Starting phenix.real_space_refine
on Tue Mar 11 14:29:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ygr_39260/03_2025/8ygr_39260.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ygr_39260/03_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_39260/03_2025/8ygr_39260.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ygr_39260/03_2025/8ygr_39260.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ygr_39260/03_2025/8ygr_39260.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ygr_39260/03_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-5624/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: 4.55, per 1000 atoms: 0.77
  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: 1.39
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.52
  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: 1.18

  Time building geometry restraints manager: 1.64 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:             1.840
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     17.200
  Find NCS groups from input model:        0.160
  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:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.120
-------------------------------------------------------------------------------
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= 0.929
  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 

*********************** 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  : 0.680 
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: 0.1577
  time to fit residues: 34.3821
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  : 0.627 
-------------------------------------------------------------------------------
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 = 39)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.104510 restraints weight = 10084.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.106728 restraints weight = 6348.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.108343 restraints weight = 4525.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7121
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= 0.300
  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 

*********************** 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  : 0.665 
Fit side-chains
REVERT: A   36 ASN cc_start: 0.8218 (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: 0.7120 (m-80) cc_final: 0.6820 (m-10)
REVERT: A  381 THR cc_start: 0.6385 (p) cc_final: 0.6052 (p)
REVERT: B  284 SER cc_start: 0.7663 (t) cc_final: 0.7349 (p)
REVERT: B  364 ASN cc_start: 0.7661 (p0) cc_final: 0.7392 (p0)
REVERT: B  365 VAL cc_start: 0.8353 (p) cc_final: 0.8143 (t)
REVERT: B  379 MET cc_start: 0.5298 (tmm) cc_final: 0.5072 (tmm)
REVERT: B  413 THR cc_start: 0.8101 (m) cc_final: 0.7858 (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: 0.7868 (t) cc_final: 0.7454 (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: 0.7494 (t0) cc_final: 0.7154 (t0)
  outliers start: 13
  outliers final: 8
  residues processed: 122
  average time/residue: 0.1634
  time to fit residues: 26.6017
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  : 0.641 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 28 optimal weight:    0.7980
   chunk 27 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0170
   chunk 61 optimal weight:    0.7980
   chunk 62 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.5818

-------------------------------------------------------------------------------
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 = 0.3400 r_free = 0.3400 target = 0.115635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.103221 restraints weight = 10160.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.105552 restraints weight = 6529.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.107061 restraints weight = 4597.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7160
moved from start:          0.3774

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= 0.259
  Angle     :  0.609   6.766   8241  Z= 0.326
  Chirality :  0.047   0.219    901
  Planarity :  0.004   0.046   1064
  Dihedral  :  5.275  23.818    818
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 12.35 %
    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: -4.10 (0.87), residues: 15
  sheet: -0.23 (0.30), residues: 289
  loop : -2.13 (0.23), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 356 
 HIS   0.003   0.001   HIS C 315 
 PHE   0.018   0.002   PHE B 328 
 TYR   0.012   0.001   TYR B  45 
 ARG   0.005   0.000   ARG B 425 

*********************** 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
  135 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 119
  time to evaluate  : 0.640 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 ASN cc_start: 0.8240 (m-40) cc_final: 0.7929 (m110)
REVERT: A   49 ASN cc_start: 0.7840 (p0) cc_final: 0.7493 (p0)
REVERT: A  281 ILE cc_start: 0.7053 (mp) cc_final: 0.6804 (mm)
REVERT: A  301 TYR cc_start: 0.7496 (t80) cc_final: 0.7231 (t80)
REVERT: A  319 SER cc_start: 0.8237 (t) cc_final: 0.7807 (m)
REVERT: B   64 LEU cc_start: 0.8378 (mt) cc_final: 0.8147 (mt)
REVERT: B  364 ASN cc_start: 0.7533 (p0) cc_final: 0.7273 (p0)
REVERT: B  367 TYR cc_start: 0.7864 (m-80) cc_final: 0.7385 (m-80)
REVERT: B  439 LEU cc_start: 0.7614 (tp) cc_final: 0.7372 (tp)
REVERT: C  312 VAL cc_start: 0.8005 (t) cc_final: 0.7629 (m)
REVERT: C  313 THR cc_start: 0.8240 (m) cc_final: 0.7936 (p)
REVERT: C  328 PHE cc_start: 0.8021 (t80) cc_final: 0.7684 (t80)
REVERT: C  338 VAL cc_start: 0.8051 (t) cc_final: 0.7776 (p)
  outliers start: 16
  outliers final: 13
  residues processed: 128
  average time/residue: 0.1767
  time to fit residues: 29.5904
Evaluate side-chains
  131 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 41 optimal weight:    0.9990
   chunk 56 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 44 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0370
   chunk 17 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 55 optimal weight:    0.0370
   overall best weight:    0.4536

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.115594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.103223 restraints weight = 10253.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.105391 restraints weight = 6442.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.107218 restraints weight = 4616.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7161
moved from start:          0.4243

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= 0.206
  Angle     :  0.559   6.952   8241  Z= 0.297
  Chirality :  0.045   0.171    901
  Planarity :  0.004   0.044   1064
  Dihedral  :  5.024  22.407    818
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 13.43 %
    Favored  : 83.18 %
  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: -1.80 (0.28), residues: 735
  helix: -3.94 (0.96), residues: 15
  sheet: -0.09 (0.30), residues: 295
  loop : -2.00 (0.24), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 356 
 HIS   0.003   0.001   HIS C 436 
 PHE   0.017   0.002   PHE B 328 
 TYR   0.020   0.001   TYR B 301 
 ARG   0.004   0.000   ARG B 427 

*********************** 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
  138 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 116
  time to evaluate  : 0.652 
Fit side-chains
REVERT: A   36 ASN cc_start: 0.8274 (m-40) cc_final: 0.7957 (m110)
REVERT: A   49 ASN cc_start: 0.7895 (p0) cc_final: 0.7539 (p0)
REVERT: A  281 ILE cc_start: 0.7078 (mp) cc_final: 0.6844 (mm)
REVERT: A  301 TYR cc_start: 0.7542 (t80) cc_final: 0.7229 (t80)
REVERT: B  364 ASN cc_start: 0.7452 (p0) cc_final: 0.7157 (p0)
REVERT: B  439 LEU cc_start: 0.7637 (tp) cc_final: 0.7410 (tp)
REVERT: C  312 VAL cc_start: 0.8043 (t) cc_final: 0.7651 (m)
REVERT: C  427 ARG cc_start: 0.7718 (ttp-170) cc_final: 0.7469 (ttp80)
  outliers start: 22
  outliers final: 18
  residues processed: 127
  average time/residue: 0.1478
  time to fit residues: 25.7094
Evaluate side-chains
  127 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 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  362 PHE
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  300 ASN
Chi-restraints excluded: chain B residue  333 LEU
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  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:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 68 optimal weight:    0.0980
   chunk 9 optimal weight:    0.6980
   chunk 43 optimal weight:    0.0980
   chunk 54 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 65 optimal weight:    0.1980
   chunk 41 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.3380

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

Flipped N/Q/H residues before XYZ refinement:
A 436 HIS
** 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 = 0.3405 r_free = 0.3405 target = 0.115980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.103542 restraints weight = 10126.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.105857 restraints weight = 6381.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.107476 restraints weight = 4523.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7152
moved from start:          0.4469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6054  Z= 0.169
  Angle     :  0.526   6.637   8241  Z= 0.280
  Chirality :  0.044   0.156    901
  Planarity :  0.004   0.042   1064
  Dihedral  :  4.844  20.756    818
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 14.66 %
    Favored  : 81.02 %
  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: -1.62 (0.28), residues: 735
  helix: -3.83 (1.01), residues: 15
  sheet:  0.05 (0.30), residues: 305
  loop : -1.93 (0.25), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 356 
 HIS   0.005   0.001   HIS A 436 
 PHE   0.017   0.002   PHE B 328 
 TYR   0.017   0.001   TYR B 301 
 ARG   0.003   0.000   ARG B 425 

*********************** 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
  139 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 111
  time to evaluate  : 0.638 
Fit side-chains
REVERT: A   40 PHE cc_start: 0.8133 (m-10) cc_final: 0.7829 (m-10)
REVERT: A  281 ILE cc_start: 0.7063 (mp) cc_final: 0.6785 (mm)
REVERT: A  418 PHE cc_start: 0.7597 (m-80) cc_final: 0.7383 (m-80)
REVERT: A  487 SER cc_start: 0.8121 (t) cc_final: 0.7764 (m)
REVERT: B  355 TYR cc_start: 0.7643 (t80) cc_final: 0.7292 (t80)
REVERT: B  364 ASN cc_start: 0.7370 (p0) cc_final: 0.7079 (p0)
REVERT: B  439 LEU cc_start: 0.7600 (tp) cc_final: 0.7373 (tp)
REVERT: C  300 ASN cc_start: 0.7605 (m-40) cc_final: 0.7353 (m110)
REVERT: C  312 VAL cc_start: 0.8045 (t) cc_final: 0.7632 (m)
REVERT: C  344 VAL cc_start: 0.8517 (t) cc_final: 0.8291 (p)
REVERT: C  427 ARG cc_start: 0.7720 (ttp-170) cc_final: 0.7453 (ttp80)
  outliers start: 28
  outliers final: 18
  residues processed: 125
  average time/residue: 0.1484
  time to fit residues: 25.2663
Evaluate side-chains
  127 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
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  300 ASN
Chi-restraints excluded: chain A residue  362 PHE
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain B residue   56 ASN
Chi-restraints excluded: chain B residue  254 ILE
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  432 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 59 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 26 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 21 optimal weight:    0.4980
   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 266 GLN
** 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 = 0.3365 r_free = 0.3365 target = 0.112970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.100658 restraints weight = 10084.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.102968 restraints weight = 6387.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.104588 restraints weight = 4530.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7202
moved from start:          0.4796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6054  Z= 0.285
  Angle     :  0.601   7.182   8241  Z= 0.319
  Chirality :  0.046   0.166    901
  Planarity :  0.004   0.042   1064
  Dihedral  :  5.291  23.195    818
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 15.12 %
    Favored  : 80.40 %
  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 (0.28), residues: 735
  helix: -3.73 (1.05), residues: 15
  sheet: -0.06 (0.31), residues: 295
  loop : -2.00 (0.24), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 356 
 HIS   0.004   0.001   HIS A 436 
 PHE   0.022   0.002   PHE C 342 
 TYR   0.016   0.001   TYR B 301 
 ARG   0.003   0.000   ARG C 307 

*********************** 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
  137 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 108
  time to evaluate  : 0.601 
Fit side-chains
REVERT: A   40 PHE cc_start: 0.8145 (m-10) cc_final: 0.7874 (m-10)
REVERT: A  369 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.7167 (mtp85)
REVERT: A  386 ASN cc_start: 0.6986 (OUTLIER) cc_final: 0.6594 (p0)
REVERT: A  487 SER cc_start: 0.8176 (t) cc_final: 0.7799 (m)
REVERT: B  364 ASN cc_start: 0.7525 (p0) cc_final: 0.7148 (p0)
REVERT: B  439 LEU cc_start: 0.7654 (tp) cc_final: 0.7437 (tp)
REVERT: B  472 SER cc_start: 0.8217 (OUTLIER) cc_final: 0.7962 (p)
REVERT: C  300 ASN cc_start: 0.7662 (m-40) cc_final: 0.7355 (m110)
REVERT: C  312 VAL cc_start: 0.8072 (t) cc_final: 0.7686 (m)
REVERT: C  412 SER cc_start: 0.7774 (t) cc_final: 0.7419 (p)
  outliers start: 29
  outliers final: 23
  residues processed: 125
  average time/residue: 0.1479
  time to fit residues: 25.3221
Evaluate side-chains
  127 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 101
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
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  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  437 PHE
Chi-restraints excluded: chain A residue  447 LEU
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  254 ILE
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain B residue  300 ASN
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  371 LEU
Chi-restraints excluded: chain C residue  396 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:    0.7980
   chunk 55 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0370
   chunk 69 optimal weight:    0.5980
   chunk 43 optimal weight:    2.9990
   chunk 63 optimal weight:    0.3980
   overall best weight:    0.5058

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

Flipped N/Q/H residues before XYZ refinement:
A 302 GLN
** 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 = 0.3373 r_free = 0.3373 target = 0.113554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.101272 restraints weight = 10141.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.103579 restraints weight = 6373.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.105233 restraints weight = 4496.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7184
moved from start:          0.4963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6054  Z= 0.224
  Angle     :  0.572   8.307   8241  Z= 0.300
  Chirality :  0.044   0.161    901
  Planarity :  0.004   0.041   1064
  Dihedral  :  5.034  21.815    818
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 16.67 %
    Favored  : 78.70 %
  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: -1.63 (0.29), residues: 735
  helix: -3.72 (1.05), residues: 15
  sheet:  0.02 (0.31), residues: 305
  loop : -1.92 (0.25), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 356 
 HIS   0.003   0.001   HIS C 436 
 PHE   0.019   0.002   PHE B 328 
 TYR   0.013   0.001   TYR B 301 
 ARG   0.002   0.000   ARG B 427 

*********************** 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
  131 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 101
  time to evaluate  : 0.602 
Fit side-chains
REVERT: A  280 THR cc_start: 0.7402 (m) cc_final: 0.7103 (t)
REVERT: A  369 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7211 (mtp85)
REVERT: A  386 ASN cc_start: 0.6965 (OUTLIER) cc_final: 0.6604 (p0)
REVERT: A  487 SER cc_start: 0.8180 (t) cc_final: 0.7828 (m)
REVERT: B  364 ASN cc_start: 0.7522 (p0) cc_final: 0.7176 (p0)
REVERT: B  439 LEU cc_start: 0.7652 (tp) cc_final: 0.7438 (tp)
REVERT: B  472 SER cc_start: 0.8214 (p) cc_final: 0.7950 (p)
REVERT: C  312 VAL cc_start: 0.8082 (t) cc_final: 0.7679 (m)
REVERT: C  344 VAL cc_start: 0.8525 (t) cc_final: 0.8270 (p)
REVERT: C  348 ASN cc_start: 0.7247 (t0) cc_final: 0.6916 (p0)
REVERT: C  349 SER cc_start: 0.7916 (t) cc_final: 0.7651 (p)
  outliers start: 30
  outliers final: 26
  residues processed: 117
  average time/residue: 0.1465
  time to fit residues: 23.4341
Evaluate side-chains
  127 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 99
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
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  271 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  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  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  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  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:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 46 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 11 optimal weight:    0.1980
   chunk 67 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 302 GLN
** 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 = 0.3382 r_free = 0.3382 target = 0.113580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.101427 restraints weight = 10021.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.103693 restraints weight = 6338.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.105286 restraints weight = 4472.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7213
moved from start:          0.5182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6054  Z= 0.289
  Angle     :  0.613   7.180   8241  Z= 0.321
  Chirality :  0.045   0.163    901
  Planarity :  0.004   0.042   1064
  Dihedral  :  5.362  23.798    818
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 16.05 %
    Favored  : 79.01 %
  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 (0.29), residues: 735
  helix: -3.84 (0.91), residues: 15
  sheet: -0.14 (0.30), residues: 320
  loop : -2.04 (0.26), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 356 
 HIS   0.004   0.001   HIS C 436 
 PHE   0.021   0.002   PHE C 342 
 TYR   0.013   0.001   TYR B 301 
 ARG   0.004   0.000   ARG C 307 

*********************** 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
  134 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 102
  time to evaluate  : 0.640 
Fit side-chains
REVERT: A  304 THR cc_start: 0.8267 (t) cc_final: 0.7938 (m)
REVERT: A  369 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.7197 (mtp85)
REVERT: A  386 ASN cc_start: 0.7012 (OUTLIER) cc_final: 0.6674 (p0)
REVERT: A  487 SER cc_start: 0.8208 (t) cc_final: 0.7858 (m)
REVERT: B  364 ASN cc_start: 0.7569 (p0) cc_final: 0.7178 (p0)
REVERT: B  439 LEU cc_start: 0.7624 (tp) cc_final: 0.7384 (tp)
REVERT: B  472 SER cc_start: 0.8160 (p) cc_final: 0.7895 (p)
REVERT: C  312 VAL cc_start: 0.8059 (t) cc_final: 0.7676 (m)
REVERT: C  348 ASN cc_start: 0.7279 (t0) cc_final: 0.6993 (p0)
REVERT: C  349 SER cc_start: 0.7967 (t) cc_final: 0.7688 (p)
REVERT: C  412 SER cc_start: 0.7848 (t) cc_final: 0.7534 (p)
  outliers start: 32
  outliers final: 28
  residues processed: 120
  average time/residue: 0.1472
  time to fit residues: 24.4030
Evaluate side-chains
  132 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 102
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
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  271 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  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  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  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  327 SER
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:    0.7980
   chunk 69 optimal weight:    0.6980
   chunk 56 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 67 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.6780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.112503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.100624 restraints weight = 10147.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.102643 restraints weight = 6486.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.104311 restraints weight = 4668.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7211
moved from start:          0.5278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   6054  Z= 0.290
  Angle     :  0.607   7.344   8241  Z= 0.319
  Chirality :  0.045   0.160    901
  Planarity :  0.004   0.041   1064
  Dihedral  :  5.373  23.557    818
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 16.67 %
    Favored  : 78.40 %
  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: -1.74 (0.30), residues: 735
  helix: -3.95 (0.79), residues: 15
  sheet: -0.13 (0.29), residues: 357
  loop : -2.14 (0.27), residues: 363

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   0.020   0.002   PHE C 342 
 TYR   0.012   0.001   TYR B 301 
 ARG   0.003   0.000   ARG C 307 

*********************** 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
  143 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 111
  time to evaluate  : 0.596 
Fit side-chains
REVERT: A  280 THR cc_start: 0.7372 (m) cc_final: 0.7034 (t)
REVERT: A  304 THR cc_start: 0.8273 (t) cc_final: 0.7946 (m)
REVERT: A  369 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.7171 (mtp85)
REVERT: A  386 ASN cc_start: 0.6993 (OUTLIER) cc_final: 0.6671 (p0)
REVERT: A  487 SER cc_start: 0.8283 (t) cc_final: 0.7950 (m)
REVERT: B  364 ASN cc_start: 0.7579 (p0) cc_final: 0.7211 (p0)
REVERT: B  439 LEU cc_start: 0.7630 (tp) cc_final: 0.7389 (tp)
REVERT: B  472 SER cc_start: 0.8114 (p) cc_final: 0.7857 (p)
REVERT: C  312 VAL cc_start: 0.8104 (t) cc_final: 0.7713 (m)
REVERT: C  348 ASN cc_start: 0.7259 (t0) cc_final: 0.6989 (p0)
REVERT: C  349 SER cc_start: 0.7943 (t) cc_final: 0.7698 (p)
REVERT: C  412 SER cc_start: 0.7889 (t) cc_final: 0.7604 (p)
  outliers start: 32
  outliers final: 28
  residues processed: 128
  average time/residue: 0.1394
  time to fit residues: 24.6651
Evaluate side-chains
  141 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 111
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
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  271 ILE
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  300 ASN
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  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  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  432 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 27 optimal weight:    0.6980
   chunk 50 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    0.2980
   chunk 41 optimal weight:    0.5980
   chunk 44 optimal weight:    0.3980
   chunk 61 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 71 optimal weight:    0.8980
   overall best weight:    0.5580

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.112381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.100417 restraints weight = 10180.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.102594 restraints weight = 6524.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.104010 restraints weight = 4663.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7206
moved from start:          0.5367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6054  Z= 0.247
  Angle     :  0.590   7.617   8241  Z= 0.311
  Chirality :  0.045   0.164    901
  Planarity :  0.004   0.042   1064
  Dihedral  :  5.215  22.783    818
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 16.82 %
    Favored  : 78.40 %
  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: -1.68 (0.30), residues: 735
  helix: -3.94 (0.81), residues: 15
  sheet: -0.03 (0.29), residues: 364
  loop : -2.23 (0.28), residues: 356

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 A 342 
 TYR   0.012   0.001   TYR B 301 
 ARG   0.002   0.000   ARG C 307 

********************** 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
  131 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 100
  time to evaluate  : 0.586 
Fit side-chains
REVERT: A  304 THR cc_start: 0.8287 (t) cc_final: 0.7955 (m)
REVERT: A  369 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7185 (mtp85)
REVERT: A  386 ASN cc_start: 0.6979 (OUTLIER) cc_final: 0.6621 (p0)
REVERT: A  487 SER cc_start: 0.8192 (t) cc_final: 0.7870 (m)
REVERT: B  364 ASN cc_start: 0.7521 (p0) cc_final: 0.7169 (p0)
REVERT: B  439 LEU cc_start: 0.7605 (tp) cc_final: 0.7359 (tp)
REVERT: B  472 SER cc_start: 0.8098 (p) cc_final: 0.7832 (p)
REVERT: C  312 VAL cc_start: 0.8097 (t) cc_final: 0.7681 (m)
REVERT: C  344 VAL cc_start: 0.8500 (t) cc_final: 0.8230 (p)
REVERT: C  348 ASN cc_start: 0.7257 (t0) cc_final: 0.7024 (p0)
REVERT: C  349 SER cc_start: 0.7945 (t) cc_final: 0.7723 (p)
REVERT: C  412 SER cc_start: 0.7888 (t) cc_final: 0.7632 (p)
  outliers start: 31
  outliers final: 28
  residues processed: 119
  average time/residue: 0.1409
  time to fit residues: 22.9873
Evaluate side-chains
  127 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 97
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
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  271 ILE
Chi-restraints excluded: chain A residue  300 ASN
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  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   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  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 10 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 73 optimal weight:    0.8980
   chunk 5 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 40 optimal weight:    0.5980
   chunk 34 optimal weight:    0.0970
   chunk 30 optimal weight:    0.0270
   chunk 67 optimal weight:    0.6980
   overall best weight:    0.3836

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

Flipped N/Q/H residues before XYZ refinement:
A 302 GLN
C 300 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.113521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.101901 restraints weight = 10157.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.103894 restraints weight = 6672.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.105310 restraints weight = 4821.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7180
moved from start:          0.5403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6054  Z= 0.190
  Angle     :  0.562   7.931   8241  Z= 0.294
  Chirality :  0.044   0.206    901
  Planarity :  0.004   0.041   1064
  Dihedral  :  4.959  21.377    818
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 18.21 %
    Favored  : 77.93 %
  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: -1.64 (0.30), residues: 735
  helix: -3.67 (0.93), residues: 15
  sheet: -0.01 (0.28), residues: 357
  loop : -2.16 (0.28), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 356 
 HIS   0.003   0.001   HIS A 405 
 PHE   0.020   0.002   PHE A 342 
 TYR   0.014   0.001   TYR B 355 
 ARG   0.002   0.000   ARG B 427 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2058.78 seconds
wall clock time: 36 minutes 30.90 seconds (2190.90 seconds total)