Starting phenix.real_space_refine
on Mon Apr 28 01:00:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ozl_17313/04_2025/8ozl_17313.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ozl_17313/04_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_17313/04_2025/8ozl_17313.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ozl_17313/04_2025/8ozl_17313.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ozl_17313/04_2025/8ozl_17313.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ozl_17313/04_2025/8ozl_17313.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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:
    C, B, E, D
  Time building chain proxies: 3.50, per 1000 atoms: 0.52
  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: 1.62
  Conformation dependent library (CDL) restraints added in 991.2 milliseconds
  

  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: 0.76
  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: 1.84

  Time building geometry restraints manager: 1.93 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

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:             4.260
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     18.580
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.450
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  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
 TRP   0.017   0.003   TRP B 327 
 HIS   0.005   0.002   HIS E 459 
 PHE   0.011   0.002   PHE D 456 
 TYR   0.008   0.002   TYR E 429 
 ARG   0.006   0.001   ARG E 477 

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

*********************** 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  : 0.692 
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: 0.2687
  time to fit residues: 27.9104
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  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    0.6980
   chunk 64 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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**
A 389 HIS
A 474 GLN
B 389 HIS
B 474 GLN
C 389 HIS
C 474 GLN
** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3035 r_free = 0.3035 target = 0.107424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.097525 restraints weight = 7854.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.2908 rms_B_bonded: 1.03
r_work: 0.2803 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.2670 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.1899

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= 0.159
  Angle     :  0.547   4.948   9280  Z= 0.308
  Chirality :  0.043   0.131   1085
  Planarity :  0.005   0.031   1220
  Dihedral  :  3.795  10.717    945
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 1.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  7.92 %
    Favored  : 91.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.27), residues: 860
  helix:  1.55 (0.19), residues: 620
  sheet:  None (None), residues: 0
  loop :  1.02 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 327 
 HIS   0.001   0.000   HIS A 309 
 PHE   0.008   0.001   PHE A 379 
 TYR   0.009   0.001   TYR E 419 
 ARG   0.002   0.000   ARG B 330 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06551 (  410)
  hydrogen bonds       : angle       4.10570 ( 1200)
  covalent geometry    : bond        0.00310 ( 6805)
  covalent geometry    : angle       0.54678 ( 9280)

*********************** 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
  102 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 99
  time to evaluate  : 0.703 
Fit side-chains
REVERT: A  396 LYS cc_start: 0.8637 (tttt) cc_final: 0.8183 (tptt)
REVERT: D  354 ILE cc_start: 0.8201 (mt) cc_final: 0.7947 (mm)
  outliers start: 3
  outliers final: 2
  residues processed: 99
  average time/residue: 0.1726
  time to fit residues: 23.1510
Evaluate side-chains
  96 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 94
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
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 50 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 83 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9980
   chunk 41 optimal weight:    0.4980
   chunk 27 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    1.2986

-------------------------------------------------------------------------------
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 = 0.2994 r_free = 0.2994 target = 0.103766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.093525 restraints weight = 8146.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.2854 rms_B_bonded: 1.09
r_work: 0.2737 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2602 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.2313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   6805  Z= 0.158
  Angle     :  0.523   5.073   9280  Z= 0.280
  Chirality :  0.042   0.130   1085
  Planarity :  0.004   0.031   1220
  Dihedral  :  3.771  12.868    945
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 1.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  9.44 %
    Favored  : 89.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.02 (0.28), residues: 860
  helix:  1.58 (0.20), residues: 620
  sheet:  None (None), residues: 0
  loop :  0.97 (0.42), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 327 
 HIS   0.002   0.001   HIS A 383 
 PHE   0.007   0.001   PHE A 456 
 TYR   0.010   0.001   TYR E 419 
 ARG   0.004   0.000   ARG D 381 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05687 (  410)
  hydrogen bonds       : angle       3.82208 ( 1200)
  covalent geometry    : bond        0.00380 ( 6805)
  covalent geometry    : angle       0.52340 ( 9280)

*********************** 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
  112 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 105
  time to evaluate  : 0.706 
Fit side-chains
REVERT: A  396 LYS cc_start: 0.8701 (tttt) cc_final: 0.8295 (tptt)
REVERT: E  319 ARG cc_start: 0.8656 (tpp-160) cc_final: 0.8320 (tpp-160)
  outliers start: 7
  outliers final: 4
  residues processed: 110
  average time/residue: 0.2549
  time to fit residues: 34.9213
Evaluate side-chains
  104 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 100
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 SER
Chi-restraints excluded: chain B residue  362 SER
Chi-restraints excluded: chain C residue  323 GLU
Chi-restraints excluded: chain E residue  323 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 78 optimal weight:    0.7980
   chunk 81 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.2989 r_free = 0.2989 target = 0.103631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.093738 restraints weight = 8194.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.2876 rms_B_bonded: 1.04
r_work: 0.2768 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.2638 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.2638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.2651

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= 0.133
  Angle     :  0.488   4.969   9280  Z= 0.257
  Chirality :  0.041   0.127   1085
  Planarity :  0.004   0.030   1220
  Dihedral  :  3.688  12.728    945
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  9.44 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.17 (0.28), residues: 860
  helix:  1.73 (0.20), residues: 620
  sheet:  None (None), residues: 0
  loop :  0.87 (0.42), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 327 
 HIS   0.002   0.001   HIS E 383 
 PHE   0.005   0.001   PHE A 456 
 TYR   0.008   0.001   TYR E 419 
 ARG   0.004   0.000   ARG D 427 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04665 (  410)
  hydrogen bonds       : angle       3.65737 ( 1200)
  covalent geometry    : bond        0.00314 ( 6805)
  covalent geometry    : angle       0.48774 ( 9280)

*********************** 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
  111 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 103
  time to evaluate  : 0.702 
Fit side-chains
REVERT: A  396 LYS cc_start: 0.8713 (tttt) cc_final: 0.8317 (tptt)
REVERT: E  319 ARG cc_start: 0.8662 (tpp-160) cc_final: 0.8308 (tpp-160)
  outliers start: 8
  outliers final: 5
  residues processed: 105
  average time/residue: 0.2324
  time to fit residues: 30.9060
Evaluate side-chains
  107 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 102
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 SER
Chi-restraints excluded: chain B residue  362 SER
Chi-restraints excluded: chain C residue  323 GLU
Chi-restraints excluded: chain E residue  323 GLU
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 11 optimal weight:    4.9990
   chunk 72 optimal weight:    0.8980
   chunk 42 optimal weight:    6.9990
   chunk 64 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 51 optimal weight:    0.4980
   chunk 28 optimal weight:    0.4980
   chunk 81 optimal weight:    0.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.3007 r_free = 0.3007 target = 0.104946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.095163 restraints weight = 8121.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.2883 rms_B_bonded: 1.01
r_work: 0.2772 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.2642 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.2642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.2863

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= 0.110
  Angle     :  0.456   4.953   9280  Z= 0.237
  Chirality :  0.039   0.127   1085
  Planarity :  0.004   0.029   1220
  Dihedral  :  3.531  12.700    945
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  :  9.31 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.32 (0.28), residues: 860
  helix:  1.87 (0.20), residues: 620
  sheet:  None (None), residues: 0
  loop :  0.85 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 327 
 HIS   0.001   0.000   HIS D 383 
 PHE   0.003   0.001   PHE A 456 
 TYR   0.007   0.001   TYR B 419 
 ARG   0.003   0.000   ARG D 427 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03898 (  410)
  hydrogen bonds       : angle       3.47419 ( 1200)
  covalent geometry    : bond        0.00248 ( 6805)
  covalent geometry    : angle       0.45609 ( 9280)

*********************** 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
  110 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.715 
Fit side-chains
REVERT: A  396 LYS cc_start: 0.8720 (tttt) cc_final: 0.8323 (tptt)
REVERT: E  319 ARG cc_start: 0.8708 (tpp-160) cc_final: 0.8378 (tpp-160)
  outliers start: 9
  outliers final: 4
  residues processed: 103
  average time/residue: 0.2348
  time to fit residues: 30.6033
Evaluate side-chains
  101 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 60 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 81 optimal weight:    0.6980
   chunk 45 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 6 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 72 optimal weight:    0.8980
   chunk 80 optimal weight:    0.7980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3000 r_free = 0.3000 target = 0.104705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.094886 restraints weight = 8156.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.2891 rms_B_bonded: 1.02
r_work: 0.2780 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.2651 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.2651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.2941

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= 0.109
  Angle     :  0.454   4.941   9280  Z= 0.234
  Chirality :  0.039   0.126   1085
  Planarity :  0.003   0.028   1220
  Dihedral  :  3.469  12.334    945
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 1.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  9.17 %
    Favored  : 90.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.38 (0.28), residues: 860
  helix:  1.93 (0.20), residues: 620
  sheet:  None (None), residues: 0
  loop :  0.83 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 327 
 HIS   0.001   0.000   HIS D 383 
 PHE   0.004   0.001   PHE D 456 
 TYR   0.008   0.001   TYR E 419 
 ARG   0.002   0.000   ARG D 427 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03842 (  410)
  hydrogen bonds       : angle       3.41439 ( 1200)
  covalent geometry    : bond        0.00249 ( 6805)
  covalent geometry    : angle       0.45441 ( 9280)

*********************** 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
  103 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 97
  time to evaluate  : 0.705 
Fit side-chains
REVERT: A  396 LYS cc_start: 0.8672 (tttt) cc_final: 0.8265 (tptt)
REVERT: E  319 ARG cc_start: 0.8695 (tpp-160) cc_final: 0.8339 (tpp-160)
  outliers start: 6
  outliers final: 5
  residues processed: 99
  average time/residue: 0.2272
  time to fit residues: 29.0207
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  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 SER
Chi-restraints excluded: chain B residue  362 SER
Chi-restraints excluded: chain C residue  323 GLU
Chi-restraints excluded: chain E residue  323 GLU
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 45 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 43 optimal weight:    0.3980
   chunk 66 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 34 optimal weight:    0.0470
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.8680

-------------------------------------------------------------------------------
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 = 0.2995 r_free = 0.2995 target = 0.104207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.094230 restraints weight = 8138.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.2870 rms_B_bonded: 1.03
r_work: 0.2764 rms_B_bonded: 1.69 restraints_weight: 0.5000
r_work: 0.2637 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.2981

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     :  0.461   4.972   9280  Z= 0.237
  Chirality :  0.039   0.126   1085
  Planarity :  0.003   0.027   1220
  Dihedral  :  3.459  12.355    945
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 1.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  9.72 %
    Favored  : 89.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.36 (0.28), residues: 860
  helix:  1.92 (0.20), residues: 620
  sheet:  None (None), residues: 0
  loop :  0.78 (0.40), residues: 240

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03970 (  410)
  hydrogen bonds       : angle       3.41355 ( 1200)
  covalent geometry    : bond        0.00269 ( 6805)
  covalent geometry    : angle       0.46087 ( 9280)

*********************** 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
  102 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.789 
Fit side-chains
REVERT: A  396 LYS cc_start: 0.8563 (tttt) cc_final: 0.8064 (tptt)
REVERT: E  319 ARG cc_start: 0.8647 (tpp-160) cc_final: 0.8254 (tpp-160)
  outliers start: 7
  outliers final: 6
  residues processed: 97
  average time/residue: 0.2242
  time to fit residues: 28.2685
Evaluate side-chains
  101 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 SER
Chi-restraints excluded: chain B residue  362 SER
Chi-restraints excluded: chain B residue  475 SER
Chi-restraints excluded: chain C residue  323 GLU
Chi-restraints excluded: chain E residue  323 GLU
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 28 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 76 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0870
   chunk 64 optimal weight:    0.8980
   chunk 77 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 27 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.6358

-------------------------------------------------------------------------------
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 = 0.3012 r_free = 0.3012 target = 0.105306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.095376 restraints weight = 8197.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.2922 rms_B_bonded: 1.03
r_work: 0.2814 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.2684 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.3073

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= 0.100
  Angle     :  0.443   4.927   9280  Z= 0.227
  Chirality :  0.039   0.126   1085
  Planarity :  0.003   0.026   1220
  Dihedral  :  3.399  12.443    945
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 1.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  9.86 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.47 (0.28), residues: 860
  helix:  2.00 (0.21), residues: 620
  sheet:  None (None), residues: 0
  loop :  0.83 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 327 
 HIS   0.001   0.000   HIS D 383 
 PHE   0.003   0.001   PHE D 456 
 TYR   0.007   0.001   TYR E 419 
 ARG   0.001   0.000   ARG D 427 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03486 (  410)
  hydrogen bonds       : angle       3.34673 ( 1200)
  covalent geometry    : bond        0.00226 ( 6805)
  covalent geometry    : angle       0.44293 ( 9280)

*********************** 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
  101 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 94
  time to evaluate  : 0.686 
Fit side-chains
REVERT: A  396 LYS cc_start: 0.8598 (tttt) cc_final: 0.8128 (tptt)
REVERT: D  396 LYS cc_start: 0.8635 (tttt) cc_final: 0.8111 (tptt)
REVERT: E  319 ARG cc_start: 0.8606 (tpp-160) cc_final: 0.8292 (tpp-160)
  outliers start: 7
  outliers final: 5
  residues processed: 96
  average time/residue: 0.2117
  time to fit residues: 26.2382
Evaluate side-chains
  98 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 93
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 SER
Chi-restraints excluded: chain B residue  362 SER
Chi-restraints excluded: chain C residue  323 GLU
Chi-restraints excluded: chain E residue  323 GLU
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 5 optimal weight:    0.0020
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 72 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 80 optimal weight:    0.7980
   chunk 26 optimal weight:    0.1980
   chunk 61 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9980
   overall best weight:    0.7990

-------------------------------------------------------------------------------
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 = 0.3000 r_free = 0.3000 target = 0.104467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.094441 restraints weight = 8211.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.2873 rms_B_bonded: 1.04
r_work: 0.2764 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.2636 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.2636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.3078

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= 0.109
  Angle     :  0.452   4.945   9280  Z= 0.232
  Chirality :  0.039   0.125   1085
  Planarity :  0.003   0.026   1220
  Dihedral  :  3.398  12.321    945
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 1.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 10.14 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.45 (0.28), residues: 860
  helix:  2.00 (0.21), residues: 620
  sheet:  None (None), residues: 0
  loop :  0.78 (0.40), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 327 
 HIS   0.001   0.000   HIS D 383 
 PHE   0.004   0.001   PHE D 456 
 TYR   0.008   0.001   TYR E 419 
 ARG   0.001   0.000   ARG D 427 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03764 (  410)
  hydrogen bonds       : angle       3.36019 ( 1200)
  covalent geometry    : bond        0.00254 ( 6805)
  covalent geometry    : angle       0.45227 ( 9280)

*********************** 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
  98 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.770 
Fit side-chains
REVERT: A  396 LYS cc_start: 0.8584 (tttt) cc_final: 0.8102 (tptt)
REVERT: D  396 LYS cc_start: 0.8605 (tttt) cc_final: 0.8066 (tptt)
REVERT: E  319 ARG cc_start: 0.8610 (tpp-160) cc_final: 0.8276 (tpp-160)
  outliers start: 6
  outliers final: 5
  residues processed: 94
  average time/residue: 0.2127
  time to fit residues: 25.9053
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  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 SER
Chi-restraints excluded: chain B residue  362 SER
Chi-restraints excluded: chain C residue  323 GLU
Chi-restraints excluded: chain E residue  323 GLU
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 11 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 68 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 81 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3004 r_free = 0.3004 target = 0.104717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.094685 restraints weight = 8282.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.2875 rms_B_bonded: 1.04
r_work: 0.2768 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.2640 rms_B_bonded: 3.04 restraints_weight: 0.2500
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.3113

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= 0.106
  Angle     :  0.448   4.955   9280  Z= 0.230
  Chirality :  0.039   0.125   1085
  Planarity :  0.003   0.026   1220
  Dihedral  :  3.385  12.370    945
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 1.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 10.14 %
    Favored  : 88.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.47 (0.28), residues: 860
  helix:  2.02 (0.21), residues: 620
  sheet:  None (None), residues: 0
  loop :  0.79 (0.40), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 327 
 HIS   0.001   0.000   HIS D 383 
 PHE   0.004   0.001   PHE D 456 
 TYR   0.008   0.001   TYR E 419 
 ARG   0.001   0.000   ARG D 311 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03638 (  410)
  hydrogen bonds       : angle       3.34510 ( 1200)
  covalent geometry    : bond        0.00246 ( 6805)
  covalent geometry    : angle       0.44848 ( 9280)

********************** 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
  98 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.711 
Fit side-chains
REVERT: A  396 LYS cc_start: 0.8582 (tttt) cc_final: 0.8099 (tptt)
  outliers start: 7
  outliers final: 6
  residues processed: 93
  average time/residue: 0.2152
  time to fit residues: 25.9670
Evaluate side-chains
  97 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 SER
Chi-restraints excluded: chain B residue  362 SER
Chi-restraints excluded: chain B residue  475 SER
Chi-restraints excluded: chain C residue  323 GLU
Chi-restraints excluded: chain E residue  323 GLU
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 62 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0980
   chunk 30 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3008 r_free = 0.3008 target = 0.104996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.094981 restraints weight = 8238.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.2878 rms_B_bonded: 1.04
r_work: 0.2764 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2633 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.2633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.3166

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= 0.101
  Angle     :  0.444   4.943   9280  Z= 0.227
  Chirality :  0.039   0.125   1085
  Planarity :  0.003   0.025   1220
  Dihedral  :  3.356  12.473    945
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 1.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 10.28 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.53 (0.28), residues: 860
  helix:  2.05 (0.21), residues: 620
  sheet:  None (None), residues: 0
  loop :  0.83 (0.40), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 327 
 HIS   0.001   0.000   HIS D 383 
 PHE   0.003   0.001   PHE D 456 
 TYR   0.007   0.001   TYR B 419 
 ARG   0.001   0.000   ARG D 427 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03447 (  410)
  hydrogen bonds       : angle       3.30814 ( 1200)
  covalent geometry    : bond        0.00231 ( 6805)
  covalent geometry    : angle       0.44423 ( 9280)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3013.13 seconds
wall clock time: 52 minutes 34.23 seconds (3154.23 seconds total)