Starting phenix.real_space_refine
on Sat May 10 10:28:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ygr_39260/05_2025/8ygr_39260.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ygr_39260/05_2025/8ygr_39260.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ygr_39260/05_2025/8ygr_39260.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ygr_39260/05_2025/8ygr_39260.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ygr_39260/05_2025/8ygr_39260.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ygr_39260/05_2025/8ygr_39260.cif"
  }
  resolution = 3.84
  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=   0.001 sd=   0.020
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      12      5.16       5
     C    3774      2.51       5
     N     990      2.21       5
     O    1124      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 5900
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2147
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 272, 2147
          Classifications: {'peptide': 272}
          Link IDs: {'PTRANS': 14, 'TRANS': 257}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2078
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 263, 2078
          Classifications: {'peptide': 263}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 249}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1675
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 1675
          Classifications: {'peptide': 210}
          Link IDs: {'PTRANS': 7, 'TRANS': 202}
  Time building chain proxies: 4.42, per 1000 atoms: 0.75
  Number of scatterers: 5900
  At special positions: 0
  Unit cell: (104, 82, 130, 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      12     16.00
     O    1124      8.00
     N     990      7.00
     C    3774      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: 1.43
  Conformation dependent library (CDL) restraints added in 710.5 milliseconds
  

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1378

  Finding SS restraints...
    Secondary structure from input PDB file:
      2 helices and 11 sheets defined
      1.6% alpha, 34.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 359 through 365
      removed outlier: 3.509A  pdb=" N   ARG A 363 " --> pdb=" O   GLN A 360 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   VAL A 365 " --> pdb=" O   PHE A 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 364
    Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34
      removed outlier: 6.921A  pdb=" N   VAL A  33 " --> pdb=" O   ASP C 325 " (cutoff:3.500A)
      removed outlier: 9.062A  pdb=" N   SER C 327 " --> pdb=" O   VAL A  33 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   PHE C 328 " --> pdb=" O   SER C 340 " (cutoff:3.500A)
      removed outlier: 4.994A  pdb=" N   SER C 340 " --> pdb=" O   PHE C 328 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   GLU C 293 " --> pdb=" O   SER C 340 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   PHE C 342 " --> pdb=" O   GLU C 293 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   SER C 295 " --> pdb=" O   PHE C 342 " (cutoff:3.500A)
      removed outlier: 8.384A  pdb=" N   VAL C 344 " --> pdb=" O   SER C 295 " (cutoff:3.500A)
      removed outlier: 11.866A  pdb=" N   LYS C 297 " --> pdb=" O   VAL C 344 " (cutoff:3.500A)
      removed outlier: 5.039A  pdb=" N   TRP C 291 " --> pdb=" O   SER C 284 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   SER C 284 " --> pdb=" O   TRP C 291 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   GLU C 293 " --> pdb=" O   ILE C 282 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ALA C 278 " --> pdb=" O   LYS C 297 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 252 through 273
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 252 through 273
    current: chain 'A' and resid 464 through 475
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 464 through 475
    current: chain 'B' and resid 462 through 470
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 279 through 282
      removed outlier: 4.124A  pdb=" N   GLU A 293 " --> pdb=" O   ILE A 282 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 291
      removed outlier: 4.089A  pdb=" N   SER A 340 " --> pdb=" O   TRP A 291 " (cutoff:3.500A)
      removed outlier: 4.834A  pdb=" N   SER A 340 " --> pdb=" O   PHE A 328 " (cutoff:3.500A)
      removed outlier: 5.578A  pdb=" N   PHE A 328 " --> pdb=" O   SER A 340 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   VAL A 323 " --> pdb=" O   THR B  59 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 299 through 306
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 353 through 357
    current: chain 'A' and resid 401 through 415
      removed outlier: 5.434A  pdb=" N   LEU A 404 " --> pdb=" O   ALA A 431 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   ALA A 431 " --> pdb=" O   LEU A 404 " (cutoff:3.500A)
      removed outlier: 5.304A  pdb=" N   SER A 406 " --> pdb=" O   ARG A 429 " (cutoff:3.500A)
      removed outlier: 5.571A  pdb=" N   ARG A 429 " --> pdb=" O   SER A 406 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   GLY A 408 " --> pdb=" O   ARG A 427 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 420 through 432
    current: chain 'B' and resid 310 through 321
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 350 through 355
    current: chain 'B' and resid 401 through 415
      removed outlier: 5.196A  pdb=" N   ARG B 427 " --> pdb=" O   ALA B 407 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   VAL B 409 " --> pdb=" O   ARG B 425 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   ARG B 425 " --> pdb=" O   VAL B 409 " (cutoff:3.500A)
      removed outlier: 4.938A  pdb=" N   LEU B 411 " --> pdb=" O   SER B 423 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   SER B 423 " --> pdb=" O   LEU B 411 " (cutoff:3.500A)
      removed outlier: 4.872A  pdb=" N   THR B 413 " --> pdb=" O   LEU B 421 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   LEU B 421 " --> pdb=" O   THR B 413 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 384 through 386
    Processing sheet with id=AA7, first strand: chain 'B' and resid 279 through 283
      removed outlier: 3.630A  pdb=" N   GLU B 293 " --> pdb=" O   ILE B 282 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   VAL B 339 " --> pdb=" O   LYS B 290 " (cutoff:3.500A)
      removed outlier: 7.134A  pdb=" N   SER B 292 " --> pdb=" O   VAL B 339 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 385 through 386
    Processing sheet with id=AA9, first strand: chain 'C' and resid 265 through 267
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 265 through 267
    current: chain 'C' and resid 462 through 472
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'C' and resid 299 through 305
      removed outlier: 3.610A  pdb=" N   ALA C 299 " --> pdb=" O   CYS C 318 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   TYR C 303 " --> pdb=" O   ALA C 314 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   LEU C 424 " --> pdb=" O   TYR C 355 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   GLY C 408 " --> pdb=" O   ARG C 427 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   ARG C 429 " --> pdb=" O   SER C 406 " (cutoff:3.500A)
      removed outlier: 5.415A  pdb=" N   SER C 406 " --> pdb=" O   ARG C 429 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   ALA C 431 " --> pdb=" O   LEU C 404 " (cutoff:3.500A)
      removed outlier: 5.456A  pdb=" N   LEU C 404 " --> pdb=" O   ALA C 431 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   VAL C 378 " --> pdb=" O   LEU C 404 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 385 through 386

    98 hydrogen bonds defined for protein.
    246 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: 1.41

  Time building geometry restraints manager: 1.68 seconds

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

  Histogram of bond lengths:
        1.14 -     1.27: 951
        1.27 -     1.41: 1674
        1.41 -     1.54: 3352
        1.54 -     1.67: 59
        1.67 -     1.81: 18
  Bond restraints: 6054
  Sorted by residual:
  bond pdb=" C   THR B 410 "
       pdb=" O   THR B 410 "
    ideal  model  delta    sigma   weight residual
    1.234  1.139  0.095 1.22e-02 6.72e+03 6.01e+01
  bond pdb=" C   VAL B 365 "
       pdb=" O   VAL B 365 "
    ideal  model  delta    sigma   weight residual
    1.238  1.165  0.073 1.18e-02 7.18e+03 3.86e+01
  bond pdb=" CA  VAL A 320 "
       pdb=" CB  VAL A 320 "
    ideal  model  delta    sigma   weight residual
    1.551  1.488  0.062 1.08e-02 8.57e+03 3.34e+01
  bond pdb=" CA  VAL A 474 "
       pdb=" C   VAL A 474 "
    ideal  model  delta    sigma   weight residual
    1.524  1.467  0.058 1.05e-02 9.07e+03 3.01e+01
  bond pdb=" CA  LYS A 438 "
       pdb=" C   LYS A 438 "
    ideal  model  delta    sigma   weight residual
    1.521  1.459  0.062 1.23e-02 6.61e+03 2.52e+01
  ... (remaining 6049 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.72: 7345
        2.72 -     5.45: 758
        5.45 -     8.17: 104
        8.17 -    10.89: 29
       10.89 -    13.61: 5
  Bond angle restraints: 8241
  Sorted by residual:
  angle pdb=" N   GLY B 285 "
        pdb=" CA  GLY B 285 "
        pdb=" C   GLY B 285 "
      ideal   model   delta    sigma   weight residual
     112.77  126.38  -13.61 1.28e+00 6.10e-01 1.13e+02
  angle pdb=" N   TYR A 480 "
        pdb=" CA  TYR A 480 "
        pdb=" C   TYR A 480 "
      ideal   model   delta    sigma   weight residual
     111.07  121.83  -10.76 1.07e+00 8.73e-01 1.01e+02
  angle pdb=" N   ARG C 307 "
        pdb=" CA  ARG C 307 "
        pdb=" C   ARG C 307 "
      ideal   model   delta    sigma   weight residual
     111.14  121.36  -10.22 1.08e+00 8.57e-01 8.95e+01
  angle pdb=" N   SER A 340 "
        pdb=" CA  SER A 340 "
        pdb=" C   SER A 340 "
      ideal   model   delta    sigma   weight residual
     111.69  121.43   -9.74 1.23e+00 6.61e-01 6.27e+01
  angle pdb=" N   ALA B 407 "
        pdb=" CA  ALA B 407 "
        pdb=" C   ALA B 407 "
      ideal   model   delta    sigma   weight residual
     108.19   98.15   10.04 1.29e+00 6.01e-01 6.05e+01
  ... (remaining 8236 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.69: 3271
       17.69 -    35.37: 209
       35.37 -    53.06: 22
       53.06 -    70.75: 7
       70.75 -    88.43: 7
  Dihedral angle restraints: 3516
    sinusoidal: 1356
      harmonic: 2160
  Sorted by residual:
  dihedral pdb=" C   TYR B 462 "
           pdb=" N   TYR B 462 "
           pdb=" CA  TYR B 462 "
           pdb=" CB  TYR B 462 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -111.16  -11.44     0      2.50e+00 1.60e-01 2.10e+01
  dihedral pdb=" C   VAL A  33 "
           pdb=" N   VAL A  33 "
           pdb=" CA  VAL A  33 "
           pdb=" CB  VAL A  33 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -111.29  -10.71     0      2.50e+00 1.60e-01 1.83e+01
  dihedral pdb=" C   VAL B 365 "
           pdb=" N   VAL B 365 "
           pdb=" CA  VAL B 365 "
           pdb=" CB  VAL B 365 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -132.68   10.68     0      2.50e+00 1.60e-01 1.82e+01
  ... (remaining 3513 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.094: 620
       0.094 -    0.188: 202
       0.188 -    0.282: 59
       0.282 -    0.376: 17
       0.376 -    0.470: 3
  Chirality restraints: 901
  Sorted by residual:
  chirality pdb=" CA  PRO B 395 "
            pdb=" N   PRO B 395 "
            pdb=" C   PRO B 395 "
            pdb=" CB  PRO B 395 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.25    0.47 2.00e-01 2.50e+01 5.53e+00
  chirality pdb=" CA  PHE C 362 "
            pdb=" N   PHE C 362 "
            pdb=" C   PHE C 362 "
            pdb=" CB  PHE C 362 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 5.15e+00
  chirality pdb=" CB  VAL B 366 "
            pdb=" CA  VAL B 366 "
            pdb=" CG1 VAL B 366 "
            pdb=" CG2 VAL B 366 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.19   -0.44 2.00e-01 2.50e+01 4.74e+00
  ... (remaining 898 not shown)

  Planarity restraints: 1064
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP B 354 "   -0.016 2.00e-02 2.50e+03   3.25e-02 1.05e+01
        pdb=" CG  ASP B 354 "    0.056 2.00e-02 2.50e+03
        pdb=" OD1 ASP B 354 "   -0.021 2.00e-02 2.50e+03
        pdb=" OD2 ASP B 354 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 389 "    0.044 5.00e-02 4.00e+02   6.73e-02 7.25e+00
        pdb=" N   PRO B 390 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO B 390 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B 390 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 372 "    0.013 2.00e-02 2.50e+03   2.65e-02 7.00e+00
        pdb=" C   ALA B 372 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   ALA B 372 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ALA B 373 "    0.015 2.00e-02 2.50e+03
  ... (remaining 1061 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1742
        2.80 -     3.33: 4938
        3.33 -     3.85: 8513
        3.85 -     4.38: 9431
        4.38 -     4.90: 17460
  Nonbonded interactions: 42084
  Sorted by model distance:
  nonbonded pdb=" O   GLY B 322 "
            pdb=" OG  SER B 349 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" N   THR A  43 "
            pdb=" O   THR A  43 "
     model   vdw
     2.301 2.496
  nonbonded pdb=" N   TYR B 462 "
            pdb=" O   TYR B 462 "
     model   vdw
     2.307 2.496
  nonbonded pdb=" N   ILE A 282 "
            pdb=" O   ILE A 282 "
     model   vdw
     2.346 2.496
  nonbonded pdb=" N   VAL B 409 "
            pdb=" O   VAL B 409 "
     model   vdw
     2.348 2.496
  ... (remaining 42079 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 32 through 476)
  selection = (chain 'B' and (resid 32 through 63 or resid 251 through 476))
}

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 group one per residue
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:             2.310
  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:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.920
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6084
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      :  0.014   0.095   6054  Z= 0.967
  Angle     :  1.778  13.614   8241  Z= 1.199
  Chirality :  0.107   0.470    901
  Planarity :  0.008   0.067   1064
  Dihedral  : 12.367  88.434   2138
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 1.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Cbeta Deviations :  0.44 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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: -2.89 (0.26), residues: 735
  helix: -3.57 (0.88), residues: 15
  sheet: -1.14 (0.26), residues: 337
  loop : -2.63 (0.25), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.004   TRP A 356 
 HIS   0.009   0.003   HIS B 436 
 PHE   0.031   0.004   PHE A 342 
 TYR   0.034   0.003   TYR B 289 
 ARG   0.007   0.001   ARG B 274 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.27865 (   98)
  hydrogen bonds       : angle       9.73326 (  246)
  covalent geometry    : bond        0.01438 ( 6054)
  covalent geometry    : angle       1.77772 ( 8241)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.607 
Fit side-chains
   revert: symmetry clash
REVERT: A  269 ARG cc_start: 0.6365 (mmt90) cc_final: 0.5751 (mmt-90)
REVERT: A  300 ASN cc_start: 0.7276 (p0) cc_final: 0.6942 (t0)
REVERT: A  321 ASN cc_start: 0.6907 (t0) cc_final: 0.6331 (p0)
REVERT: A  326 PHE cc_start: 0.7212 (m-80) cc_final: 0.6484 (m-10)
REVERT: A  391 VAL cc_start: 0.6933 (t) cc_final: 0.6607 (m)
REVERT: A  454 ASN cc_start: 0.6150 (t0) cc_final: 0.5294 (t0)
REVERT: B   49 ASN cc_start: 0.7358 (m110) cc_final: 0.7078 (p0)
REVERT: B  273 ILE cc_start: 0.5006 (pt) cc_final: 0.4641 (mt)
REVERT: B  301 TYR cc_start: 0.6955 (t80) cc_final: 0.6177 (t80)
REVERT: B  350 TYR cc_start: 0.7150 (m-80) cc_final: 0.6549 (m-10)
REVERT: B  427 ARG cc_start: 0.6821 (mtp180) cc_final: 0.5831 (mtp180)
REVERT: C  282 ILE cc_start: 0.7185 (tt) cc_final: 0.6826 (pt)
REVERT: C  306 THR cc_start: 0.7283 (p) cc_final: 0.7077 (m)
REVERT: C  339 VAL cc_start: 0.6739 (t) cc_final: 0.6461 (p)
REVERT: C  348 ASN cc_start: 0.7275 (t0) cc_final: 0.6754 (t0)
REVERT: C  350 TYR cc_start: 0.6946 (m-80) cc_final: 0.6594 (m-80)
REVERT: C  364 ASN cc_start: 0.6450 (m-40) cc_final: 0.6166 (m-40)
REVERT: C  440 THR cc_start: 0.7224 (m) cc_final: 0.6935 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.1558
  time to fit residues: 33.7786
Evaluate side-chains
  131 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    0.6980
   chunk 56 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 37 optimal weight:    0.6980
   chunk 29 optimal weight:    0.3980
   chunk 58 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9990
   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 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 GLN
B 329 ASN
B 386 ASN
C 266 GLN
C 300 ASN
C 414 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.116711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.104499 restraints weight = 10084.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.106727 restraints weight = 6367.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.108321 restraints weight = 4528.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7122
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      :  0.005   0.034   6054  Z= 0.197
  Angle     :  0.664   7.275   8241  Z= 0.356
  Chirality :  0.048   0.180    901
  Planarity :  0.005   0.055   1064
  Dihedral  :  5.491  25.193    818
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 10.65 %
    Favored  : 87.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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 (0.27), residues: 735
  helix: -3.47 (0.92), residues: 15
  sheet: -0.85 (0.26), residues: 363
  loop : -2.28 (0.26), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 356 
 HIS   0.005   0.001   HIS C 315 
 PHE   0.022   0.003   PHE C 437 
 TYR   0.013   0.002   TYR B 462 
 ARG   0.005   0.001   ARG B 425 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04961 (   98)
  hydrogen bonds       : angle       6.19634 (  246)
  covalent geometry    : bond        0.00460 ( 6054)
  covalent geometry    : angle       0.66366 ( 8241)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 0.680 
Fit side-chains
REVERT: A   36 ASN cc_start: 0.8217 (m-40) cc_final: 0.7849 (m110)
REVERT: A   49 ASN cc_start: 0.7849 (p0) cc_final: 0.7517 (p0)
REVERT: A  326 PHE cc_start: 0.7121 (m-80) cc_final: 0.6821 (m-10)
REVERT: A  381 THR cc_start: 0.6382 (p) cc_final: 0.6049 (p)
REVERT: B  284 SER cc_start: 0.7663 (t) cc_final: 0.7350 (p)
REVERT: B  364 ASN cc_start: 0.7661 (p0) cc_final: 0.7391 (p0)
REVERT: B  365 VAL cc_start: 0.8353 (p) cc_final: 0.8143 (t)
REVERT: B  379 MET cc_start: 0.5297 (tmm) cc_final: 0.5073 (tmm)
REVERT: B  413 THR cc_start: 0.8102 (m) cc_final: 0.7859 (t)
REVERT: B  439 LEU cc_start: 0.7417 (tp) cc_final: 0.7204 (tp)
REVERT: B  445 SER cc_start: 0.8410 (t) cc_final: 0.8030 (m)
REVERT: C  312 VAL cc_start: 0.7867 (t) cc_final: 0.7453 (m)
REVERT: C  313 THR cc_start: 0.8187 (m) cc_final: 0.7974 (p)
REVERT: C  328 PHE cc_start: 0.7956 (t80) cc_final: 0.7569 (t80)
REVERT: C  338 VAL cc_start: 0.8090 (t) cc_final: 0.7745 (p)
REVERT: C  348 ASN cc_start: 0.7493 (t0) cc_final: 0.7153 (t0)
  outliers start: 13
  outliers final: 8
  residues processed: 122
  average time/residue: 0.1674
  time to fit residues: 27.2161
Evaluate side-chains
  117 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 109
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  471 ILE
Chi-restraints excluded: chain B residue  300 ASN
Chi-restraints excluded: chain B residue  345 ILE
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  474 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 26 optimal weight:    0.1980
   chunk 28 optimal weight:    0.7980
   chunk 27 optimal weight:    0.3980
   chunk 45 optimal weight:    6.9990
   chunk 61 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
C 266 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.115407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.102998 restraints weight = 10154.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.105297 restraints weight = 6528.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.106815 restraints weight = 4585.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7168
moved from start:          0.3895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6054  Z= 0.177
  Angle     :  0.620   6.736   8241  Z= 0.331
  Chirality :  0.047   0.220    901
  Planarity :  0.004   0.047   1064
  Dihedral  :  5.340  24.023    818
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 12.19 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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 (0.27), residues: 735
  helix: -4.09 (0.87), residues: 15
  sheet: -0.21 (0.30), residues: 288
  loop : -2.14 (0.23), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 356 
 HIS   0.003   0.001   HIS C 315 
 PHE   0.019   0.002   PHE B 328 
 TYR   0.012   0.001   TYR B  45 
 ARG   0.005   0.000   ARG B 425 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04641 (   98)
  hydrogen bonds       : angle       5.80039 (  246)
  covalent geometry    : bond        0.00416 ( 6054)
  covalent geometry    : angle       0.61963 ( 8241)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.704 
Fit side-chains
REVERT: A   36 ASN cc_start: 0.8244 (m-40) cc_final: 0.7932 (m110)
REVERT: A   49 ASN cc_start: 0.7841 (p0) cc_final: 0.7491 (p0)
REVERT: A  281 ILE cc_start: 0.7044 (mp) cc_final: 0.6811 (mm)
REVERT: A  319 SER cc_start: 0.8241 (t) cc_final: 0.7827 (m)
REVERT: A  454 ASN cc_start: 0.6988 (t0) cc_final: 0.6785 (t0)
REVERT: B   64 LEU cc_start: 0.8371 (mt) cc_final: 0.8140 (mt)
REVERT: B  364 ASN cc_start: 0.7512 (p0) cc_final: 0.7255 (p0)
REVERT: B  367 TYR cc_start: 0.7876 (m-80) cc_final: 0.7412 (m-80)
REVERT: B  439 LEU cc_start: 0.7660 (tp) cc_final: 0.7435 (tp)
REVERT: C  312 VAL cc_start: 0.7998 (t) cc_final: 0.7643 (m)
REVERT: C  313 THR cc_start: 0.8244 (m) cc_final: 0.7932 (p)
REVERT: C  328 PHE cc_start: 0.8041 (t80) cc_final: 0.7702 (t80)
REVERT: C  338 VAL cc_start: 0.8099 (t) cc_final: 0.7833 (p)
  outliers start: 17
  outliers final: 13
  residues processed: 128
  average time/residue: 0.2139
  time to fit residues: 36.2285
Evaluate side-chains
  127 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  362 PHE
Chi-restraints excluded: chain A residue  364 ASN
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain B residue   56 ASN
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  396 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 73 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   chunk 56 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 266 GLN
A 436 HIS
** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 266 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.113955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.101666 restraints weight = 10211.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.103928 restraints weight = 6435.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.105547 restraints weight = 4583.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7196
moved from start:          0.4483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   6054  Z= 0.195
  Angle     :  0.621   7.492   8241  Z= 0.329
  Chirality :  0.046   0.171    901
  Planarity :  0.004   0.047   1064
  Dihedral  :  5.514  24.943    818
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 13.58 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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 (0.28), residues: 735
  helix: -3.92 (0.96), residues: 15
  sheet: -0.24 (0.30), residues: 291
  loop : -2.12 (0.25), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 356 
 HIS   0.006   0.002   HIS A 436 
 PHE   0.021   0.002   PHE C 342 
 TYR   0.020   0.002   TYR B 301 
 ARG   0.004   0.001   ARG B 427 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04441 (   98)
  hydrogen bonds       : angle       5.40811 (  246)
  covalent geometry    : bond        0.00466 ( 6054)
  covalent geometry    : angle       0.62069 ( 8241)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 117
  time to evaluate  : 0.666 
Fit side-chains
REVERT: A   36 ASN cc_start: 0.8281 (m-40) cc_final: 0.7908 (m110)
REVERT: A   49 ASN cc_start: 0.7885 (p0) cc_final: 0.7548 (p0)
REVERT: A  304 THR cc_start: 0.8267 (t) cc_final: 0.7876 (m)
REVERT: A  346 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7604 (mtpp)
REVERT: A  454 ASN cc_start: 0.7146 (t0) cc_final: 0.6934 (t0)
REVERT: A  487 SER cc_start: 0.8155 (t) cc_final: 0.7830 (m)
REVERT: B   43 THR cc_start: 0.8582 (m) cc_final: 0.8346 (p)
REVERT: B   64 LEU cc_start: 0.8395 (mt) cc_final: 0.8190 (mt)
REVERT: B  260 SER cc_start: 0.8332 (OUTLIER) cc_final: 0.8131 (m)
REVERT: B  364 ASN cc_start: 0.7574 (p0) cc_final: 0.7272 (p0)
REVERT: C  312 VAL cc_start: 0.8013 (t) cc_final: 0.7651 (m)
REVERT: C  313 THR cc_start: 0.8155 (m) cc_final: 0.7928 (p)
REVERT: C  328 PHE cc_start: 0.8143 (t80) cc_final: 0.7874 (t80)
REVERT: C  338 VAL cc_start: 0.8109 (t) cc_final: 0.7882 (p)
  outliers start: 29
  outliers final: 23
  residues processed: 132
  average time/residue: 0.1488
  time to fit residues: 26.8623
Evaluate side-chains
  135 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  346 LYS
Chi-restraints excluded: chain A residue  362 PHE
Chi-restraints excluded: chain A residue  364 ASN
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain B residue   56 ASN
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  260 SER
Chi-restraints excluded: chain B residue  300 ASN
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  413 THR
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  472 SER
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain C residue  306 THR
Chi-restraints excluded: chain C residue  396 VAL
Chi-restraints excluded: chain C residue  432 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 15 optimal weight:    0.6980
   chunk 48 optimal weight:    0.0980
   chunk 68 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 54 optimal weight:    0.7980
   chunk 70 optimal weight:    0.1980
   chunk 65 optimal weight:    0.9990
   chunk 41 optimal weight:    0.4980
   chunk 55 optimal weight:    0.8980
   chunk 46 optimal weight:    0.5980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
A 302 GLN
** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 266 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.114183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.101768 restraints weight = 10133.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.104097 restraints weight = 6486.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.105618 restraints weight = 4601.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7177
moved from start:          0.4665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6054  Z= 0.127
  Angle     :  0.551   7.803   8241  Z= 0.290
  Chirality :  0.044   0.156    901
  Planarity :  0.004   0.045   1064
  Dihedral  :  5.059  21.927    818
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 15.43 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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: -1.78 (0.29), residues: 735
  helix: -3.86 (0.97), residues: 15
  sheet: -0.10 (0.30), residues: 306
  loop : -2.01 (0.25), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 356 
 HIS   0.002   0.001   HIS A 436 
 PHE   0.017   0.002   PHE B 328 
 TYR   0.016   0.001   TYR B 301 
 ARG   0.006   0.000   ARG B 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03814 (   98)
  hydrogen bonds       : angle       5.22510 (  246)
  covalent geometry    : bond        0.00298 ( 6054)
  covalent geometry    : angle       0.55093 ( 8241)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 108
  time to evaluate  : 0.672 
Fit side-chains
REVERT: A  281 ILE cc_start: 0.7040 (mp) cc_final: 0.6800 (mm)
REVERT: A  369 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7164 (mtp85)
REVERT: A  386 ASN cc_start: 0.7183 (OUTLIER) cc_final: 0.6750 (p0)
REVERT: A  454 ASN cc_start: 0.7087 (t0) cc_final: 0.6835 (t0)
REVERT: A  487 SER cc_start: 0.8174 (t) cc_final: 0.7795 (m)
REVERT: B   43 THR cc_start: 0.8580 (m) cc_final: 0.8348 (p)
REVERT: B  260 SER cc_start: 0.8301 (OUTLIER) cc_final: 0.8056 (m)
REVERT: B  364 ASN cc_start: 0.7442 (p0) cc_final: 0.7144 (p0)
REVERT: B  439 LEU cc_start: 0.7593 (tp) cc_final: 0.7379 (tp)
REVERT: C  312 VAL cc_start: 0.8054 (t) cc_final: 0.7670 (m)
REVERT: C  328 PHE cc_start: 0.7930 (t80) cc_final: 0.7681 (t80)
REVERT: C  344 VAL cc_start: 0.8493 (t) cc_final: 0.8276 (p)
  outliers start: 25
  outliers final: 17
  residues processed: 123
  average time/residue: 0.1521
  time to fit residues: 25.6635
Evaluate side-chains
  127 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  362 PHE
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  369 ARG
Chi-restraints excluded: chain A residue  386 ASN
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain B residue   56 ASN
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  260 SER
Chi-restraints excluded: chain B residue  300 ASN
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  413 THR
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain C residue  371 LEU
Chi-restraints excluded: chain C residue  396 VAL
Chi-restraints excluded: chain C residue  432 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    0.0020
   chunk 59 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 26 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 61 optimal weight:    0.3980
   chunk 21 optimal weight:    0.0050
   overall best weight:    0.4202

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

Flipped N/Q/H residues before XYZ refinement:
A 302 GLN
** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 360 GLN
C 266 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.113998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.101773 restraints weight = 10050.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.103993 restraints weight = 6338.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.105672 restraints weight = 4541.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7177
moved from start:          0.4868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6054  Z= 0.129
  Angle     :  0.551   6.976   8241  Z= 0.290
  Chirality :  0.044   0.156    901
  Planarity :  0.004   0.044   1064
  Dihedral  :  4.971  21.411    818
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 14.51 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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: -1.75 (0.28), residues: 735
  helix: -3.75 (1.05), residues: 15
  sheet: -0.06 (0.31), residues: 292
  loop : -1.95 (0.25), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 356 
 HIS   0.002   0.001   HIS C 436 
 PHE   0.019   0.002   PHE B 328 
 TYR   0.014   0.001   TYR B 301 
 ARG   0.006   0.000   ARG B 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03751 (   98)
  hydrogen bonds       : angle       5.10648 (  246)
  covalent geometry    : bond        0.00304 ( 6054)
  covalent geometry    : angle       0.55095 ( 8241)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 114
  time to evaluate  : 0.674 
Fit side-chains
REVERT: A   40 PHE cc_start: 0.8158 (m-10) cc_final: 0.7852 (m-10)
REVERT: A  280 THR cc_start: 0.7387 (m) cc_final: 0.7088 (t)
REVERT: A  386 ASN cc_start: 0.6983 (OUTLIER) cc_final: 0.6754 (p0)
REVERT: A  454 ASN cc_start: 0.7053 (t0) cc_final: 0.6778 (t0)
REVERT: A  487 SER cc_start: 0.8147 (t) cc_final: 0.7850 (m)
REVERT: B  260 SER cc_start: 0.8297 (OUTLIER) cc_final: 0.8083 (m)
REVERT: B  364 ASN cc_start: 0.7447 (p0) cc_final: 0.7099 (p0)
REVERT: B  439 LEU cc_start: 0.7602 (tp) cc_final: 0.7401 (tp)
REVERT: B  472 SER cc_start: 0.8252 (p) cc_final: 0.7975 (p)
REVERT: C  312 VAL cc_start: 0.8042 (t) cc_final: 0.7623 (m)
REVERT: C  328 PHE cc_start: 0.7919 (t80) cc_final: 0.7654 (t80)
REVERT: C  344 VAL cc_start: 0.8493 (t) cc_final: 0.8248 (p)
REVERT: C  346 LYS cc_start: 0.8255 (mtpt) cc_final: 0.8009 (mtmt)
REVERT: C  348 ASN cc_start: 0.7246 (t0) cc_final: 0.6893 (p0)
REVERT: C  349 SER cc_start: 0.7915 (t) cc_final: 0.7606 (p)
  outliers start: 34
  outliers final: 26
  residues processed: 133
  average time/residue: 0.1461
  time to fit residues: 26.8050
Evaluate side-chains
  135 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  362 PHE
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  386 ASN
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  469 SER
Chi-restraints excluded: chain B residue   56 ASN
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  260 SER
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain B residue  300 ASN
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  413 THR
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  445 SER
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain C residue  371 LEU
Chi-restraints excluded: chain C residue  396 VAL
Chi-restraints excluded: chain C residue  402 VAL
Chi-restraints excluded: chain C residue  432 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 73 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0000
   chunk 69 optimal weight:    0.9980
   chunk 43 optimal weight:    0.7980
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.6384

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

Flipped N/Q/H residues before XYZ refinement:
A 302 GLN
** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 266 GLN
C 300 ASN
C 302 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.112152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.099863 restraints weight = 10130.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.102144 restraints weight = 6411.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.103724 restraints weight = 4551.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7205
moved from start:          0.5087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6054  Z= 0.176
  Angle     :  0.602   7.239   8241  Z= 0.317
  Chirality :  0.045   0.161    901
  Planarity :  0.004   0.042   1064
  Dihedral  :  5.283  23.371    818
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 15.59 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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: -1.82 (0.29), residues: 735
  helix: -3.85 (0.97), residues: 15
  sheet: -0.06 (0.32), residues: 286
  loop : -2.01 (0.25), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 356 
 HIS   0.003   0.001   HIS C 436 
 PHE   0.021   0.002   PHE C 342 
 TYR   0.015   0.001   TYR A 301 
 ARG   0.006   0.000   ARG B 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04114 (   98)
  hydrogen bonds       : angle       5.15798 (  246)
  covalent geometry    : bond        0.00424 ( 6054)
  covalent geometry    : angle       0.60187 ( 8241)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 110
  time to evaluate  : 0.743 
Fit side-chains
REVERT: A  369 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.7196 (mtp85)
REVERT: A  386 ASN cc_start: 0.7032 (OUTLIER) cc_final: 0.6646 (p0)
REVERT: A  454 ASN cc_start: 0.6985 (t0) cc_final: 0.6690 (t0)
REVERT: A  487 SER cc_start: 0.8213 (t) cc_final: 0.7860 (m)
REVERT: B  364 ASN cc_start: 0.7547 (p0) cc_final: 0.7194 (p0)
REVERT: B  439 LEU cc_start: 0.7620 (tp) cc_final: 0.7407 (tp)
REVERT: B  472 SER cc_start: 0.8207 (p) cc_final: 0.7937 (p)
REVERT: C  312 VAL cc_start: 0.8005 (t) cc_final: 0.7637 (m)
REVERT: C  348 ASN cc_start: 0.7276 (t0) cc_final: 0.6986 (p0)
REVERT: C  349 SER cc_start: 0.7968 (t) cc_final: 0.7667 (p)
REVERT: C  412 SER cc_start: 0.7871 (t) cc_final: 0.7540 (p)
  outliers start: 34
  outliers final: 27
  residues processed: 131
  average time/residue: 0.1634
  time to fit residues: 28.8615
Evaluate side-chains
  136 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 107
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  353 ILE
Chi-restraints excluded: chain A residue  362 PHE
Chi-restraints excluded: chain A residue  364 ASN
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  369 ARG
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  386 ASN
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  469 SER
Chi-restraints excluded: chain B residue   56 ASN
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain B residue  300 ASN
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  413 THR
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  445 SER
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain C residue  371 LEU
Chi-restraints excluded: chain C residue  396 VAL
Chi-restraints excluded: chain C residue  402 VAL
Chi-restraints excluded: chain C residue  432 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 47 optimal weight:    0.2980
   chunk 16 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    0.3980
   chunk 67 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 302 GLN
** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 266 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.111842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.099747 restraints weight = 9896.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.101989 restraints weight = 6290.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.103595 restraints weight = 4469.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7209
moved from start:          0.5260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6054  Z= 0.175
  Angle     :  0.595   7.122   8241  Z= 0.312
  Chirality :  0.045   0.158    901
  Planarity :  0.004   0.043   1064
  Dihedral  :  5.298  23.058    818
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 16.51 %
    Favored  : 78.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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: -1.85 (0.29), residues: 735
  helix: -3.87 (0.95), residues: 15
  sheet: -0.11 (0.31), residues: 300
  loop : -2.07 (0.25), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 356 
 HIS   0.003   0.001   HIS C 436 
 PHE   0.019   0.002   PHE C 342 
 TYR   0.015   0.001   TYR A 301 
 ARG   0.006   0.000   ARG B 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04037 (   98)
  hydrogen bonds       : angle       5.11422 (  246)
  covalent geometry    : bond        0.00419 ( 6054)
  covalent geometry    : angle       0.59514 ( 8241)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 103
  time to evaluate  : 0.701 
Fit side-chains
REVERT: A  281 ILE cc_start: 0.7031 (mp) cc_final: 0.6824 (mm)
REVERT: A  304 THR cc_start: 0.8252 (t) cc_final: 0.7867 (m)
REVERT: A  386 ASN cc_start: 0.7002 (OUTLIER) cc_final: 0.6659 (p0)
REVERT: A  454 ASN cc_start: 0.6874 (t0) cc_final: 0.6609 (t0)
REVERT: A  487 SER cc_start: 0.8306 (t) cc_final: 0.7954 (m)
REVERT: B  260 SER cc_start: 0.8473 (m) cc_final: 0.8256 (m)
REVERT: B  364 ASN cc_start: 0.7504 (p0) cc_final: 0.7151 (p0)
REVERT: B  439 LEU cc_start: 0.7628 (tp) cc_final: 0.7391 (tp)
REVERT: B  472 SER cc_start: 0.8163 (p) cc_final: 0.7907 (p)
REVERT: C  312 VAL cc_start: 0.8026 (t) cc_final: 0.7641 (m)
REVERT: C  344 VAL cc_start: 0.8481 (t) cc_final: 0.8208 (p)
REVERT: C  348 ASN cc_start: 0.7287 (t0) cc_final: 0.7053 (p0)
REVERT: C  349 SER cc_start: 0.7949 (t) cc_final: 0.7692 (p)
REVERT: C  412 SER cc_start: 0.7871 (t) cc_final: 0.7592 (p)
  outliers start: 34
  outliers final: 28
  residues processed: 124
  average time/residue: 0.1487
  time to fit residues: 25.2812
Evaluate side-chains
  131 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 102
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  353 ILE
Chi-restraints excluded: chain A residue  362 PHE
Chi-restraints excluded: chain A residue  364 ASN
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  386 ASN
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  469 SER
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain B residue  300 ASN
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  413 THR
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  445 SER
Chi-restraints excluded: chain B residue  463 GLU
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain C residue  371 LEU
Chi-restraints excluded: chain C residue  396 VAL
Chi-restraints excluded: chain C residue  402 VAL
Chi-restraints excluded: chain C residue  432 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9990
   chunk 56 optimal weight:    0.5980
   chunk 46 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   chunk 67 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 34 optimal weight:    0.3980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 302 GLN
** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 266 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.112425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.100585 restraints weight = 10147.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.102780 restraints weight = 6452.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.104227 restraints weight = 4583.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.5363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6054  Z= 0.170
  Angle     :  0.597   8.137   8241  Z= 0.312
  Chirality :  0.044   0.159    901
  Planarity :  0.004   0.043   1064
  Dihedral  :  5.284  23.243    818
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 16.82 %
    Favored  : 78.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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: -1.84 (0.30), residues: 735
  helix: -4.02 (0.87), residues: 15
  sheet: -0.18 (0.31), residues: 319
  loop : -2.06 (0.26), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 356 
 HIS   0.003   0.001   HIS C 436 
 PHE   0.019   0.002   PHE C 342 
 TYR   0.014   0.001   TYR A 301 
 ARG   0.004   0.000   ARG A 369 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04006 (   98)
  hydrogen bonds       : angle       5.14288 (  246)
  covalent geometry    : bond        0.00409 ( 6054)
  covalent geometry    : angle       0.59655 ( 8241)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 105
  time to evaluate  : 0.630 
Fit side-chains
REVERT: A  281 ILE cc_start: 0.7043 (mp) cc_final: 0.6816 (mm)
REVERT: A  304 THR cc_start: 0.8226 (t) cc_final: 0.7839 (m)
REVERT: A  386 ASN cc_start: 0.7024 (OUTLIER) cc_final: 0.6636 (p0)
REVERT: A  454 ASN cc_start: 0.6876 (t0) cc_final: 0.6578 (t0)
REVERT: A  487 SER cc_start: 0.8221 (t) cc_final: 0.7905 (m)
REVERT: B  260 SER cc_start: 0.8472 (m) cc_final: 0.8258 (m)
REVERT: B  364 ASN cc_start: 0.7520 (p0) cc_final: 0.7167 (p0)
REVERT: B  439 LEU cc_start: 0.7619 (tp) cc_final: 0.7395 (tp)
REVERT: B  472 SER cc_start: 0.8142 (p) cc_final: 0.7885 (p)
REVERT: C  312 VAL cc_start: 0.7994 (t) cc_final: 0.7624 (m)
REVERT: C  348 ASN cc_start: 0.7311 (t0) cc_final: 0.7027 (p0)
REVERT: C  349 SER cc_start: 0.7962 (t) cc_final: 0.7675 (p)
REVERT: C  412 SER cc_start: 0.7858 (t) cc_final: 0.7589 (p)
  outliers start: 33
  outliers final: 29
  residues processed: 125
  average time/residue: 0.1587
  time to fit residues: 27.1925
Evaluate side-chains
  135 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 105
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  353 ILE
Chi-restraints excluded: chain A residue  362 PHE
Chi-restraints excluded: chain A residue  364 ASN
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  386 ASN
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  469 SER
Chi-restraints excluded: chain B residue   56 ASN
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain B residue  300 ASN
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  356 TRP
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  413 THR
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  445 SER
Chi-restraints excluded: chain B residue  463 GLU
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain C residue  371 LEU
Chi-restraints excluded: chain C residue  396 VAL
Chi-restraints excluded: chain C residue  402 VAL
Chi-restraints excluded: chain C residue  432 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 50 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    0.3980
   chunk 41 optimal weight:    0.1980
   chunk 44 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   chunk 58 optimal weight:    0.3980
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 302 GLN
A 324 ASN
** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 266 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.112251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.100364 restraints weight = 10173.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.102568 restraints weight = 6468.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.104151 restraints weight = 4587.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7202
moved from start:          0.5401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6054  Z= 0.144
  Angle     :  0.586   9.008   8241  Z= 0.302
  Chirality :  0.044   0.154    901
  Planarity :  0.004   0.043   1064
  Dihedral  :  5.117  22.380    818
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 17.59 %
    Favored  : 77.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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: -1.79 (0.30), residues: 735
  helix: -4.01 (0.88), residues: 15
  sheet: -0.02 (0.29), residues: 338
  loop : -2.25 (0.27), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 356 
 HIS   0.003   0.001   HIS C 436 
 PHE   0.020   0.002   PHE B 328 
 TYR   0.012   0.001   TYR A 301 
 ARG   0.003   0.000   ARG A 269 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03794 (   98)
  hydrogen bonds       : angle       5.08298 (  246)
  covalent geometry    : bond        0.00343 ( 6054)
  covalent geometry    : angle       0.58558 ( 8241)

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 106
  time to evaluate  : 0.614 
Fit side-chains
REVERT: A  281 ILE cc_start: 0.7025 (mp) cc_final: 0.6813 (mm)
REVERT: A  386 ASN cc_start: 0.6901 (OUTLIER) cc_final: 0.6568 (p0)
REVERT: A  454 ASN cc_start: 0.6827 (t0) cc_final: 0.6528 (t0)
REVERT: A  487 SER cc_start: 0.8207 (t) cc_final: 0.7866 (m)
REVERT: B  364 ASN cc_start: 0.7467 (p0) cc_final: 0.7103 (p0)
REVERT: B  439 LEU cc_start: 0.7626 (tp) cc_final: 0.7396 (tp)
REVERT: B  472 SER cc_start: 0.8102 (p) cc_final: 0.7840 (p)
REVERT: C  312 VAL cc_start: 0.8009 (t) cc_final: 0.7647 (m)
REVERT: C  344 VAL cc_start: 0.8475 (t) cc_final: 0.8229 (p)
REVERT: C  348 ASN cc_start: 0.7283 (t0) cc_final: 0.7056 (p0)
REVERT: C  349 SER cc_start: 0.7951 (t) cc_final: 0.7710 (p)
REVERT: C  412 SER cc_start: 0.7880 (t) cc_final: 0.7600 (p)
  outliers start: 32
  outliers final: 28
  residues processed: 125
  average time/residue: 0.1469
  time to fit residues: 25.4946
Evaluate side-chains
  133 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 104
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  353 ILE
Chi-restraints excluded: chain A residue  362 PHE
Chi-restraints excluded: chain A residue  364 ASN
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  369 ARG
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  386 ASN
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  469 SER
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain B residue  300 ASN
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  356 TRP
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  413 THR
Chi-restraints excluded: chain B residue  445 SER
Chi-restraints excluded: chain B residue  463 GLU
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain C residue  371 LEU
Chi-restraints excluded: chain C residue  396 VAL
Chi-restraints excluded: chain C residue  402 VAL
Chi-restraints excluded: chain C residue  432 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 49 optimal weight:    0.6980
   chunk 11 optimal weight:    0.1980
   chunk 53 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 302 GLN
A 324 ASN
** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 266 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.111425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.099381 restraints weight = 10185.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.101549 restraints weight = 6504.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.103068 restraints weight = 4650.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7218
moved from start:          0.5469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6054  Z= 0.171
  Angle     :  0.601   9.432   8241  Z= 0.314
  Chirality :  0.044   0.159    901
  Planarity :  0.004   0.042   1064
  Dihedral  :  5.263  23.346    818
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 17.44 %
    Favored  : 77.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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: -1.79 (0.30), residues: 735
  helix: -4.11 (0.81), residues: 15
  sheet: -0.06 (0.29), residues: 354
  loop : -2.29 (0.28), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 356 
 HIS   0.003   0.001   HIS C 436 
 PHE   0.019   0.002   PHE B 468 
 TYR   0.013   0.001   TYR A 301 
 ARG   0.005   0.000   ARG A 269 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04032 (   98)
  hydrogen bonds       : angle       5.08591 (  246)
  covalent geometry    : bond        0.00411 ( 6054)
  covalent geometry    : angle       0.60052 ( 8241)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2215.19 seconds
wall clock time: 39 minutes 36.01 seconds (2376.01 seconds total)