Starting phenix.real_space_refine
on Fri Oct 10 14:43:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ozl_17313/10_2025/8ozl_17313.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ozl_17313/10_2025/8ozl_17313.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ozl_17313/10_2025/8ozl_17313.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ozl_17313/10_2025/8ozl_17313.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ozl_17313/10_2025/8ozl_17313.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ozl_17313/10_2025/8ozl_17313.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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      25      5.16       5
     C    4220      2.51       5
     N    1205      2.21       5
     O    1225      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  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: 6675
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1335
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 174, 1335
          Classifications: {'peptide': 174}
          Link IDs: {'PTRANS': 11, 'TRANS': 162}
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 1.25, per 1000 atoms: 0.19
  Number of scatterers: 6675
  At special positions: 0
  Unit cell: (111.24, 110.16, 51.84, 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      25     16.00
     O    1225      8.00
     N    1205      7.00
     C    4220      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: 0.38
  Conformation dependent library (CDL) restraints added in 369.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1560

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 0 sheets defined
      81.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 306 through 315
      removed outlier: 3.760A  pdb=" N   ILE A 310 " --> pdb=" O   PRO A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 322
      No H-bonds generated for 'chain 'A' and resid 320 through 322'
    Processing helix  chain 'A' and resid 323 through 339
      Proline residue:  A 333  - end of helix
    Processing helix  chain 'A' and resid 343 through 355
    Processing helix  chain 'A' and resid 364 through 369
      removed outlier: 4.077A  pdb=" N   LEU A 369 " --> pdb=" O   GLY A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 383
    Processing helix  chain 'A' and resid 386 through 389
      removed outlier: 3.566A  pdb=" N   HIS A 389 " --> pdb=" O   PHE A 386 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 386 through 389'
    Processing helix  chain 'A' and resid 390 through 402
      removed outlier: 3.541A  pdb=" N   ASP A 400 " --> pdb=" O   LYS A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 415
    Processing helix  chain 'A' and resid 418 through 430
      removed outlier: 3.692A  pdb=" N   GLY A 428 " --> pdb=" O   GLY A 424 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   TYR A 429 " --> pdb=" O   ILE A 425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 446
      removed outlier: 3.706A  pdb=" N   VAL A 436 " --> pdb=" O   GLY A 432 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLU A 446 " --> pdb=" O   ARG A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 455
    Processing helix  chain 'A' and resid 455 through 467
    Processing helix  chain 'B' and resid 306 through 315
      removed outlier: 3.760A  pdb=" N   ILE B 310 " --> pdb=" O   PRO B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 320 through 322
      No H-bonds generated for 'chain 'B' and resid 320 through 322'
    Processing helix  chain 'B' and resid 323 through 339
      Proline residue:  B 333  - end of helix
    Processing helix  chain 'B' and resid 343 through 355
    Processing helix  chain 'B' and resid 364 through 369
      removed outlier: 4.077A  pdb=" N   LEU B 369 " --> pdb=" O   GLY B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 383
    Processing helix  chain 'B' and resid 386 through 389
      removed outlier: 3.566A  pdb=" N   HIS B 389 " --> pdb=" O   PHE B 386 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 386 through 389'
    Processing helix  chain 'B' and resid 390 through 402
      removed outlier: 3.542A  pdb=" N   ASP B 400 " --> pdb=" O   LYS B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 415
    Processing helix  chain 'B' and resid 418 through 430
      removed outlier: 3.691A  pdb=" N   GLY B 428 " --> pdb=" O   GLY B 424 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   TYR B 429 " --> pdb=" O   ILE B 425 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 446
      removed outlier: 3.706A  pdb=" N   VAL B 436 " --> pdb=" O   GLY B 432 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLU B 446 " --> pdb=" O   ARG B 442 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 455
    Processing helix  chain 'B' and resid 455 through 467
    Processing helix  chain 'C' and resid 306 through 315
      removed outlier: 3.760A  pdb=" N   ILE C 310 " --> pdb=" O   PRO C 306 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 320 through 322
      No H-bonds generated for 'chain 'C' and resid 320 through 322'
    Processing helix  chain 'C' and resid 323 through 339
      Proline residue:  C 333  - end of helix
    Processing helix  chain 'C' and resid 343 through 355
    Processing helix  chain 'C' and resid 364 through 369
      removed outlier: 4.078A  pdb=" N   LEU C 369 " --> pdb=" O   GLY C 366 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 370 through 383
    Processing helix  chain 'C' and resid 386 through 389
      removed outlier: 3.566A  pdb=" N   HIS C 389 " --> pdb=" O   PHE C 386 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 386 through 389'
    Processing helix  chain 'C' and resid 390 through 402
      removed outlier: 3.541A  pdb=" N   ASP C 400 " --> pdb=" O   LYS C 396 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 403 through 415
    Processing helix  chain 'C' and resid 418 through 430
      removed outlier: 3.692A  pdb=" N   GLY C 428 " --> pdb=" O   GLY C 424 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   TYR C 429 " --> pdb=" O   ILE C 425 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 432 through 446
      removed outlier: 3.706A  pdb=" N   VAL C 436 " --> pdb=" O   GLY C 432 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   GLU C 446 " --> pdb=" O   ARG C 442 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 448 through 455
    Processing helix  chain 'C' and resid 455 through 467
    Processing helix  chain 'D' and resid 306 through 315
      removed outlier: 3.760A  pdb=" N   ILE D 310 " --> pdb=" O   PRO D 306 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 320 through 322
      No H-bonds generated for 'chain 'D' and resid 320 through 322'
    Processing helix  chain 'D' and resid 323 through 339
      Proline residue:  D 333  - end of helix
    Processing helix  chain 'D' and resid 343 through 355
    Processing helix  chain 'D' and resid 364 through 369
      removed outlier: 4.078A  pdb=" N   LEU D 369 " --> pdb=" O   GLY D 366 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 370 through 383
    Processing helix  chain 'D' and resid 386 through 389
      removed outlier: 3.566A  pdb=" N   HIS D 389 " --> pdb=" O   PHE D 386 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 386 through 389'
    Processing helix  chain 'D' and resid 390 through 402
      removed outlier: 3.542A  pdb=" N   ASP D 400 " --> pdb=" O   LYS D 396 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 403 through 415
    Processing helix  chain 'D' and resid 418 through 430
      removed outlier: 3.691A  pdb=" N   GLY D 428 " --> pdb=" O   GLY D 424 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   TYR D 429 " --> pdb=" O   ILE D 425 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 432 through 446
      removed outlier: 3.706A  pdb=" N   VAL D 436 " --> pdb=" O   GLY D 432 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   GLU D 446 " --> pdb=" O   ARG D 442 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 448 through 455
    Processing helix  chain 'D' and resid 455 through 467
    Processing helix  chain 'E' and resid 306 through 315
      removed outlier: 3.760A  pdb=" N   ILE E 310 " --> pdb=" O   PRO E 306 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 320 through 322
      No H-bonds generated for 'chain 'E' and resid 320 through 322'
    Processing helix  chain 'E' and resid 323 through 339
      Proline residue:  E 333  - end of helix
    Processing helix  chain 'E' and resid 343 through 355
    Processing helix  chain 'E' and resid 364 through 369
      removed outlier: 4.078A  pdb=" N   LEU E 369 " --> pdb=" O   GLY E 366 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 370 through 383
    Processing helix  chain 'E' and resid 386 through 389
      removed outlier: 3.566A  pdb=" N   HIS E 389 " --> pdb=" O   PHE E 386 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 386 through 389'
    Processing helix  chain 'E' and resid 390 through 402
      removed outlier: 3.542A  pdb=" N   ASP E 400 " --> pdb=" O   LYS E 396 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 403 through 415
    Processing helix  chain 'E' and resid 418 through 430
      removed outlier: 3.691A  pdb=" N   GLY E 428 " --> pdb=" O   GLY E 424 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   TYR E 429 " --> pdb=" O   ILE E 425 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 432 through 446
      removed outlier: 3.706A  pdb=" N   VAL E 436 " --> pdb=" O   GLY E 432 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   GLU E 446 " --> pdb=" O   ARG E 442 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 448 through 455
    Processing helix  chain 'E' and resid 455 through 467

    410 hydrogen bonds defined for protein.
    1200 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: 0.85

  Time building geometry restraints manager: 0.56 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1366
        1.33 -     1.45: 1444
        1.45 -     1.57: 3955
        1.57 -     1.69: 0
        1.69 -     1.81: 40
  Bond restraints: 6805
  Sorted by residual:
  bond pdb=" C   PRO B 317 "
       pdb=" O   PRO B 317 "
    ideal  model  delta    sigma   weight residual
    1.246  1.208  0.038 8.50e-03 1.38e+04 1.99e+01
  bond pdb=" C   PRO A 317 "
       pdb=" O   PRO A 317 "
    ideal  model  delta    sigma   weight residual
    1.246  1.208  0.037 8.50e-03 1.38e+04 1.94e+01
  bond pdb=" C   PRO E 317 "
       pdb=" O   PRO E 317 "
    ideal  model  delta    sigma   weight residual
    1.246  1.208  0.037 8.50e-03 1.38e+04 1.93e+01
  bond pdb=" C   PRO D 317 "
       pdb=" O   PRO D 317 "
    ideal  model  delta    sigma   weight residual
    1.246  1.208  0.037 8.50e-03 1.38e+04 1.91e+01
  bond pdb=" C   PRO C 317 "
       pdb=" O   PRO C 317 "
    ideal  model  delta    sigma   weight residual
    1.246  1.209  0.037 8.50e-03 1.38e+04 1.90e+01
  ... (remaining 6800 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.03: 4806
        1.03 -     2.05: 2739
        2.05 -     3.08: 1355
        3.08 -     4.11: 315
        4.11 -     5.13: 65
  Bond angle restraints: 9280
  Sorted by residual:
  angle pdb=" C   PRO A 431 "
        pdb=" CA  PRO A 431 "
        pdb=" CB  PRO A 431 "
      ideal   model   delta    sigma   weight residual
     111.87  107.00    4.87 8.40e-01 1.42e+00 3.37e+01
  angle pdb=" C   PRO B 431 "
        pdb=" CA  PRO B 431 "
        pdb=" CB  PRO B 431 "
      ideal   model   delta    sigma   weight residual
     111.87  107.00    4.87 8.40e-01 1.42e+00 3.36e+01
  angle pdb=" C   PRO D 431 "
        pdb=" CA  PRO D 431 "
        pdb=" CB  PRO D 431 "
      ideal   model   delta    sigma   weight residual
     111.87  107.03    4.84 8.40e-01 1.42e+00 3.32e+01
  angle pdb=" C   PRO E 431 "
        pdb=" CA  PRO E 431 "
        pdb=" CB  PRO E 431 "
      ideal   model   delta    sigma   weight residual
     111.87  107.03    4.84 8.40e-01 1.42e+00 3.32e+01
  angle pdb=" C   PRO C 431 "
        pdb=" CA  PRO C 431 "
        pdb=" CB  PRO C 431 "
      ideal   model   delta    sigma   weight residual
     111.87  107.05    4.82 8.40e-01 1.42e+00 3.29e+01
  ... (remaining 9275 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.61: 3455
        9.61 -    19.22: 396
       19.22 -    28.83: 134
       28.83 -    38.44: 55
       38.44 -    48.05: 30
  Dihedral angle restraints: 4070
    sinusoidal: 1625
      harmonic: 2445
  Sorted by residual:
  dihedral pdb=" N   GLN D 308 "
           pdb=" C   GLN D 308 "
           pdb=" CA  GLN D 308 "
           pdb=" CB  GLN D 308 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  130.47   -7.67     0      2.50e+00 1.60e-01 9.41e+00
  dihedral pdb=" N   GLN C 308 "
           pdb=" C   GLN C 308 "
           pdb=" CA  GLN C 308 "
           pdb=" CB  GLN C 308 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  130.47   -7.67     0      2.50e+00 1.60e-01 9.41e+00
  dihedral pdb=" N   GLN A 308 "
           pdb=" C   GLN A 308 "
           pdb=" CA  GLN A 308 "
           pdb=" CB  GLN A 308 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  130.47   -7.67     0      2.50e+00 1.60e-01 9.40e+00
  ... (remaining 4067 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 415
       0.054 -    0.108: 326
       0.108 -    0.162: 287
       0.162 -    0.216: 40
       0.216 -    0.270: 17
  Chirality restraints: 1085
  Sorted by residual:
  chirality pdb=" CA  GLN D 308 "
            pdb=" N   GLN D 308 "
            pdb=" C   GLN D 308 "
            pdb=" CB  GLN D 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.83e+00
  chirality pdb=" CA  GLN B 308 "
            pdb=" N   GLN B 308 "
            pdb=" C   GLN B 308 "
            pdb=" CB  GLN B 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.82e+00
  chirality pdb=" CA  GLN A 308 "
            pdb=" N   GLN A 308 "
            pdb=" C   GLN A 308 "
            pdb=" CB  GLN A 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.82e+00
  ... (remaining 1082 not shown)

  Planarity restraints: 1220
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE C 310 "    0.006 2.00e-02 2.50e+03   1.26e-02 1.58e+00
        pdb=" C   ILE C 310 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   ILE C 310 "    0.008 2.00e-02 2.50e+03
        pdb=" N   ARG C 311 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE E 310 "   -0.006 2.00e-02 2.50e+03   1.25e-02 1.57e+00
        pdb=" C   ILE E 310 "    0.022 2.00e-02 2.50e+03
        pdb=" O   ILE E 310 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   ARG E 311 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 310 "    0.006 2.00e-02 2.50e+03   1.24e-02 1.54e+00
        pdb=" C   ILE A 310 "   -0.021 2.00e-02 2.50e+03
        pdb=" O   ILE A 310 "    0.008 2.00e-02 2.50e+03
        pdb=" N   ARG A 311 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1217 not shown)

  Histogram of nonbonded interaction distances:
        2.57 -     3.04: 3716
        3.04 -     3.50: 6788
        3.50 -     3.97: 10310
        3.97 -     4.43: 10865
        4.43 -     4.90: 19040
  Nonbonded interactions: 50719
  Sorted by model distance:
  nonbonded pdb=" O   THR E 364 "
            pdb=" OD1 ASP E 367 "
     model   vdw
     2.574 3.040
  nonbonded pdb=" O   THR C 364 "
            pdb=" OD1 ASP C 367 "
     model   vdw
     2.574 3.040
  nonbonded pdb=" O   THR A 364 "
            pdb=" OD1 ASP A 367 "
     model   vdw
     2.574 3.040
  nonbonded pdb=" O   THR B 364 "
            pdb=" OD1 ASP B 367 "
     model   vdw
     2.574 3.040
  nonbonded pdb=" O   THR D 364 "
            pdb=" OD1 ASP D 367 "
     model   vdw
     2.575 3.040
  ... (remaining 50714 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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:             3.140
  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:                    0.030
  Process input model:                     6.870
  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:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6921
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      :  0.012   0.042   6805  Z= 0.954
  Angle     :  1.519   5.132   9280  Z= 1.240
  Chirality :  0.097   0.270   1085
  Planarity :  0.005   0.019   1220
  Dihedral  : 10.880  48.048   2510
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 1.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  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:  2.33 (0.27), residues: 860
  helix:  1.83 (0.19), residues: 610
  sheet:  None (None), residues: 0
  loop :  1.07 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 477 
 TYR   0.008   0.002   TYR E 429 
 PHE   0.011   0.002   PHE D 456 
 TRP   0.017   0.003   TRP B 327 
 HIS   0.005   0.002   HIS E 459 

Details of bonding type rmsd
  covalent geometry    : bond        0.01233 ( 6805)
  covalent geometry    : angle       1.51883 ( 9280)
  hydrogen bonds       : bond        0.29389 (  410)
  hydrogen bonds       : angle       5.83728 ( 1200)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.238 
Fit side-chains
REVERT: C  412 MET cc_start: 0.7114 (mtp) cc_final: 0.6796 (mmm)
REVERT: D  412 MET cc_start: 0.7158 (mtp) cc_final: 0.6858 (mtp)
REVERT: E  412 MET cc_start: 0.7100 (mtp) cc_final: 0.6823 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1114
  time to fit residues: 11.6251
Evaluate side-chains
  79 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 389 HIS
A 474 GLN
B 389 HIS
B 474 GLN
C 389 HIS
C 474 GLN
D 389 HIS
D 474 GLN
E 389 HIS
E 474 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.107911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.100240 restraints weight = 7920.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.2928 rms_B_bonded: 0.80
r_work: 0.2824 rms_B_bonded: 1.52 restraints_weight: 0.5000
r_work: 0.2699 rms_B_bonded: 2.81 restraints_weight: 0.2500
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.1793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   6805  Z= 0.165
  Angle     :  0.555   4.881   9280  Z= 0.314
  Chirality :  0.043   0.132   1085
  Planarity :  0.005   0.032   1220
  Dihedral  :  3.801  10.580    945
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 1.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  7.36 %
    Favored  : 91.53 %
  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:  2.07 (0.27), residues: 860
  helix:  1.60 (0.19), residues: 620
  sheet:  None (None), residues: 0
  loop :  1.02 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 330 
 TYR   0.010   0.001   TYR E 419 
 PHE   0.008   0.001   PHE A 379 
 TRP   0.010   0.001   TRP C 327 
 HIS   0.002   0.001   HIS A 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 6805)
  covalent geometry    : angle       0.55532 ( 9280)
  hydrogen bonds       : bond        0.07176 (  410)
  hydrogen bonds       : angle       4.15539 ( 1200)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.242 
Fit side-chains
REVERT: A  396 LYS cc_start: 0.8696 (tttt) cc_final: 0.8331 (tptt)
  outliers start: 8
  outliers final: 2
  residues processed: 101
  average time/residue: 0.0747
  time to fit residues: 10.2484
Evaluate side-chains
  91 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 89
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 SER
Chi-restraints excluded: chain B residue  362 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 72 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.101312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.091557 restraints weight = 8188.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.2848 rms_B_bonded: 1.01
r_work: 0.2738 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.2609 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.2609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.2394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026   6805  Z= 0.184
  Angle     :  0.565   5.236   9280  Z= 0.302
  Chirality :  0.043   0.129   1085
  Planarity :  0.004   0.032   1220
  Dihedral  :  3.862  11.434    945
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 1.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  : 10.14 %
    Favored  : 89.44 %
  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:  1.83 (0.27), residues: 860
  helix:  1.50 (0.20), residues: 620
  sheet:  None (None), residues: 0
  loop :  0.71 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 381 
 TYR   0.011   0.001   TYR E 419 
 PHE   0.009   0.002   PHE A 456 
 TRP   0.010   0.001   TRP C 327 
 HIS   0.002   0.001   HIS A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 ( 6805)
  covalent geometry    : angle       0.56451 ( 9280)
  hydrogen bonds       : bond        0.06142 (  410)
  hydrogen bonds       : angle       3.89230 ( 1200)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 101
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A  396 LYS cc_start: 0.8698 (tttt) cc_final: 0.8321 (tptt)
REVERT: E  322 ARG cc_start: 0.8566 (mtt90) cc_final: 0.8340 (mtp85)
  outliers start: 3
  outliers final: 3
  residues processed: 101
  average time/residue: 0.1085
  time to fit residues: 13.6945
Evaluate side-chains
  102 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 99
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 SER
Chi-restraints excluded: chain B residue  362 SER
Chi-restraints excluded: chain E residue  388 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 68 optimal weight:    0.9980
   chunk 18 optimal weight:    0.3980
   chunk 20 optimal weight:    0.0980
   chunk 44 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 3 optimal weight:    0.0270
   chunk 63 optimal weight:    0.9980
   chunk 61 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 81 optimal weight:    1.9990
   overall best weight:    0.3838

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

Flipped N/Q/H residues before XYZ refinement:
** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.107904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.098169 restraints weight = 8090.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.2907 rms_B_bonded: 0.99
r_work: 0.2802 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.2675 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.2776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6805  Z= 0.101
  Angle     :  0.450   4.902   9280  Z= 0.236
  Chirality :  0.039   0.128   1085
  Planarity :  0.004   0.031   1220
  Dihedral  :  3.603  11.664    945
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 1.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  9.31 %
    Favored  : 90.14 %
  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:  2.33 (0.28), residues: 860
  helix:  1.86 (0.20), residues: 615
  sheet:  None (None), residues: 0
  loop :  0.92 (0.41), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 472 
 TYR   0.007   0.001   TYR D 419 
 PHE   0.004   0.001   PHE C 379 
 TRP   0.009   0.001   TRP A 327 
 HIS   0.001   0.000   HIS A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 ( 6805)
  covalent geometry    : angle       0.45035 ( 9280)
  hydrogen bonds       : bond        0.03545 (  410)
  hydrogen bonds       : angle       3.58751 ( 1200)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 106
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A  396 LYS cc_start: 0.8688 (tttt) cc_final: 0.8288 (tptt)
REVERT: E  319 ARG cc_start: 0.8457 (tpp-160) cc_final: 0.8089 (tpp-160)
  outliers start: 4
  outliers final: 3
  residues processed: 106
  average time/residue: 0.0971
  time to fit residues: 13.0396
Evaluate side-chains
  104 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 101
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  388 MET
Chi-restraints excluded: chain A residue  415 SER
Chi-restraints excluded: chain E residue  388 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 42 optimal weight:    6.9990
   chunk 77 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 39 optimal weight:    0.2980
   chunk 11 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.103742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.093954 restraints weight = 8232.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.2859 rms_B_bonded: 1.02
r_work: 0.2753 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.2625 rms_B_bonded: 3.06 restraints_weight: 0.2500
r_work (final): 0.2625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8436
moved from start:          0.2779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   6805  Z= 0.130
  Angle     :  0.478   4.995   9280  Z= 0.248
  Chirality :  0.040   0.126   1085
  Planarity :  0.004   0.029   1220
  Dihedral  :  3.562  11.349    945
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 1.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 10.28 %
    Favored  : 89.17 %
  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:  2.25 (0.28), residues: 860
  helix:  1.81 (0.20), residues: 620
  sheet:  None (None), residues: 0
  loop :  0.85 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 381 
 TYR   0.008   0.001   TYR E 419 
 PHE   0.006   0.001   PHE A 456 
 TRP   0.008   0.001   TRP A 327 
 HIS   0.002   0.000   HIS A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 6805)
  covalent geometry    : angle       0.47786 ( 9280)
  hydrogen bonds       : bond        0.04421 (  410)
  hydrogen bonds       : angle       3.55228 ( 1200)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 99
  time to evaluate  : 0.153 
Fit side-chains
REVERT: A  396 LYS cc_start: 0.8689 (tttt) cc_final: 0.8269 (tptt)
REVERT: E  319 ARG cc_start: 0.8611 (tpp-160) cc_final: 0.8292 (tpp-160)
  outliers start: 4
  outliers final: 3
  residues processed: 99
  average time/residue: 0.0970
  time to fit residues: 12.3883
Evaluate side-chains
  100 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 SER
Chi-restraints excluded: chain B residue  362 SER
Chi-restraints excluded: chain E residue  388 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 45 optimal weight:    4.9990
   chunk 68 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 76 optimal weight:    5.9990
   chunk 11 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 445 GLN
** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.104175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.094251 restraints weight = 8266.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.2869 rms_B_bonded: 1.04
r_work: 0.2764 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.2637 rms_B_bonded: 3.03 restraints_weight: 0.2500
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.2922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6805  Z= 0.111
  Angle     :  0.457   4.956   9280  Z= 0.236
  Chirality :  0.039   0.126   1085
  Planarity :  0.003   0.028   1220
  Dihedral  :  3.492  10.903    945
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 1.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 10.42 %
    Favored  : 89.03 %
  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:  2.34 (0.28), residues: 860
  helix:  1.90 (0.20), residues: 620
  sheet:  None (None), residues: 0
  loop :  0.82 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 319 
 TYR   0.008   0.001   TYR E 419 
 PHE   0.004   0.001   PHE A 379 
 TRP   0.009   0.001   TRP A 327 
 HIS   0.002   0.000   HIS A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 6805)
  covalent geometry    : angle       0.45695 ( 9280)
  hydrogen bonds       : bond        0.03892 (  410)
  hydrogen bonds       : angle       3.45368 ( 1200)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.205 
Fit side-chains
REVERT: A  396 LYS cc_start: 0.8629 (tttt) cc_final: 0.8180 (tptt)
REVERT: E  319 ARG cc_start: 0.8571 (tpp-160) cc_final: 0.8208 (tpp-160)
  outliers start: 4
  outliers final: 2
  residues processed: 92
  average time/residue: 0.0971
  time to fit residues: 11.7107
Evaluate side-chains
  94 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 92
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 SER
Chi-restraints excluded: chain E residue  388 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 58 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 61 optimal weight:    3.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.103698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.093858 restraints weight = 8245.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.2864 rms_B_bonded: 1.03
r_work: 0.2757 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.2629 rms_B_bonded: 3.06 restraints_weight: 0.2500
r_work (final): 0.2629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          0.2971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   6805  Z= 0.115
  Angle     :  0.460   4.989   9280  Z= 0.237
  Chirality :  0.039   0.126   1085
  Planarity :  0.004   0.026   1220
  Dihedral  :  3.471  10.730    945
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 1.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 10.69 %
    Favored  : 88.75 %
  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:  2.34 (0.28), residues: 860
  helix:  1.91 (0.20), residues: 620
  sheet:  None (None), residues: 0
  loop :  0.78 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 381 
 TYR   0.008   0.001   TYR E 419 
 PHE   0.004   0.001   PHE D 456 
 TRP   0.009   0.001   TRP A 327 
 HIS   0.001   0.000   HIS D 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 6805)
  covalent geometry    : angle       0.45978 ( 9280)
  hydrogen bonds       : bond        0.04006 (  410)
  hydrogen bonds       : angle       3.43709 ( 1200)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 92
  time to evaluate  : 0.204 
Fit side-chains
REVERT: A  396 LYS cc_start: 0.8674 (tttt) cc_final: 0.8215 (tptt)
REVERT: E  319 ARG cc_start: 0.8572 (tpp-160) cc_final: 0.8196 (tpp-160)
  outliers start: 4
  outliers final: 3
  residues processed: 92
  average time/residue: 0.1006
  time to fit residues: 12.0044
Evaluate side-chains
  95 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 92
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 SER
Chi-restraints excluded: chain B residue  362 SER
Chi-restraints excluded: chain E residue  388 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   chunk 17 optimal weight:    0.3980
   chunk 20 optimal weight:    0.7980
   chunk 31 optimal weight:    0.0020
   chunk 75 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   chunk 42 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.8190

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

Flipped N/Q/H residues before XYZ refinement:
** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.104555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.094818 restraints weight = 8212.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 1.02
r_work: 0.2765 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.2638 rms_B_bonded: 2.97 restraints_weight: 0.2500
r_work (final): 0.2638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.3034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   6805  Z= 0.111
  Angle     :  0.455   4.952   9280  Z= 0.234
  Chirality :  0.039   0.126   1085
  Planarity :  0.003   0.025   1220
  Dihedral  :  3.441  10.772    945
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 10.83 %
    Favored  : 88.47 %
  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:  2.37 (0.28), residues: 860
  helix:  1.94 (0.20), residues: 620
  sheet:  None (None), residues: 0
  loop :  0.79 (0.40), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 322 
 TYR   0.008   0.001   TYR E 419 
 PHE   0.004   0.001   PHE D 456 
 TRP   0.009   0.001   TRP A 327 
 HIS   0.001   0.000   HIS D 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 6805)
  covalent geometry    : angle       0.45489 ( 9280)
  hydrogen bonds       : bond        0.03809 (  410)
  hydrogen bonds       : angle       3.40314 ( 1200)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 0.233 
Fit side-chains
REVERT: A  396 LYS cc_start: 0.8668 (tttt) cc_final: 0.8178 (tptt)
REVERT: E  319 ARG cc_start: 0.8514 (tpp-160) cc_final: 0.8175 (tpp-160)
  outliers start: 5
  outliers final: 4
  residues processed: 92
  average time/residue: 0.0921
  time to fit residues: 11.1196
Evaluate side-chains
  96 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 92
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  388 MET
Chi-restraints excluded: chain A residue  415 SER
Chi-restraints excluded: chain B residue  362 SER
Chi-restraints excluded: chain E residue  388 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 72 optimal weight:    0.0270
   chunk 29 optimal weight:    0.6980
   chunk 84 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 71 optimal weight:    0.3980
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.105378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.095615 restraints weight = 8275.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.2889 rms_B_bonded: 1.02
r_work: 0.2783 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.2655 rms_B_bonded: 3.07 restraints_weight: 0.2500
r_work (final): 0.2655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.3145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6805  Z= 0.096
  Angle     :  0.438   4.914   9280  Z= 0.224
  Chirality :  0.039   0.126   1085
  Planarity :  0.003   0.025   1220
  Dihedral  :  3.361  10.728    945
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 1.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 10.69 %
    Favored  : 88.61 %
  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:  2.49 (0.28), residues: 860
  helix:  1.96 (0.21), residues: 625
  sheet:  None (None), residues: 0
  loop :  1.00 (0.41), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 311 
 TYR   0.007   0.001   TYR E 419 
 PHE   0.003   0.001   PHE D 456 
 TRP   0.009   0.001   TRP D 327 
 HIS   0.001   0.000   HIS D 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 6805)
  covalent geometry    : angle       0.43759 ( 9280)
  hydrogen bonds       : bond        0.03292 (  410)
  hydrogen bonds       : angle       3.31257 ( 1200)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 95
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A  396 LYS cc_start: 0.8677 (tttt) cc_final: 0.8220 (tptt)
REVERT: E  319 ARG cc_start: 0.8547 (tpp-160) cc_final: 0.8218 (tpp-160)
  outliers start: 5
  outliers final: 4
  residues processed: 95
  average time/residue: 0.0983
  time to fit residues: 12.1515
Evaluate side-chains
  95 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  388 MET
Chi-restraints excluded: chain A residue  415 SER
Chi-restraints excluded: chain B residue  362 SER
Chi-restraints excluded: chain E residue  388 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 8 optimal weight:    0.1980
   chunk 30 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.103855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.093934 restraints weight = 8307.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.2891 rms_B_bonded: 1.05
r_work: 0.2780 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.2648 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.2648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.3103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   6805  Z= 0.113
  Angle     :  0.456   4.978   9280  Z= 0.233
  Chirality :  0.039   0.125   1085
  Planarity :  0.003   0.025   1220
  Dihedral  :  3.385  10.633    945
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 1.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 10.97 %
    Favored  : 88.47 %
  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:  2.42 (0.28), residues: 860
  helix:  2.00 (0.21), residues: 620
  sheet:  None (None), residues: 0
  loop :  0.73 (0.40), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 472 
 TYR   0.008   0.001   TYR B 419 
 PHE   0.004   0.001   PHE D 456 
 TRP   0.008   0.001   TRP A 327 
 HIS   0.001   0.000   HIS D 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 6805)
  covalent geometry    : angle       0.45563 ( 9280)
  hydrogen bonds       : bond        0.03852 (  410)
  hydrogen bonds       : angle       3.37330 ( 1200)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 90
  time to evaluate  : 0.262 
Fit side-chains
REVERT: A  396 LYS cc_start: 0.8609 (tttt) cc_final: 0.8131 (tptt)
REVERT: E  319 ARG cc_start: 0.8571 (tpp-160) cc_final: 0.8228 (tpp-160)
  outliers start: 4
  outliers final: 4
  residues processed: 91
  average time/residue: 0.0984
  time to fit residues: 11.7472
Evaluate side-chains
  94 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 90
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  388 MET
Chi-restraints excluded: chain A residue  415 SER
Chi-restraints excluded: chain B residue  362 SER
Chi-restraints excluded: chain E residue  388 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 74 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0980
   chunk 63 optimal weight:    0.8980
   chunk 69 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 25 optimal weight:    6.9990
   chunk 26 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.104741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.094908 restraints weight = 8222.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.2884 rms_B_bonded: 1.03
r_work: 0.2772 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.2641 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.2641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.3174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6805  Z= 0.099
  Angle     :  0.441   4.945   9280  Z= 0.226
  Chirality :  0.039   0.125   1085
  Planarity :  0.003   0.026   1220
  Dihedral  :  3.349  10.702    945
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 1.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 10.69 %
    Favored  : 88.61 %
  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:  2.47 (0.28), residues: 860
  helix:  1.97 (0.21), residues: 625
  sheet:  None (None), residues: 0
  loop :  0.90 (0.41), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 319 
 TYR   0.007   0.001   TYR E 419 
 PHE   0.003   0.001   PHE D 456 
 TRP   0.009   0.001   TRP D 327 
 HIS   0.001   0.000   HIS D 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 6805)
  covalent geometry    : angle       0.44149 ( 9280)
  hydrogen bonds       : bond        0.03411 (  410)
  hydrogen bonds       : angle       3.31714 ( 1200)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1418.05 seconds
wall clock time: 24 minutes 55.33 seconds (1495.33 seconds total)