' and resid 497 through 499'
    Processing helix  chain 'A' and resid 500 through 519
      removed outlier: 3.636A  pdb=" N   ASN A 504 " --> pdb=" O   LEU A 500 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   PHE A 509 " --> pdb=" O   PHE A 505 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ASP A 515 " --> pdb=" O   ILE A 511 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   SER A 517 " --> pdb=" O   MET A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 547
    Processing helix  chain 'A' and resid 567 through 584
      removed outlier: 3.602A  pdb=" N   ILE A 571 " --> pdb=" O   TRP A 567 " (cutoff:3.500A)
      Proline residue:  A 581  - end of helix
    Processing helix  chain 'B' and resid 17 through 39
    Processing helix  chain 'B' and resid 40 through 42
      No H-bonds generated for 'chain 'B' and resid 40 through 42'
    Processing helix  chain 'B' and resid 43 through 49
    Processing helix  chain 'B' and resid 134 through 159
      removed outlier: 5.067A  pdb=" N   LYS B 141 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      removed outlier: 4.859A  pdb=" N   ALA B 142 " --> pdb=" O   PHE B 138 " (cutoff:3.500A)
      Proline residue:  B 150  - end of helix
    Processing helix  chain 'B' and resid 161 through 182
      removed outlier: 3.868A  pdb=" N   MET B 165 " --> pdb=" O   TYR B 161 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   PHE B 166 " --> pdb=" O   PRO B 162 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   THR B 167 " --> pdb=" O   ILE B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 184 through 214
      removed outlier: 3.602A  pdb=" N   TYR B 214 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 249
      removed outlier: 4.313A  pdb=" N   VAL B 235 " --> pdb=" O   LEU B 231 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   LEU B 236 " --> pdb=" O   ALA B 232 " (cutoff:3.500A)
      Proline residue:  B 239  - end of helix
    Processing helix  chain 'B' and resid 252 through 272
    Processing helix  chain 'B' and resid 297 through 314
      removed outlier: 3.650A  pdb=" N   ALA B 312 " --> pdb=" O   ASN B 308 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LEU B 314 " --> pdb=" O   GLY B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 318 through 329
      removed outlier: 3.833A  pdb=" N   MET B 323 " --> pdb=" O   PRO B 319 " (cutoff:3.500A)
      removed outlier: 5.264A  pdb=" N   GLU B 324 " --> pdb=" O   ILE B 320 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 330 through 338
    Processing helix  chain 'B' and resid 338 through 348
      removed outlier: 4.167A  pdb=" N   ILE B 342 " --> pdb=" O   LEU B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 349 through 371
      removed outlier: 4.456A  pdb=" N   THR B 368 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   LEU B 369 " --> pdb=" O   ASN B 365 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 394
    Processing helix  chain 'B' and resid 424 through 433
      removed outlier: 3.630A  pdb=" N   ASP B 433 " --> pdb=" O   GLY B 429 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 454 through 491
      removed outlier: 3.939A  pdb=" N   ARG B 467 " --> pdb=" O   LYS B 463 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 497 through 499
      No H-bonds generated for 'chain 'B' and resid 497 through 499'
    Processing helix  chain 'B' and resid 500 through 519
      removed outlier: 3.735A  pdb=" N   ASN B 504 " --> pdb=" O   LEU B 500 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   PHE B 509 " --> pdb=" O   PHE B 505 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ASP B 515 " --> pdb=" O   ILE B 511 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   SER B 517 " --> pdb=" O   MET B 513 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 524 through 547
      removed outlier: 3.509A  pdb=" N   MET B 547 " --> pdb=" O   VAL B 543 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 567 through 584
      removed outlier: 3.646A  pdb=" N   ILE B 571 " --> pdb=" O   TRP B 567 " (cutoff:3.500A)
      Proline residue:  B 581  - end of helix

    502 hydrogen bonds defined for protein.
    1506 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: 1.62

  Time building geometry restraints manager: 1.73 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1824
        1.34 -     1.46: 1310
        1.46 -     1.58: 2886
        1.58 -     1.69: 0
        1.69 -     1.81: 104
  Bond restraints: 6124
  Sorted by residual:
  bond pdb=" CA  LEU B 338 "
       pdb=" C   LEU B 338 "
    ideal  model  delta    sigma   weight residual
    1.524  1.536 -0.012 1.26e-02 6.30e+03 9.08e-01
  bond pdb=" CA  THR B 348 "
       pdb=" C   THR B 348 "
    ideal  model  delta    sigma   weight residual
    1.522  1.535 -0.013 1.38e-02 5.25e+03 8.63e-01
  bond pdb=" CA  LEU A 338 "
       pdb=" C   LEU A 338 "
    ideal  model  delta    sigma   weight residual
    1.522  1.533 -0.011 1.26e-02 6.30e+03 7.92e-01
  bond pdb=" CA  ASN A 149 "
       pdb=" C   ASN A 149 "
    ideal  model  delta    sigma   weight residual
    1.520  1.531 -0.011 1.23e-02 6.61e+03 7.92e-01
  bond pdb=" CA  ASN B 149 "
       pdb=" C   ASN B 149 "
    ideal  model  delta    sigma   weight residual
    1.520  1.531 -0.010 1.23e-02 6.61e+03 6.88e-01
  ... (remaining 6119 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 8057
        1.64 -     3.28: 181
        3.28 -     4.92: 46
        4.92 -     6.57: 9
        6.57 -     8.21: 3
  Bond angle restraints: 8296
  Sorted by residual:
  angle pdb=" N   LEU B 338 "
        pdb=" CA  LEU B 338 "
        pdb=" C   LEU B 338 "
      ideal   model   delta    sigma   weight residual
     109.81  118.02   -8.21 2.21e+00 2.05e-01 1.38e+01
  angle pdb=" CA  PRO B 316 "
        pdb=" C   PRO B 316 "
        pdb=" N   ALA B 317 "
      ideal   model   delta    sigma   weight residual
     114.58  117.79   -3.21 1.16e+00 7.43e-01 7.67e+00
  angle pdb=" N   TYR B 161 "
        pdb=" CA  TYR B 161 "
        pdb=" C   TYR B 161 "
      ideal   model   delta    sigma   weight residual
     109.81  115.59   -5.78 2.21e+00 2.05e-01 6.84e+00
  angle pdb=" N   PRO B 239 "
        pdb=" CA  PRO B 239 "
        pdb=" C   PRO B 239 "
      ideal   model   delta    sigma   weight residual
     110.70  113.77   -3.07 1.22e+00 6.72e-01 6.33e+00
  angle pdb=" CA  MET B 326 "
        pdb=" CB  MET B 326 "
        pdb=" CG  MET B 326 "
      ideal   model   delta    sigma   weight residual
     114.10  119.02   -4.92 2.00e+00 2.50e-01 6.06e+00
  ... (remaining 8291 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.09: 3254
       17.09 -    34.17: 267
       34.17 -    51.25: 54
       51.25 -    68.34: 10
       68.34 -    85.42: 5
  Dihedral angle restraints: 3590
    sinusoidal: 1364
      harmonic: 2226
  Sorted by residual:
  dihedral pdb=" CG  ARG B 192 "
           pdb=" CD  ARG B 192 "
           pdb=" NE  ARG B 192 "
           pdb=" CZ  ARG B 192 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.70   44.30     2      1.50e+01 4.44e-03 1.04e+01
  dihedral pdb=" CG  ARG A 192 "
           pdb=" CD  ARG A 192 "
           pdb=" NE  ARG A 192 "
           pdb=" CZ  ARG A 192 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.77   44.23     2      1.50e+01 4.44e-03 1.04e+01
  dihedral pdb=" CB  GLU B 466 "
           pdb=" CG  GLU B 466 "
           pdb=" CD  GLU B 466 "
           pdb=" OE1 GLU B 466 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -85.42   85.42     1      3.00e+01 1.11e-03 9.82e+00
  ... (remaining 3587 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 732
       0.040 -    0.081: 203
       0.081 -    0.121: 47
       0.121 -    0.161: 6
       0.161 -    0.201: 2
  Chirality restraints: 990
  Sorted by residual:
  chirality pdb=" CA  LEU B 338 "
            pdb=" N   LEU B 338 "
            pdb=" C   LEU B 338 "
            pdb=" CB  LEU B 338 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CA  LEU A 338 "
            pdb=" N   LEU A 338 "
            pdb=" C   LEU A 338 "
            pdb=" CB  LEU A 338 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.42e-01
  chirality pdb=" CA  ILE A 491 "
            pdb=" N   ILE A 491 "
            pdb=" C   ILE A 491 "
            pdb=" CB  ILE A 491 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.28    0.15 2.00e-01 2.50e+01 5.51e-01
  ... (remaining 987 not shown)

  Planarity restraints: 1012
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 534 "    0.020 2.00e-02 2.50e+03   1.77e-02 6.23e+00
        pdb=" CG  TYR A 534 "   -0.043 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 534 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 534 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 534 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 534 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 534 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 534 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 534 "   -0.020 2.00e-02 2.50e+03   1.76e-02 6.22e+00
        pdb=" CG  TYR B 534 "    0.043 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 534 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 534 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 534 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 534 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 534 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR B 534 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 580 "    0.034 5.00e-02 4.00e+02   5.18e-02 4.30e+00
        pdb=" N   PRO B 581 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO B 581 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 581 "    0.029 5.00e-02 4.00e+02
  ... (remaining 1009 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1471
        2.81 -     3.33: 6264
        3.33 -     3.85: 9558
        3.85 -     4.38: 9689
        4.38 -     4.90: 18147
  Nonbonded interactions: 45129
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN B  34 "
            pdb=" O   LEU B 231 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" OG  SER B 175 "
            pdb=" O   ALA B 191 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" ND2 ASN A  34 "
            pdb=" O   LEU A 231 "
     model   vdw
     2.338 3.120
  nonbonded pdb=" OG  SER A 175 "
            pdb=" O   ALA A 191 "
     model   vdw
     2.341 3.040
  nonbonded pdb=" O   ASP B 387 "
            pdb=" OG1 THR B 390 "
     model   vdw
     2.471 3.040
  ... (remaining 45124 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             1.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     18.250
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
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   0.032   6124  Z= 0.151
  Angle     :  0.644   8.208   8296  Z= 0.333
  Chirality :  0.040   0.201    990
  Planarity :  0.005   0.052   1012
  Dihedral  : 13.312  85.423   2162
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  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:  3.41 (0.32), residues: 756
  helix:  2.84 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -2.88 (0.62), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 321 
 HIS   0.001   0.000   HIS B 530 
 PHE   0.018   0.001   PHE B 241 
 TYR   0.043   0.002   TYR A 534 
 ARG   0.003   0.000   ARG B 469 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13662 (  502)
  hydrogen bonds       : angle       4.37259 ( 1506)
  covalent geometry    : bond        0.00327 ( 6124)
  covalent geometry    : angle       0.64421 ( 8296)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.612 
Fit side-chains
REVERT: B  233 MET cc_start: 0.8575 (ppp) cc_final: 0.8301 (tmm)
REVERT: B  323 MET cc_start: 0.6273 (tpt) cc_final: 0.5950 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1714
  time to fit residues: 23.1873
Evaluate side-chains
  94 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    5.9990
   chunk 59 optimal weight:   10.0000
   chunk 32 optimal weight:    0.9980
   chunk 20 optimal weight:    8.9990
   chunk 39 optimal weight:    5.9990
   chunk 31 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
A 358 GLN
B  34 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.169547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.119509 restraints weight = 7510.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 2.66
r_work: 0.3225 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.0936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6124  Z= 0.169
  Angle     :  0.648  12.404   8296  Z= 0.325
  Chirality :  0.040   0.160    990
  Planarity :  0.005   0.049   1012
  Dihedral  :  3.687  14.833    826
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  9.66 %
    Favored  : 89.88 %
  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:  3.81 (0.32), residues: 756
  helix:  3.10 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop : -3.01 (0.61), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 321 
 HIS   0.002   0.001   HIS B 329 
 PHE   0.017   0.001   PHE B 241 
 TYR   0.026   0.002   TYR A 534 
 ARG   0.002   0.000   ARG A 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06188 (  502)
  hydrogen bonds       : angle       3.47429 ( 1506)
  covalent geometry    : bond        0.00390 ( 6124)
  covalent geometry    : angle       0.64824 ( 8296)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 95
  time to evaluate  : 0.657 
Fit side-chains
REVERT: A  462 GLN cc_start: 0.8062 (mp10) cc_final: 0.7790 (mp10)
REVERT: B  233 MET cc_start: 0.9053 (ppp) cc_final: 0.8739 (tmm)
  outliers start: 3
  outliers final: 2
  residues processed: 97
  average time/residue: 0.1716
  time to fit residues: 22.2063
Evaluate side-chains
  94 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 92
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain B residue  362 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 66 optimal weight:    9.9990
   chunk 69 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 65 optimal weight:    6.9990
   chunk 36 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 56 optimal weight:    4.9990
   chunk 17 optimal weight:    0.0870
   chunk 9 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.9960

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

Flipped N/Q/H residues before XYZ refinement:
A 358 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.170891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.121364 restraints weight = 7525.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 2.50
r_work: 0.3250 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.1144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6124  Z= 0.150
  Angle     :  0.621  13.757   8296  Z= 0.307
  Chirality :  0.038   0.146    990
  Planarity :  0.004   0.043   1012
  Dihedral  :  3.583  14.429    826
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 11.37 %
    Favored  : 87.54 %
  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:  3.96 (0.32), residues: 756
  helix:  3.24 (0.20), residues: 670
  sheet:  None (None), residues: 0
  loop : -3.16 (0.58), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 321 
 HIS   0.001   0.000   HIS B 329 
 PHE   0.017   0.001   PHE B 241 
 TYR   0.017   0.001   TYR A 534 
 ARG   0.003   0.000   ARG A 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05591 (  502)
  hydrogen bonds       : angle       3.35946 ( 1506)
  covalent geometry    : bond        0.00333 ( 6124)
  covalent geometry    : angle       0.62145 ( 8296)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.608 
Fit side-chains
REVERT: A  326 MET cc_start: 0.8301 (ppp) cc_final: 0.7833 (ppp)
REVERT: B  233 MET cc_start: 0.9038 (ppp) cc_final: 0.8789 (tmm)
  outliers start: 7
  outliers final: 5
  residues processed: 105
  average time/residue: 0.1610
  time to fit residues: 22.8228
Evaluate side-chains
  100 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 95
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  326 MET
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  577 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 1 optimal weight:    0.3980
   chunk 25 optimal weight:    0.9980
   chunk 72 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   chunk 36 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0980
   chunk 35 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 15 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 358 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.173561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.124442 restraints weight = 7470.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.3530 rms_B_bonded: 2.55
r_work: 0.3259 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.1345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6124  Z= 0.131
  Angle     :  0.597  13.892   8296  Z= 0.291
  Chirality :  0.037   0.137    990
  Planarity :  0.004   0.039   1012
  Dihedral  :  3.523  15.744    826
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 13.24 %
    Favored  : 85.36 %
  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:  4.09 (0.32), residues: 756
  helix:  3.36 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -3.31 (0.56), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 321 
 HIS   0.001   0.000   HIS B  17 
 PHE   0.015   0.001   PHE B 241 
 TYR   0.015   0.001   TYR A 534 
 ARG   0.001   0.000   ARG A 356 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04638 (  502)
  hydrogen bonds       : angle       3.24408 ( 1506)
  covalent geometry    : bond        0.00265 ( 6124)
  covalent geometry    : angle       0.59686 ( 8296)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.704 
Fit side-chains
REVERT: A  326 MET cc_start: 0.8334 (ppp) cc_final: 0.7966 (ppp)
REVERT: A  432 ASP cc_start: 0.6803 (m-30) cc_final: 0.6598 (m-30)
REVERT: B  233 MET cc_start: 0.8992 (ppp) cc_final: 0.8755 (tmm)
  outliers start: 9
  outliers final: 5
  residues processed: 106
  average time/residue: 0.1610
  time to fit residues: 23.3545
Evaluate side-chains
  101 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 CYS
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  326 MET
Chi-restraints excluded: chain B residue  362 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 76 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 27 optimal weight:   20.0000
   chunk 25 optimal weight:    5.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
A 358 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.169972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.120309 restraints weight = 7459.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 2.64
r_work: 0.3197 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.1436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6124  Z= 0.154
  Angle     :  0.635  14.745   8296  Z= 0.307
  Chirality :  0.038   0.138    990
  Planarity :  0.004   0.039   1012
  Dihedral  :  3.464  15.131    826
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 14.80 %
    Favored  : 83.33 %
  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:  4.01 (0.32), residues: 756
  helix:  3.31 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -3.41 (0.55), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 366 
 HIS   0.001   0.000   HIS B 530 
 PHE   0.015   0.001   PHE B 241 
 TYR   0.011   0.001   TYR B 344 
 ARG   0.003   0.000   ARG B 393 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05381 (  502)
  hydrogen bonds       : angle       3.26088 ( 1506)
  covalent geometry    : bond        0.00362 ( 6124)
  covalent geometry    : angle       0.63454 ( 8296)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.757 
Fit side-chains
REVERT: A  326 MET cc_start: 0.8371 (ppp) cc_final: 0.8020 (ppp)
REVERT: A  432 ASP cc_start: 0.6874 (m-30) cc_final: 0.6618 (m-30)
REVERT: B  233 MET cc_start: 0.9046 (ppp) cc_final: 0.8785 (tmm)
  outliers start: 12
  outliers final: 7
  residues processed: 106
  average time/residue: 0.1913
  time to fit residues: 27.6756
Evaluate side-chains
  102 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 CYS
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  326 MET
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  577 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 67 optimal weight:    7.9990
   chunk 10 optimal weight:    0.5980
   chunk 39 optimal weight:    5.9990
   chunk 76 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 358 GLN
B 195 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.169702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.120716 restraints weight = 7404.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 2.42
r_work: 0.3218 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.1465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6124  Z= 0.157
  Angle     :  0.630  14.888   8296  Z= 0.307
  Chirality :  0.038   0.141    990
  Planarity :  0.004   0.038   1012
  Dihedral  :  3.492  16.107    826
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.64 %
    Favored  : 83.18 %
  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:  3.95 (0.32), residues: 756
  helix:  3.28 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -3.52 (0.55), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 366 
 HIS   0.001   0.000   HIS A 530 
 PHE   0.015   0.001   PHE B 241 
 TYR   0.012   0.001   TYR B 538 
 ARG   0.001   0.000   ARG B 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05514 (  502)
  hydrogen bonds       : angle       3.27372 ( 1506)
  covalent geometry    : bond        0.00376 ( 6124)
  covalent geometry    : angle       0.62973 ( 8296)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 1.301 
Fit side-chains
REVERT: A  326 MET cc_start: 0.8342 (ppp) cc_final: 0.8023 (ppp)
REVERT: A  519 MET cc_start: 0.7795 (mmm) cc_final: 0.7409 (mmp)
REVERT: B  233 MET cc_start: 0.8968 (ppp) cc_final: 0.8736 (tmm)
  outliers start: 14
  outliers final: 10
  residues processed: 111
  average time/residue: 0.1809
  time to fit residues: 27.7529
Evaluate side-chains
  105 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  476 CYS
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  326 MET
Chi-restraints excluded: chain B residue  348 THR
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  543 VAL
Chi-restraints excluded: chain B residue  577 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 26 optimal weight:    9.9990
   chunk 36 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 45 optimal weight:    0.1980
   chunk 43 optimal weight:    0.9990
   chunk 2 optimal weight:    0.3980
   chunk 6 optimal weight:    0.3980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 358 GLN
A 462 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.172690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.121866 restraints weight = 7419.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 2.65
r_work: 0.3243 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.1638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6124  Z= 0.131
  Angle     :  0.617  15.382   8296  Z= 0.297
  Chirality :  0.037   0.135    990
  Planarity :  0.004   0.037   1012
  Dihedral  :  3.497  17.514    826
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.95 %
    Favored  : 82.87 %
  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:  4.17 (0.32), residues: 756
  helix:  3.38 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop : -3.34 (0.56), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 321 
 HIS   0.001   0.000   HIS A 530 
 PHE   0.014   0.001   PHE B 241 
 TYR   0.010   0.001   TYR B 344 
 ARG   0.001   0.000   ARG B 393 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04585 (  502)
  hydrogen bonds       : angle       3.18040 ( 1506)
  covalent geometry    : bond        0.00279 ( 6124)
  covalent geometry    : angle       0.61746 ( 8296)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.641 
Fit side-chains
REVERT: A  326 MET cc_start: 0.8377 (ppp) cc_final: 0.8101 (ppp)
REVERT: B  233 MET cc_start: 0.8968 (ppp) cc_final: 0.8710 (tmm)
REVERT: B  251 LYS cc_start: 0.8523 (tptt) cc_final: 0.8317 (mmmt)
  outliers start: 14
  outliers final: 13
  residues processed: 111
  average time/residue: 0.1505
  time to fit residues: 22.9832
Evaluate side-chains
  110 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain B residue  200 SER
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  326 MET
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  348 THR
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  543 VAL
Chi-restraints excluded: chain B residue  577 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 52 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0970
   chunk 9 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0980
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
A 358 GLN
B 462 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.174118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.123532 restraints weight = 7555.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3525 rms_B_bonded: 2.58
r_work: 0.3279 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.1738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6124  Z= 0.126
  Angle     :  0.621  15.776   8296  Z= 0.294
  Chirality :  0.037   0.132    990
  Planarity :  0.004   0.036   1012
  Dihedral  :  3.437  16.793    826
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.58 %
    Favored  : 82.24 %
  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:  4.16 (0.32), residues: 756
  helix:  3.37 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop : -3.32 (0.55), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 321 
 HIS   0.001   0.000   HIS B  17 
 PHE   0.014   0.001   PHE B 241 
 TYR   0.009   0.001   TYR B 344 
 ARG   0.002   0.000   ARG A 393 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04282 (  502)
  hydrogen bonds       : angle       3.14997 ( 1506)
  covalent geometry    : bond        0.00264 ( 6124)
  covalent geometry    : angle       0.62124 ( 8296)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.636 
Fit side-chains
REVERT: A  326 MET cc_start: 0.8329 (ppp) cc_final: 0.8029 (ppp)
REVERT: B  233 MET cc_start: 0.8906 (ppp) cc_final: 0.8661 (tmm)
REVERT: B  251 LYS cc_start: 0.8535 (tptt) cc_final: 0.8314 (mmmt)
  outliers start: 14
  outliers final: 14
  residues processed: 115
  average time/residue: 0.1465
  time to fit residues: 23.3445
Evaluate side-chains
  113 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain A residue  248 PHE
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  476 CYS
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain B residue  200 SER
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  326 MET
Chi-restraints excluded: chain B residue  338 LEU
Chi-restraints excluded: chain B residue  348 THR
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  577 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 27 optimal weight:   10.0000
   chunk 53 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 358 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.172684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.122743 restraints weight = 7522.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 2.51
r_work: 0.3249 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6124  Z= 0.135
  Angle     :  0.632  15.180   8296  Z= 0.302
  Chirality :  0.038   0.156    990
  Planarity :  0.004   0.036   1012
  Dihedral  :  3.430  16.579    826
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 15.58 %
    Favored  : 81.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.13 (0.32), residues: 756
  helix:  3.35 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop : -3.33 (0.55), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 321 
 HIS   0.001   0.000   HIS B 329 
 PHE   0.013   0.001   PHE B 241 
 TYR   0.010   0.001   TYR B 344 
 ARG   0.003   0.000   ARG B 393 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04577 (  502)
  hydrogen bonds       : angle       3.18696 ( 1506)
  covalent geometry    : bond        0.00303 ( 6124)
  covalent geometry    : angle       0.63209 ( 8296)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.609 
Fit side-chains
REVERT: A  326 MET cc_start: 0.8334 (ppp) cc_final: 0.7993 (ppp)
REVERT: A  462 GLN cc_start: 0.8066 (mm110) cc_final: 0.7847 (mm-40)
REVERT: B  233 MET cc_start: 0.8932 (ppp) cc_final: 0.8702 (tmm)
REVERT: B  251 LYS cc_start: 0.8529 (tptt) cc_final: 0.8300 (mmmt)
REVERT: B  264 LEU cc_start: 0.7454 (mt) cc_final: 0.7237 (tp)
  outliers start: 16
  outliers final: 14
  residues processed: 114
  average time/residue: 0.1475
  time to fit residues: 23.2005
Evaluate side-chains
  114 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain A residue  248 PHE
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  476 CYS
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain B residue  200 SER
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  326 MET
Chi-restraints excluded: chain B residue  348 THR
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  577 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 70 optimal weight:    0.0030
   chunk 15 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 63 optimal weight:    6.9990
   overall best weight:    0.9196

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

Flipped N/Q/H residues before XYZ refinement:
A 358 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.172177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.121773 restraints weight = 7486.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 2.56
r_work: 0.3244 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.1785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6124  Z= 0.141
  Angle     :  0.645  16.082   8296  Z= 0.306
  Chirality :  0.038   0.157    990
  Planarity :  0.004   0.037   1012
  Dihedral  :  3.454  18.307    826
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 16.04 %
    Favored  : 81.62 %
  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:  4.12 (0.32), residues: 756
  helix:  3.34 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop : -3.32 (0.54), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 366 
 HIS   0.001   0.000   HIS B  17 
 PHE   0.014   0.001   PHE B 241 
 TYR   0.010   0.001   TYR B 344 
 ARG   0.002   0.000   ARG B 393 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04836 (  502)
  hydrogen bonds       : angle       3.18837 ( 1506)
  covalent geometry    : bond        0.00326 ( 6124)
  covalent geometry    : angle       0.64547 ( 8296)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.760 
Fit side-chains
REVERT: A  326 MET cc_start: 0.8342 (ppp) cc_final: 0.8011 (ppp)
REVERT: A  462 GLN cc_start: 0.8023 (mm110) cc_final: 0.7821 (mm-40)
REVERT: B  233 MET cc_start: 0.8964 (ppp) cc_final: 0.8723 (tmm)
REVERT: B  251 LYS cc_start: 0.8553 (tptt) cc_final: 0.8330 (mmmt)
REVERT: B  264 LEU cc_start: 0.7527 (mt) cc_final: 0.7292 (tp)
  outliers start: 15
  outliers final: 13
  residues processed: 111
  average time/residue: 0.1623
  time to fit residues: 24.6758
Evaluate side-chains
  111 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  200 SER
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  476 CYS
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain B residue  200 SER
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  326 MET
Chi-restraints excluded: chain B residue  348 THR
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  543 VAL
Chi-restraints excluded: chain B residue  577 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 51 optimal weight:    5.9990
   chunk 5 optimal weight:    0.8980
   chunk 17 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 66 optimal weight:    5.9990
   chunk 76 optimal weight:    0.2980
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 358 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.172008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.121761 restraints weight = 7609.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 2.60
r_work: 0.3228 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.1813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6124  Z= 0.138
  Angle     :  0.644  16.066   8296  Z= 0.306
  Chirality :  0.038   0.150    990
  Planarity :  0.004   0.037   1012
  Dihedral  :  3.445  17.434    826
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 16.04 %
    Favored  : 81.46 %
  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:  4.10 (0.32), residues: 756
  helix:  3.33 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop : -3.30 (0.55), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 321 
 HIS   0.001   0.000   HIS B 530 
 PHE   0.013   0.001   PHE B 241 
 TYR   0.010   0.001   TYR B 344 
 ARG   0.004   0.000   ARG B 393 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04768 (  502)
  hydrogen bonds       : angle       3.19101 ( 1506)
  covalent geometry    : bond        0.00316 ( 6124)
  covalent geometry    : angle       0.64375 ( 8296)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3403.99 seconds
wall clock time: 59 minutes 45.51 seconds (3585.51 seconds total)