Starting phenix.real_space_refine
on Fri Oct 10 13:19:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xit_38389/10_2025/8xit_38389.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xit_38389/10_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xit_38389/10_2025/8xit_38389.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xit_38389/10_2025/8xit_38389.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xit_38389/10_2025/8xit_38389.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xit_38389/10_2025/8xit_38389.map"
  }
  resolution = 3.2
  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=   0.002 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 1.56, per 1000 atoms: 0.26
  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: 0.31
  Conformation dependent library (CDL) restraints added in 244.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.21
  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: 0.97

  Time building geometry restraints manager: 0.41 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: 0.01
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:             1.190
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.010
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.840
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  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:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.480
-------------------------------------------------------------------------------
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 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:  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
 ARG   0.003   0.000   ARG B 469 
 TYR   0.043   0.002   TYR A 534 
 PHE   0.018   0.001   PHE B 241 
 TRP   0.011   0.001   TRP B 321 
 HIS   0.001   0.000   HIS B 530 

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

*********************** 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  : 0.228 
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: 0.0858
  time to fit residues: 11.5807
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  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.0170
   chunk 38 optimal weight:    0.2980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.5618

-------------------------------------------------------------------------------
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 = 0.4080 r_free = 0.4080 target = 0.173104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.118823 restraints weight = 7656.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 2.29
r_work: 0.3313 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.0883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6124  Z= 0.144
  Angle     :  0.624  11.809   8296  Z= 0.311
  Chirality :  0.038   0.152    990
  Planarity :  0.004   0.044   1012
  Dihedral  :  3.659  14.783    826
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  8.26 %
    Favored  : 91.28 %
  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:  3.98 (0.32), residues: 756
  helix:  3.22 (0.20), residues: 670
  sheet:  None (None), residues: 0
  loop : -2.86 (0.62), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 457 
 TYR   0.024   0.001   TYR A 534 
 PHE   0.017   0.001   PHE B 241 
 TRP   0.010   0.001   TRP B 321 
 HIS   0.003   0.001   HIS B 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6124)
  covalent geometry    : angle       0.62421 ( 8296)
  hydrogen bonds       : bond        0.05493 (  502)
  hydrogen bonds       : angle       3.40457 ( 1506)

*********************** 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
  102 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 99
  time to evaluate  : 0.225 
Fit side-chains
REVERT: B  233 MET cc_start: 0.8920 (ppp) cc_final: 0.8626 (tmm)
  outliers start: 3
  outliers final: 2
  residues processed: 101
  average time/residue: 0.0776
  time to fit residues: 10.4971
Evaluate side-chains
  93 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 91
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
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 46 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0980
   chunk 44 optimal weight:    0.6980
   chunk 39 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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 = 0.4045 r_free = 0.4045 target = 0.169363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.119658 restraints weight = 7589.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 2.49
r_work: 0.3209 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
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      :  0.004   0.037   6124  Z= 0.168
  Angle     :  0.636  13.195   8296  Z= 0.316
  Chirality :  0.039   0.151    990
  Planarity :  0.004   0.042   1012
  Dihedral  :  3.583  16.014    826
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 10.75 %
    Favored  : 88.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  3.92 (0.32), residues: 756
  helix:  3.18 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop : -3.13 (0.60), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 457 
 TYR   0.021   0.002   TYR A 534 
 PHE   0.015   0.001   PHE B 241 
 TRP   0.005   0.001   TRP B 366 
 HIS   0.001   0.000   HIS A 530 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 6124)
  covalent geometry    : angle       0.63572 ( 8296)
  hydrogen bonds       : bond        0.05974 (  502)
  hydrogen bonds       : angle       3.37926 ( 1506)

*********************** 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
  103 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 0.183 
Fit side-chains
REVERT: A  326 MET cc_start: 0.8316 (ppp) cc_final: 0.7834 (ppp)
REVERT: B  233 MET cc_start: 0.9056 (ppp) cc_final: 0.8806 (tmm)
  outliers start: 7
  outliers final: 5
  residues processed: 100
  average time/residue: 0.0605
  time to fit residues: 8.1866
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  : 0.209 
-------------------------------------------------------------------------------
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 18 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 70 optimal weight:    0.0070
   chunk 57 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 71 optimal weight:    0.0020
   chunk 39 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.5208

-------------------------------------------------------------------------------
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 = 0.4089 r_free = 0.4089 target = 0.173696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.124217 restraints weight = 7451.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.3531 rms_B_bonded: 2.56
r_work: 0.3285 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.1348

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= 0.130
  Angle     :  0.591  14.007   8296  Z= 0.290
  Chirality :  0.037   0.138    990
  Planarity :  0.004   0.038   1012
  Dihedral  :  3.529  14.738    826
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 14.02 %
    Favored  : 84.74 %
  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:  4.08 (0.32), residues: 756
  helix:  3.36 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -3.34 (0.56), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 393 
 TYR   0.014   0.001   TYR A 534 
 PHE   0.016   0.001   PHE B 241 
 TRP   0.007   0.001   TRP B 321 
 HIS   0.001   0.000   HIS B  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 6124)
  covalent geometry    : angle       0.59117 ( 8296)
  hydrogen bonds       : bond        0.04627 (  502)
  hydrogen bonds       : angle       3.23605 ( 1506)

*********************** 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
  106 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A  326 MET cc_start: 0.8317 (ppp) cc_final: 0.7934 (ppp)
REVERT: A  432 ASP cc_start: 0.6788 (m-30) cc_final: 0.6552 (m-30)
REVERT: B  233 MET cc_start: 0.8975 (ppp) cc_final: 0.8737 (tmm)
  outliers start: 8
  outliers final: 4
  residues processed: 104
  average time/residue: 0.0602
  time to fit residues: 8.7488
Evaluate side-chains
  101 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 63 optimal weight:    7.9990
   chunk 73 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 75 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 72 optimal weight:    2.9990
   chunk 59 optimal weight:    9.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.4062 r_free = 0.4062 target = 0.171005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.121528 restraints weight = 7620.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 2.54
r_work: 0.3230 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.1427

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= 0.147
  Angle     :  0.625  14.743   8296  Z= 0.302
  Chirality :  0.038   0.135    990
  Planarity :  0.004   0.038   1012
  Dihedral  :  3.443  14.613    826
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 14.33 %
    Favored  : 84.11 %
  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:  4.03 (0.32), residues: 756
  helix:  3.32 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -3.41 (0.55), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 393 
 TYR   0.012   0.001   TYR B 344 
 PHE   0.014   0.001   PHE B 241 
 TRP   0.005   0.001   TRP B 366 
 HIS   0.001   0.000   HIS B 530 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 6124)
  covalent geometry    : angle       0.62458 ( 8296)
  hydrogen bonds       : bond        0.05196 (  502)
  hydrogen bonds       : angle       3.23933 ( 1506)

*********************** 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: 10
    poor density    : 98
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A  326 MET cc_start: 0.8367 (ppp) cc_final: 0.8002 (ppp)
REVERT: A  432 ASP cc_start: 0.6871 (m-30) cc_final: 0.6614 (m-30)
REVERT: B  233 MET cc_start: 0.9005 (ppp) cc_final: 0.8773 (tmm)
  outliers start: 10
  outliers final: 6
  residues processed: 106
  average time/residue: 0.0668
  time to fit residues: 9.7780
Evaluate side-chains
  104 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 31 optimal weight:    0.3980
   chunk 49 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   chunk 61 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 70 optimal weight:    0.0060
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.4796

-------------------------------------------------------------------------------
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 = 0.4093 r_free = 0.4093 target = 0.174212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.124634 restraints weight = 7547.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3537 rms_B_bonded: 2.57
r_work: 0.3283 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.1565

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= 0.126
  Angle     :  0.608  15.333   8296  Z= 0.292
  Chirality :  0.037   0.136    990
  Planarity :  0.004   0.036   1012
  Dihedral  :  3.449  15.790    826
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 15.42 %
    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 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:  4.14 (0.32), residues: 756
  helix:  3.41 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -3.42 (0.55), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 393 
 TYR   0.010   0.001   TYR B 344 
 PHE   0.014   0.001   PHE B 241 
 TRP   0.006   0.001   TRP B 321 
 HIS   0.001   0.000   HIS A 530 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 6124)
  covalent geometry    : angle       0.60792 ( 8296)
  hydrogen bonds       : bond        0.04476 (  502)
  hydrogen bonds       : angle       3.17302 ( 1506)

*********************** 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
  117 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A  326 MET cc_start: 0.8298 (ppp) cc_final: 0.8011 (ppp)
REVERT: B  233 MET cc_start: 0.8906 (ppp) cc_final: 0.8700 (tmm)
REVERT: B  251 LYS cc_start: 0.8548 (tptt) cc_final: 0.8300 (mmmt)
  outliers start: 15
  outliers final: 10
  residues processed: 115
  average time/residue: 0.0576
  time to fit residues: 9.2547
Evaluate side-chains
  107 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  577 ILE
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 76 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 74 optimal weight:    0.5980
   chunk 73 optimal weight:    1.9990
   chunk 56 optimal weight:    0.2980
   chunk 38 optimal weight:    0.6980
   chunk 14 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4089 r_free = 0.4089 target = 0.173830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.125206 restraints weight = 7553.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 2.42
r_work: 0.3267 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.1657

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= 0.130
  Angle     :  0.632  15.666   8296  Z= 0.299
  Chirality :  0.038   0.155    990
  Planarity :  0.004   0.036   1012
  Dihedral  :  3.450  17.041    826
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 15.89 %
    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 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:  4.18 (0.31), residues: 756
  helix:  3.43 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -3.42 (0.54), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 393 
 TYR   0.010   0.001   TYR B 344 
 PHE   0.014   0.001   PHE B 241 
 TRP   0.005   0.001   TRP B 321 
 HIS   0.001   0.000   HIS B  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 6124)
  covalent geometry    : angle       0.63221 ( 8296)
  hydrogen bonds       : bond        0.04517 (  502)
  hydrogen bonds       : angle       3.16922 ( 1506)

*********************** 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
  110 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.197 
Fit side-chains
REVERT: A  326 MET cc_start: 0.8303 (ppp) cc_final: 0.8032 (ppp)
REVERT: B  233 MET cc_start: 0.8942 (ppp) cc_final: 0.8702 (tmm)
REVERT: B  251 LYS cc_start: 0.8521 (tptt) cc_final: 0.8280 (mmmt)
  outliers start: 12
  outliers final: 10
  residues processed: 108
  average time/residue: 0.0641
  time to fit residues: 9.6206
Evaluate side-chains
  107 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  338 LEU
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 39 optimal weight:    5.9990
   chunk 64 optimal weight:    8.9990
   chunk 4 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   chunk 22 optimal weight:    0.4980
   overall best weight:    1.4786

-------------------------------------------------------------------------------
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 = 0.4034 r_free = 0.4034 target = 0.168407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.119019 restraints weight = 7522.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 2.46
r_work: 0.3198 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6124  Z= 0.176
  Angle     :  0.669  14.673   8296  Z= 0.324
  Chirality :  0.040   0.153    990
  Planarity :  0.004   0.039   1012
  Dihedral  :  3.516  17.123    826
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 16.51 %
    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 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:  3.98 (0.31), residues: 756
  helix:  3.24 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop : -3.32 (0.56), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 393 
 TYR   0.013   0.001   TYR A 538 
 PHE   0.014   0.001   PHE A 166 
 TRP   0.004   0.001   TRP B 366 
 HIS   0.001   0.000   HIS B 530 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 6124)
  covalent geometry    : angle       0.66872 ( 8296)
  hydrogen bonds       : bond        0.05863 (  502)
  hydrogen bonds       : angle       3.29637 ( 1506)

*********************** 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
  113 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.150 
Fit side-chains
REVERT: A  326 MET cc_start: 0.8325 (ppp) cc_final: 0.8027 (ppp)
REVERT: B  233 MET cc_start: 0.9004 (ppp) cc_final: 0.8756 (tmm)
  outliers start: 12
  outliers final: 9
  residues processed: 111
  average time/residue: 0.0601
  time to fit residues: 9.2031
Evaluate side-chains
  109 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 50 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 70 optimal weight:    0.0870
   chunk 63 optimal weight:    9.9990
   chunk 15 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.8164

-------------------------------------------------------------------------------
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 = 0.4067 r_free = 0.4067 target = 0.171576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.121552 restraints weight = 7571.470|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 2.64
r_work: 0.3237 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.1705

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     :  0.651  16.264   8296  Z= 0.311
  Chirality :  0.038   0.139    990
  Planarity :  0.004   0.036   1012
  Dihedral  :  3.522  16.888    826
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 16.82 %
    Favored  : 81.15 %
  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:  4.09 (0.31), residues: 756
  helix:  3.32 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop : -3.29 (0.56), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 393 
 TYR   0.011   0.001   TYR B 538 
 PHE   0.014   0.001   PHE B 241 
 TRP   0.004   0.001   TRP B 366 
 HIS   0.001   0.000   HIS B  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6124)
  covalent geometry    : angle       0.65117 ( 8296)
  hydrogen bonds       : bond        0.05015 (  502)
  hydrogen bonds       : angle       3.23824 ( 1506)

*********************** 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
  114 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.215 
Fit side-chains
REVERT: A  326 MET cc_start: 0.8325 (ppp) cc_final: 0.8015 (ppp)
REVERT: B  233 MET cc_start: 0.8968 (ppp) cc_final: 0.8725 (tmm)
REVERT: B  251 LYS cc_start: 0.8550 (tptt) cc_final: 0.8341 (mmmt)
  outliers start: 13
  outliers final: 10
  residues processed: 112
  average time/residue: 0.0630
  time to fit residues: 9.7277
Evaluate side-chains
  109 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
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  338 LEU
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain B residue  200 SER
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 1 optimal weight:    2.9990
   chunk 58 optimal weight:    4.9990
   chunk 26 optimal weight:    6.9990
   chunk 54 optimal weight:    0.7980
   chunk 33 optimal weight:    4.9990
   chunk 50 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0050
   chunk 47 optimal weight:    1.9990
   chunk 21 optimal weight:    0.4980
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.8596

-------------------------------------------------------------------------------
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 = 0.4067 r_free = 0.4067 target = 0.171613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.120184 restraints weight = 7530.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 2.65
r_work: 0.3229 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.1748

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= 0.143
  Angle     :  0.669  16.605   8296  Z= 0.316
  Chirality :  0.039   0.169    990
  Planarity :  0.004   0.036   1012
  Dihedral  :  3.529  17.112    826
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 17.13 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  4.09 (0.31), residues: 756
  helix:  3.32 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop : -3.33 (0.56), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 469 
 TYR   0.011   0.001   TYR B 538 
 PHE   0.013   0.001   PHE B 241 
 TRP   0.006   0.001   TRP B 321 
 HIS   0.001   0.000   HIS B 530 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 6124)
  covalent geometry    : angle       0.66927 ( 8296)
  hydrogen bonds       : bond        0.04996 (  502)
  hydrogen bonds       : angle       3.26487 ( 1506)

********************** 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
  109 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A  326 MET cc_start: 0.8338 (ppp) cc_final: 0.8030 (ppp)
REVERT: B  233 MET cc_start: 0.8989 (ppp) cc_final: 0.8749 (tmm)
  outliers start: 13
  outliers final: 11
  residues processed: 107
  average time/residue: 0.0608
  time to fit residues: 8.9504
Evaluate side-chains
  106 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
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  338 LEU
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain B residue  200 SER
Chi-restraints excluded: chain B residue  268 ILE
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 4 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9990
   chunk 64 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.5188

-------------------------------------------------------------------------------
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 = 0.4032 r_free = 0.4032 target = 0.168347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.116892 restraints weight = 7558.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 2.80
r_work: 0.3184 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.1803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6124  Z= 0.179
  Angle     :  0.698  16.379   8296  Z= 0.335
  Chirality :  0.040   0.147    990
  Planarity :  0.004   0.037   1012
  Dihedral  :  3.560  16.971    826
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 16.51 %
    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 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:  3.94 (0.31), residues: 756
  helix:  3.21 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop : -3.29 (0.56), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 220 
 TYR   0.013   0.001   TYR B 538 
 PHE   0.014   0.001   PHE A 166 
 TRP   0.008   0.001   TRP B 321 
 HIS   0.001   0.000   HIS B  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 6124)
  covalent geometry    : angle       0.69785 ( 8296)
  hydrogen bonds       : bond        0.05911 (  502)
  hydrogen bonds       : angle       3.35027 ( 1506)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1507.94 seconds
wall clock time: 26 minutes 30.17 seconds (1590.17 seconds total)