Starting phenix.real_space_refine
on Wed Sep 17 04:25:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sro_40736/09_2025/8sro_40736.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sro_40736/09_2025/8sro_40736.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sro_40736/09_2025/8sro_40736.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sro_40736/09_2025/8sro_40736.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sro_40736/09_2025/8sro_40736.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sro_40736/09_2025/8sro_40736.map"
  }
  resolution = 3.3
  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=   0.001 sd=   0.070
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      72      5.49       5
     S       9      5.16       5
     C    2447      2.51       5
     N     748      2.21       5
     O     856      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4132
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 682
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 682
          Classifications: {'peptide': 87}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 4, 'TRANS': 82}
          Unresolved non-hydrogen bonds: 86
          Unresolved non-hydrogen angles: 108
          Unresolved non-hydrogen dihedrals: 75
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 58
    Chain: "D"
      Number of atoms: 626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 626
          Classifications: {'peptide': 85}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 4, 'TRANS': 80}
          Unresolved non-hydrogen bonds: 127
          Unresolved non-hydrogen angles: 161
          Unresolved non-hydrogen dihedrals: 112
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 2, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 86
    Chain: "B"
      Number of atoms: 695
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 695
          Classifications: {'peptide': 87}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 4, 'TRANS': 82}
          Unresolved non-hydrogen bonds: 72
          Unresolved non-hydrogen angles: 92
          Unresolved non-hydrogen dihedrals: 61
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 53
    Chain: "C"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 653
          Classifications: {'peptide': 86}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 4, 'TRANS': 81}
          Unresolved non-hydrogen bonds: 106
          Unresolved non-hydrogen angles: 134
          Unresolved non-hydrogen dihedrals: 93
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ASN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'GLN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 74
    Chain: "J"
      Number of atoms: 370
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 370
          Classifications: {'DNA': 18}
          Link IDs: {'rna3p': 17}
    Chain: "I"
      Number of atoms: 368
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 368
          Classifications: {'DNA': 18}
          Link IDs: {'rna3p': 17}
    Chain: "F"
      Number of atoms: 370
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 370
          Classifications: {'DNA': 18}
          Link IDs: {'rna3p': 17}
    Chain: "E"
      Number of atoms: 368
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 368
          Classifications: {'DNA': 18}
          Link IDs: {'rna3p': 17}
  Time building chain proxies: 1.31, per 1000 atoms: 0.32
  Number of scatterers: 4132
  At special positions: 0
  Unit cell: (59.08, 88.62, 81.868, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       9     16.00
     P      72     15.00
     O     856      8.00
     N     748      7.00
     C    2447      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: 0.40
  Conformation dependent library (CDL) restraints added in 89.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  682

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 4 sheets defined
      50.7% alpha, 9.0% beta
      29 base pairs and 58 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 327 through 333
      removed outlier: 3.876A  pdb=" N   PHE A 331 " --> pdb=" O   ASN A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 351
    Processing helix  chain 'A' and resid 359 through 371
    Processing helix  chain 'A' and resid 379 through 392
      removed outlier: 3.616A  pdb=" N   ALA A 384 " --> pdb=" O   THR A 380 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   ILE A 385 " --> pdb=" O   TRP A 381 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 329 through 334
    Processing helix  chain 'D' and resid 341 through 351
    Processing helix  chain 'D' and resid 359 through 371
      removed outlier: 3.599A  pdb=" N   HIS D 365 " --> pdb=" O   ASN D 361 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 379 through 392
      removed outlier: 3.650A  pdb=" N   ALA D 384 " --> pdb=" O   THR D 380 " (cutoff:3.500A)
      removed outlier: 5.200A  pdb=" N   ILE D 385 " --> pdb=" O   TRP D 381 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 328 through 333
      removed outlier: 3.996A  pdb=" N   LYS B 332 " --> pdb=" O   MET B 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 341 through 351
    Processing helix  chain 'B' and resid 360 through 371
      removed outlier: 3.793A  pdb=" N   HIS B 365 " --> pdb=" O   ASN B 361 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 392
      removed outlier: 4.151A  pdb=" N   ALA B 384 " --> pdb=" O   THR B 380 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   ILE B 385 " --> pdb=" O   TRP B 381 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 329 through 333
      removed outlier: 3.538A  pdb=" N   LYS C 332 " --> pdb=" O   ASP C 329 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 341 through 351
    Processing helix  chain 'C' and resid 359 through 371
      removed outlier: 3.874A  pdb=" N   HIS C 365 " --> pdb=" O   ASN C 361 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 379 through 392
      removed outlier: 3.549A  pdb=" N   ALA C 384 " --> pdb=" O   THR C 380 " (cutoff:3.500A)
      removed outlier: 4.713A  pdb=" N   ILE C 385 " --> pdb=" O   TRP C 381 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 395 through 399
    Processing sheet with id=AA2, first strand: chain 'D' and resid 395 through 399
    Processing sheet with id=AA3, first strand: chain 'B' and resid 358 through 359
      removed outlier: 3.538A  pdb=" N   THR B 407 " --> pdb=" O   VAL B 396 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 395 through 399

    115 hydrogen bonds defined for protein.
    336 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      66 hydrogen bonds
      132 hydrogen bond angles
      0 basepair planarities
      29 basepair parallelities
      58 stacking parallelities
  Total time for adding SS restraints: 0.49

  Time building geometry restraints manager: 0.49 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 891
        1.33 -     1.45: 1384
        1.45 -     1.57: 1974
        1.57 -     1.69: 140
        1.69 -     1.81: 14
  Bond restraints: 4403
  Sorted by residual:
  bond pdb=" N   ARG B 356 "
       pdb=" CA  ARG B 356 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.49e-02 4.50e+03 4.48e+00
  bond pdb=" N   PHE A 411 "
       pdb=" CA  PHE A 411 "
    ideal  model  delta    sigma   weight residual
    1.456  1.476 -0.020 1.28e-02 6.10e+03 2.39e+00
  bond pdb=" N   GLU A 412 "
       pdb=" CA  GLU A 412 "
    ideal  model  delta    sigma   weight residual
    1.458  1.479 -0.021 1.90e-02 2.77e+03 1.19e+00
  bond pdb=" C   GLU B 355 "
       pdb=" N   ARG B 356 "
    ideal  model  delta    sigma   weight residual
    1.333  1.346 -0.013 1.39e-02 5.18e+03 8.87e-01
  bond pdb=" CA  ASP D 409 "
       pdb=" C   ASP D 409 "
    ideal  model  delta    sigma   weight residual
    1.529  1.519  0.010 1.04e-02 9.25e+03 8.63e-01
  ... (remaining 4398 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.05: 5964
        1.05 -     2.10: 224
        2.10 -     3.16: 97
        3.16 -     4.21: 11
        4.21 -     5.26: 12
  Bond angle restraints: 6308
  Sorted by residual:
  angle pdb=" N   ASP A 409 "
        pdb=" CA  ASP A 409 "
        pdb=" C   ASP A 409 "
      ideal   model   delta    sigma   weight residual
     114.56  111.16    3.40 1.27e+00 6.20e-01 7.18e+00
  angle pdb=" C3'  DC F  20 "
        pdb=" C2'  DC F  20 "
        pdb=" C1'  DC F  20 "
      ideal   model   delta    sigma   weight residual
     101.60   97.80    3.80 1.50e+00 4.44e-01 6.43e+00
  angle pdb=" N   VAL D 408 "
        pdb=" CA  VAL D 408 "
        pdb=" C   VAL D 408 "
      ideal   model   delta    sigma   weight residual
     106.53  110.02   -3.49 1.41e+00 5.03e-01 6.13e+00
  angle pdb=" N   ALA C 353 "
        pdb=" CA  ALA C 353 "
        pdb=" C   ALA C 353 "
      ideal   model   delta    sigma   weight residual
     109.81  115.07   -5.26 2.21e+00 2.05e-01 5.67e+00
  angle pdb=" N   ALA D 353 "
        pdb=" CA  ALA D 353 "
        pdb=" C   ALA D 353 "
      ideal   model   delta    sigma   weight residual
     109.81  115.02   -5.21 2.21e+00 2.05e-01 5.55e+00
  ... (remaining 6303 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 1600
       17.58 -    35.16: 425
       35.16 -    52.73: 268
       52.73 -    70.31: 84
       70.31 -    87.89: 3
  Dihedral angle restraints: 2380
    sinusoidal: 1341
      harmonic: 1039
  Sorted by residual:
  dihedral pdb=" CD  ARG B 356 "
           pdb=" NE  ARG B 356 "
           pdb=" CZ  ARG B 356 "
           pdb=" NH1 ARG B 356 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -85.30   85.30     1      1.00e+01 1.00e-02 8.81e+01
  dihedral pdb=" CG  ARG B 356 "
           pdb=" CD  ARG B 356 "
           pdb=" NE  ARG B 356 "
           pdb=" CZ  ARG B 356 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00   -2.11  -87.89     2      1.50e+01 4.44e-03 2.13e+01
  dihedral pdb=" CA  PRO B 354 "
           pdb=" C   PRO B 354 "
           pdb=" N   GLU B 355 "
           pdb=" CA  GLU B 355 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.58  -16.42     0      5.00e+00 4.00e-02 1.08e+01
  ... (remaining 2377 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 558
       0.042 -    0.083: 113
       0.083 -    0.125: 18
       0.125 -    0.166: 1
       0.166 -    0.208: 1
  Chirality restraints: 691
  Sorted by residual:
  chirality pdb=" CA  GLU A 412 "
            pdb=" N   GLU A 412 "
            pdb=" C   GLU A 412 "
            pdb=" CB  GLU A 412 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" C1'  DC F  20 "
            pdb=" O4'  DC F  20 "
            pdb=" C2'  DC F  20 "
            pdb=" N1   DC F  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.31    0.16 2.00e-01 2.50e+01 6.41e-01
  chirality pdb=" CA  VAL A 408 "
            pdb=" N   VAL A 408 "
            pdb=" C   VAL A 408 "
            pdb=" CB  VAL A 408 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.52e-01
  ... (remaining 688 not shown)

  Planarity restraints: 551
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 356 "    1.099 9.50e-02 1.11e+02   4.92e-01 1.46e+02
        pdb=" NE  ARG B 356 "   -0.066 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 356 "   -0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 356 "    0.013 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 356 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 410 "    0.006 2.00e-02 2.50e+03   1.26e-02 1.60e+00
        pdb=" C   GLU A 410 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   GLU A 410 "    0.008 2.00e-02 2.50e+03
        pdb=" N   PHE A 411 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC F  20 "    0.014 2.00e-02 2.50e+03   7.79e-03 1.36e+00
        pdb=" N1   DC F  20 "   -0.017 2.00e-02 2.50e+03
        pdb=" C2   DC F  20 "   -0.006 2.00e-02 2.50e+03
        pdb=" O2   DC F  20 "    0.002 2.00e-02 2.50e+03
        pdb=" N3   DC F  20 "    0.001 2.00e-02 2.50e+03
        pdb=" C4   DC F  20 "    0.002 2.00e-02 2.50e+03
        pdb=" N4   DC F  20 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DC F  20 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DC F  20 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 548 not shown)

  Histogram of nonbonded interaction distances:
        2.41 -     2.91: 1530
        2.91 -     3.41: 3812
        3.41 -     3.90: 7566
        3.90 -     4.40: 8473
        4.40 -     4.90: 12239
  Nonbonded interactions: 33620
  Sorted by model distance:
  nonbonded pdb=" O   ALA C 384 "
            pdb=" ND2 ASN C 388 "
     model   vdw
     2.409 3.120
  nonbonded pdb=" OD1 ASN B 383 "
            pdb=" NH2 ARG B 386 "
     model   vdw
     2.415 3.120
  nonbonded pdb=" O   VAL B 408 "
            pdb=" CG1 VAL B 408 "
     model   vdw
     2.519 3.460
  nonbonded pdb=" NH2 ARG B 397 "
            pdb=" O5'  DG E  27 "
     model   vdw
     2.520 3.120
  nonbonded pdb=" O   TYR A 373 "
            pdb=" N   ARG A 375 "
     model   vdw
     2.527 3.120
  ... (remaining 33615 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and ((resid 328 through 330 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 331 or (resid 332 through 334 and (name N or name CA or \ 
 name C or name O or name CB )) or resid 335 or (resid 336 and (name N or name C \ 
A or name C or name O or name CB )) or resid 337 through 339 or (resid 340 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 341 through 351 or  \ 
(resid 352 through 353 and (name N or name CA or name C or name O or name CB ))  \ 
or resid 354 through 356 or (resid 357 through 359 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 360 through 361 or (resid 362 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 363 through 374 or (resid 3 \ 
75 through 376 and (name N or name CA or name C or name O or name CB )) or resid \ 
 377 through 397 or (resid 398 and (name N or name CA or name C or name O or nam \ 
e CB )) or resid 399 through 407 or (resid 408 through 412 and (name N or name C \ 
A or name C or name O or name CB ))))
  selection = (chain 'B' and ((resid 328 through 330 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 331 or (resid 332 through 334 and (name N or name CA or \ 
 name C or name O or name CB )) or resid 335 or (resid 336 and (name N or name C \ 
A or name C or name O or name CB )) or resid 337 through 339 or (resid 340 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 341 through 351 or  \ 
(resid 352 through 353 and (name N or name CA or name C or name O or name CB ))  \ 
or resid 354 through 355 or (resid 356 through 359 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 360 through 381 or (resid 382 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 383 through 392 or (resid 3 \ 
93 and (name N or name CA or name C or name O or name CB )) or resid 394 through \ 
 397 or (resid 398 and (name N or name CA or name C or name O or name CB )) or r \ 
esid 399 through 407 or (resid 408 through 412 and (name N or name CA or name C  \ 
or name O or name CB ))))
  selection = (chain 'C' and (resid 328 through 333 or (resid 334 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 335 or (resid 336 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 337 through 339 or (resid 340 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 341 through 357 or (re \ 
sid 358 through 359 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 360 through 392 or (resid 393 and (name N or name CA or name C or name O o \ 
r name CB )) or resid 394 through 397 or (resid 398 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 399 through 407 or (resid 408 through 412  \ 
and (name N or name CA or name C or name O or name CB ))))
  selection = (chain 'D' and (resid 328 through 351 or (resid 352 through 353 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 354 through 374 or (resid 375  \ 
through 376 and (name N or name CA or name C or name O or name CB )) or resid 37 \ 
7 through 392 or (resid 393 and (name N or name CA or name C or name O or name C \ 
B )) or resid 394 through 412))
}
ncs_group {
  reference = chain 'E'
  selection = chain 'I'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'J'
}

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:             4.570
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.840
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.000
  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:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
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   0.046   4403  Z= 0.148
  Angle     :  0.559   5.262   6308  Z= 0.332
  Chirality :  0.034   0.208    691
  Planarity :  0.021   0.492    551
  Dihedral  : 26.264  87.888   1698
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 21.08 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.78 (0.43), residues: 337
  helix: -1.09 (0.37), residues: 185
  sheet: -0.10 (0.78), residues: 46
  loop : -1.50 (0.54), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 358 
 TYR   0.014   0.002   TYR D 364 
 PHE   0.011   0.001   PHE A 340 
 TRP   0.012   0.001   TRP C 366 
 HIS   0.001   0.000   HIS B 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 4403)
  covalent geometry    : angle       0.55862 ( 6308)
  hydrogen bonds       : bond        0.20959 (  181)
  hydrogen bonds       : angle       7.75662 (  468)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 57
  time to evaluate  : 0.122 
Fit side-chains
REVERT: A  336 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.6574 (tmm)
  outliers start: 2
  outliers final: 0
  residues processed: 57
  average time/residue: 0.0750
  time to fit residues: 5.4237
Evaluate side-chains
  56 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 55
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 26 optimal weight:    0.0470
   chunk 2 optimal weight:    0.0570
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.4980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.4996

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.142974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.122639 restraints weight = 8471.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.3739 rms_B_bonded: 2.52
r_work: 0.3588 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.0931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   4403  Z= 0.156
  Angle     :  0.555   5.131   6308  Z= 0.328
  Chirality :  0.034   0.167    691
  Planarity :  0.004   0.023    551
  Dihedral  : 27.784  63.713   1204
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 20.63 %
    Favored  : 77.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.16 (0.46), residues: 337
  helix: -0.38 (0.40), residues: 185
  sheet: -0.11 (0.75), residues: 46
  loop : -1.52 (0.55), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 358 
 TYR   0.018   0.002   TYR D 364 
 PHE   0.011   0.001   PHE A 340 
 TRP   0.008   0.001   TRP C 366 
 HIS   0.003   0.001   HIS B 392 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 4403)
  covalent geometry    : angle       0.55465 ( 6308)
  hydrogen bonds       : bond        0.04334 (  181)
  hydrogen bonds       : angle       5.39188 (  468)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.109 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 61
  average time/residue: 0.0991
  time to fit residues: 7.2870
Evaluate side-chains
  61 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 58
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  380 THR
Chi-restraints excluded: chain C residue  380 THR
Chi-restraints excluded: chain C residue  390 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0870
   chunk 28 optimal weight:    0.2980
   chunk 19 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0050
   chunk 10 optimal weight:    0.0570
   chunk 30 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.2090

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.145185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.125392 restraints weight = 8404.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3777 rms_B_bonded: 2.49
r_work: 0.3627 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.1330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4403  Z= 0.134
  Angle     :  0.534   5.046   6308  Z= 0.315
  Chirality :  0.034   0.188    691
  Planarity :  0.004   0.035    551
  Dihedral  : 27.574  64.302   1201
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 18.83 %
    Favored  : 78.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.08 (0.45), residues: 337
  helix: -0.23 (0.40), residues: 185
  sheet: -0.14 (0.74), residues: 46
  loop : -1.65 (0.54), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 358 
 TYR   0.013   0.002   TYR B 364 
 PHE   0.010   0.001   PHE A 340 
 TRP   0.005   0.001   TRP B 406 
 HIS   0.002   0.000   HIS A 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 4403)
  covalent geometry    : angle       0.53385 ( 6308)
  hydrogen bonds       : bond        0.03636 (  181)
  hydrogen bonds       : angle       4.70847 (  468)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A  336 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.6284 (tmm)
REVERT: B  330 TYR cc_start: 0.7011 (t80) cc_final: 0.6785 (t80)
  outliers start: 6
  outliers final: 3
  residues processed: 68
  average time/residue: 0.0853
  time to fit residues: 7.0529
Evaluate side-chains
  63 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 59
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 MET
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain C residue  390 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 28 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.8382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.142797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.122500 restraints weight = 8455.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3736 rms_B_bonded: 2.50
r_work: 0.3587 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.1495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4403  Z= 0.178
  Angle     :  0.558   5.246   6308  Z= 0.328
  Chirality :  0.035   0.192    691
  Planarity :  0.004   0.029    551
  Dihedral  : 27.637  64.682   1201
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 19.73 %
    Favored  : 77.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.21 (0.45), residues: 337
  helix: -0.32 (0.39), residues: 186
  sheet: -0.19 (0.73), residues: 46
  loop : -1.76 (0.54), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 358 
 TYR   0.013   0.002   TYR C 364 
 PHE   0.010   0.001   PHE A 340 
 TRP   0.012   0.001   TRP B 366 
 HIS   0.010   0.001   HIS B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 4403)
  covalent geometry    : angle       0.55768 ( 6308)
  hydrogen bonds       : bond        0.03696 (  181)
  hydrogen bonds       : angle       4.50786 (  468)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.120 
Fit side-chains
  outliers start: 7
  outliers final: 7
  residues processed: 63
  average time/residue: 0.0922
  time to fit residues: 7.0508
Evaluate side-chains
  66 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain D residue  380 THR
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain C residue  380 THR
Chi-restraints excluded: chain C residue  390 SER
Chi-restraints excluded: chain C residue  405 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 17 optimal weight:    0.0870
   chunk 33 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 24 optimal weight:   10.0000
   chunk 12 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.6760

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.143219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.123081 restraints weight = 8482.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3744 rms_B_bonded: 2.49
r_work: 0.3596 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.1606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4403  Z= 0.158
  Angle     :  0.547   5.242   6308  Z= 0.322
  Chirality :  0.035   0.199    691
  Planarity :  0.004   0.023    551
  Dihedral  : 27.629  64.341   1201
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 19.73 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.13 (0.45), residues: 337
  helix: -0.25 (0.39), residues: 186
  sheet: -0.18 (0.73), residues: 46
  loop : -1.71 (0.55), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 358 
 TYR   0.017   0.002   TYR A 373 
 PHE   0.016   0.001   PHE A 340 
 TRP   0.014   0.001   TRP B 366 
 HIS   0.008   0.001   HIS B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 4403)
  covalent geometry    : angle       0.54718 ( 6308)
  hydrogen bonds       : bond        0.03430 (  181)
  hydrogen bonds       : angle       4.40262 (  468)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.135 
Fit side-chains
REVERT: D  366 TRP cc_start: 0.8027 (t60) cc_final: 0.7803 (t60)
  outliers start: 8
  outliers final: 7
  residues processed: 64
  average time/residue: 0.0979
  time to fit residues: 7.4828
Evaluate side-chains
  66 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain D residue  380 THR
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain C residue  380 THR
Chi-restraints excluded: chain C residue  390 SER
Chi-restraints excluded: chain C residue  405 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0060
   chunk 9 optimal weight:    0.0030
   chunk 35 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 24 optimal weight:    9.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.5006

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.143886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.123741 restraints weight = 8623.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3753 rms_B_bonded: 2.52
r_work: 0.3605 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
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   0.047   4403  Z= 0.147
  Angle     :  0.546   5.405   6308  Z= 0.320
  Chirality :  0.035   0.224    691
  Planarity :  0.003   0.024    551
  Dihedral  : 27.609  64.510   1201
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 19.28 %
    Favored  : 77.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.04 (0.46), residues: 337
  helix: -0.21 (0.40), residues: 186
  sheet: -0.14 (0.73), residues: 50
  loop : -1.66 (0.57), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 375 
 TYR   0.014   0.002   TYR A 373 
 PHE   0.015   0.001   PHE A 340 
 TRP   0.015   0.001   TRP B 366 
 HIS   0.007   0.001   HIS B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 4403)
  covalent geometry    : angle       0.54601 ( 6308)
  hydrogen bonds       : bond        0.03269 (  181)
  hydrogen bonds       : angle       4.31957 (  468)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.125 
Fit side-chains
REVERT: D  366 TRP cc_start: 0.7976 (t60) cc_final: 0.7707 (t60)
  outliers start: 8
  outliers final: 8
  residues processed: 63
  average time/residue: 0.0865
  time to fit residues: 6.7320
Evaluate side-chains
  66 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  377 HIS
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain D residue  380 THR
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain C residue  335 ASN
Chi-restraints excluded: chain C residue  390 SER
Chi-restraints excluded: chain C residue  405 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 10 optimal weight:    0.0050
   chunk 7 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0060
   chunk 0 optimal weight:    5.9990
   chunk 3 optimal weight:    0.0170
   chunk 32 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 19 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.2448

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.146428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.126419 restraints weight = 8647.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.3792 rms_B_bonded: 2.52
r_work: 0.3645 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.1953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4403  Z= 0.133
  Angle     :  0.537   5.374   6308  Z= 0.315
  Chirality :  0.034   0.223    691
  Planarity :  0.003   0.024    551
  Dihedral  : 27.525  65.498   1201
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 19.73 %
    Favored  : 77.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.87 (0.46), residues: 337
  helix: -0.03 (0.41), residues: 186
  sheet: -0.21 (0.75), residues: 46
  loop : -1.53 (0.54), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 375 
 TYR   0.014   0.002   TYR B 330 
 PHE   0.011   0.001   PHE A 340 
 TRP   0.021   0.001   TRP B 366 
 HIS   0.008   0.001   HIS B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 4403)
  covalent geometry    : angle       0.53669 ( 6308)
  hydrogen bonds       : bond        0.02959 (  181)
  hydrogen bonds       : angle       4.12151 (  468)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.105 
Fit side-chains
REVERT: B  334 HIS cc_start: 0.7596 (m-70) cc_final: 0.7041 (m170)
REVERT: C  399 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7450 (mt-10)
  outliers start: 7
  outliers final: 6
  residues processed: 62
  average time/residue: 0.0733
  time to fit residues: 5.6803
Evaluate side-chains
  65 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain C residue  340 PHE
Chi-restraints excluded: chain C residue  380 THR
Chi-restraints excluded: chain C residue  390 SER
Chi-restraints excluded: chain C residue  405 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 11 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   overall best weight:    1.0584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.142321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.121828 restraints weight = 8558.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3728 rms_B_bonded: 2.50
r_work: 0.3581 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.1955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   4403  Z= 0.198
  Angle     :  0.580   5.628   6308  Z= 0.339
  Chirality :  0.036   0.222    691
  Planarity :  0.004   0.033    551
  Dihedral  : 27.645  64.745   1201
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 19.28 %
    Favored  : 76.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.96 (0.46), residues: 337
  helix: -0.15 (0.40), residues: 186
  sheet: -0.15 (0.74), residues: 50
  loop : -1.59 (0.58), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 375 
 TYR   0.015   0.002   TYR A 373 
 PHE   0.018   0.001   PHE A 340 
 TRP   0.034   0.002   TRP D 366 
 HIS   0.006   0.001   HIS B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 4403)
  covalent geometry    : angle       0.57984 ( 6308)
  hydrogen bonds       : bond        0.03869 (  181)
  hydrogen bonds       : angle       4.33868 (  468)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.128 
Fit side-chains
REVERT: C  337 ARG cc_start: 0.7110 (tpp80) cc_final: 0.6821 (tpt170)
  outliers start: 10
  outliers final: 10
  residues processed: 64
  average time/residue: 0.0821
  time to fit residues: 6.4978
Evaluate side-chains
  69 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  377 HIS
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain D residue  380 THR
Chi-restraints excluded: chain D residue  394 CYS
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain C residue  335 ASN
Chi-restraints excluded: chain C residue  380 THR
Chi-restraints excluded: chain C residue  390 SER
Chi-restraints excluded: chain C residue  405 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 23 optimal weight:    0.0980
   chunk 21 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 8 optimal weight:   10.0000
   chunk 17 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0060
   chunk 3 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.4596

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.144641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.124486 restraints weight = 8663.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3767 rms_B_bonded: 2.51
r_work: 0.3618 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.2048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4403  Z= 0.144
  Angle     :  0.556   5.519   6308  Z= 0.324
  Chirality :  0.034   0.244    691
  Planarity :  0.003   0.025    551
  Dihedral  : 27.569  65.090   1201
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 21.97 %
    Favored  : 75.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.73 (0.47), residues: 337
  helix:  0.03 (0.41), residues: 186
  sheet: -0.17 (0.74), residues: 50
  loop : -1.40 (0.59), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 375 
 TYR   0.013   0.002   TYR B 330 
 PHE   0.013   0.001   PHE A 340 
 TRP   0.024   0.001   TRP D 366 
 HIS   0.007   0.001   HIS B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 4403)
  covalent geometry    : angle       0.55603 ( 6308)
  hydrogen bonds       : bond        0.03211 (  181)
  hydrogen bonds       : angle       4.21638 (  468)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.131 
Fit side-chains
  outliers start: 5
  outliers final: 5
  residues processed: 61
  average time/residue: 0.0768
  time to fit residues: 5.9196
Evaluate side-chains
  64 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain C residue  380 THR
Chi-restraints excluded: chain C residue  390 SER
Chi-restraints excluded: chain C residue  405 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 8 optimal weight:   10.0000
   chunk 19 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 4 optimal weight:    0.2980
   chunk 28 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.7982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.143651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.123340 restraints weight = 8580.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.3750 rms_B_bonded: 2.50
r_work: 0.3604 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.2069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4403  Z= 0.172
  Angle     :  0.570   5.824   6308  Z= 0.332
  Chirality :  0.035   0.251    691
  Planarity :  0.004   0.036    551
  Dihedral  : 27.603  65.013   1201
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 21.97 %
    Favored  : 75.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.83 (0.47), residues: 337
  helix: -0.02 (0.40), residues: 186
  sheet: -0.22 (0.74), residues: 50
  loop : -1.53 (0.59), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 375 
 TYR   0.015   0.002   TYR A 373 
 PHE   0.017   0.001   PHE A 340 
 TRP   0.024   0.002   TRP D 366 
 HIS   0.006   0.001   HIS B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 4403)
  covalent geometry    : angle       0.56953 ( 6308)
  hydrogen bonds       : bond        0.03501 (  181)
  hydrogen bonds       : angle       4.23078 (  468)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.132 
Fit side-chains
  outliers start: 6
  outliers final: 6
  residues processed: 62
  average time/residue: 0.0974
  time to fit residues: 7.3068
Evaluate side-chains
  65 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  377 HIS
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain C residue  380 THR
Chi-restraints excluded: chain C residue  390 SER
Chi-restraints excluded: chain C residue  405 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 27 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 21 optimal weight:    5.9990
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.143019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.122599 restraints weight = 8544.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.3741 rms_B_bonded: 2.50
r_work: 0.3595 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   4403  Z= 0.175
  Angle     :  0.573   6.009   6308  Z= 0.333
  Chirality :  0.035   0.221    691
  Planarity :  0.004   0.040    551
  Dihedral  : 27.630  65.012   1201
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.12 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 21.97 %
    Favored  : 75.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.86 (0.47), residues: 337
  helix: -0.07 (0.40), residues: 186
  sheet: -0.19 (0.74), residues: 50
  loop : -1.49 (0.60), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 375 
 TYR   0.014   0.002   TYR A 373 
 PHE   0.012   0.001   PHE A 340 
 TRP   0.023   0.002   TRP B 366 
 HIS   0.006   0.001   HIS B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 4403)
  covalent geometry    : angle       0.57297 ( 6308)
  hydrogen bonds       : bond        0.03555 (  181)
  hydrogen bonds       : angle       4.29675 (  468)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1143.86 seconds
wall clock time: 20 minutes 18.13 seconds (1218.13 seconds total)