Starting phenix.real_space_refine
on Fri Aug 22 16:38:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ygr_39260/08_2025/8ygr_39260.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ygr_39260/08_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_39260/08_2025/8ygr_39260.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ygr_39260/08_2025/8ygr_39260.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ygr_39260/08_2025/8ygr_39260.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ygr_39260/08_2025/8ygr_39260.cif"
  }
  resolution = 3.84
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.020
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.75, per 1000 atoms: 0.30
  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: 0.48
  Conformation dependent library (CDL) restraints added in 203.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.19
  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: 0.72

  Time building geometry restraints manager: 0.67 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:             4.540
  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:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.230
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.620
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.89 (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
 ARG   0.007   0.001   ARG B 274 
 TYR   0.034   0.003   TYR B 289 
 PHE   0.031   0.004   PHE A 342 
 TRP   0.037   0.004   TRP A 356 
 HIS   0.009   0.003   HIS B 436 

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

*********************** 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  : 0.231 
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  294 ILE cc_start: 0.6567 (mt) cc_final: 0.6365 (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  385 TYR cc_start: 0.7765 (t80) cc_final: 0.7555 (t80)
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: 0.6753 (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: 0.0757
  time to fit residues: 16.6016
Evaluate side-chains
  132 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.2980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0770
   overall best weight:    0.4938

-------------------------------------------------------------------------------
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 = 0.3448 r_free = 0.3448 target = 0.118640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.106876 restraints weight = 10197.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.109006 restraints weight = 6576.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.110416 restraints weight = 4727.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.111475 restraints weight = 3716.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.112263 restraints weight = 3057.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7053
moved from start:          0.2926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6054  Z= 0.162
  Angle     :  0.629   7.239   8241  Z= 0.336
  Chirality :  0.047   0.177    901
  Planarity :  0.005   0.050   1064
  Dihedral  :  5.312  23.305    818
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.29 (0.27), residues: 735
  helix: -3.44 (0.89), residues: 15
  sheet: -0.67 (0.26), residues: 350
  loop : -2.32 (0.25), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 425 
 TYR   0.013   0.001   TYR B 462 
 PHE   0.022   0.002   PHE C 437 
 TRP   0.019   0.002   TRP A 356 
 HIS   0.004   0.001   HIS C 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 6054)
  covalent geometry    : angle       0.62915 ( 8241)
  hydrogen bonds       : bond        0.04290 (   98)
  hydrogen bonds       : angle       6.13117 (  246)

*********************** 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
  126 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.226 
Fit side-chains
REVERT: A   36 ASN cc_start: 0.8199 (m-40) cc_final: 0.7827 (m110)
REVERT: A   49 ASN cc_start: 0.7854 (p0) cc_final: 0.7532 (p0)
REVERT: A  326 PHE cc_start: 0.7098 (m-80) cc_final: 0.6771 (m-10)
REVERT: A  472 SER cc_start: 0.7970 (p) cc_final: 0.7756 (t)
REVERT: B  284 SER cc_start: 0.7510 (t) cc_final: 0.7181 (p)
REVERT: B  364 ASN cc_start: 0.7596 (p0) cc_final: 0.7344 (p0)
REVERT: B  365 VAL cc_start: 0.8321 (p) cc_final: 0.8099 (t)
REVERT: B  379 MET cc_start: 0.5239 (tmm) cc_final: 0.5004 (tmm)
REVERT: B  413 THR cc_start: 0.8077 (m) cc_final: 0.7823 (t)
REVERT: B  445 SER cc_start: 0.8418 (t) cc_final: 0.8082 (m)
REVERT: C  348 ASN cc_start: 0.7460 (t0) cc_final: 0.7089 (t0)
  outliers start: 13
  outliers final: 8
  residues processed: 117
  average time/residue: 0.0492
  time to fit residues: 8.2662
Evaluate side-chains
  113 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 105
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
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  364 ASN
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 10 optimal weight:    0.1980
   chunk 47 optimal weight:    0.2980
   chunk 34 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 52 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.5380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.115713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.103422 restraints weight = 10067.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.105720 restraints weight = 6359.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.107342 restraints weight = 4499.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.108431 restraints weight = 3445.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.109294 restraints weight = 2822.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7112
moved from start:          0.3639

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= 0.160
  Angle     :  0.599   6.741   8241  Z= 0.319
  Chirality :  0.047   0.233    901
  Planarity :  0.004   0.043   1064
  Dihedral  :  5.156  23.160    818
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 12.19 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.96 (0.27), residues: 735
  helix: -3.97 (0.95), residues: 15
  sheet: -0.30 (0.29), residues: 302
  loop : -2.05 (0.24), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 425 
 TYR   0.012   0.001   TYR B 462 
 PHE   0.017   0.002   PHE C 342 
 TRP   0.018   0.002   TRP A 356 
 HIS   0.003   0.001   HIS C 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 6054)
  covalent geometry    : angle       0.59894 ( 8241)
  hydrogen bonds       : bond        0.04457 (   98)
  hydrogen bonds       : angle       5.80215 (  246)

*********************** 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
  133 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 ASN cc_start: 0.8218 (m-40) cc_final: 0.7894 (m110)
REVERT: A   49 ASN cc_start: 0.7840 (p0) cc_final: 0.7497 (p0)
REVERT: A  281 ILE cc_start: 0.7028 (mp) cc_final: 0.6787 (mm)
REVERT: A  326 PHE cc_start: 0.7194 (m-80) cc_final: 0.6918 (m-10)
REVERT: B  355 TYR cc_start: 0.7548 (t80) cc_final: 0.7343 (t80)
REVERT: B  364 ASN cc_start: 0.7505 (p0) cc_final: 0.7238 (p0)
REVERT: B  367 TYR cc_start: 0.7861 (m-80) cc_final: 0.7333 (m-80)
REVERT: B  413 THR cc_start: 0.8112 (m) cc_final: 0.7909 (t)
REVERT: C  312 VAL cc_start: 0.7971 (t) cc_final: 0.7591 (m)
REVERT: C  328 PHE cc_start: 0.7920 (t80) cc_final: 0.7485 (t80)
REVERT: C  338 VAL cc_start: 0.8146 (t) cc_final: 0.7863 (p)
  outliers start: 16
  outliers final: 14
  residues processed: 125
  average time/residue: 0.0811
  time to fit residues: 13.3538
Evaluate side-chains
  124 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
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  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  254 ILE
Chi-restraints excluded: chain B residue  375 LEU
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  396 VAL
Chi-restraints excluded: chain C residue  432 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 13 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 52 optimal weight:    0.7980
   chunk 63 optimal weight:    0.3980
   chunk 38 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   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 302 GLN
** 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 = 0.3363 r_free = 0.3363 target = 0.112707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.100325 restraints weight = 10124.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.102643 restraints weight = 6377.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.104253 restraints weight = 4516.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.105367 restraints weight = 3468.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.106195 restraints weight = 2850.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7161
moved from start:          0.4360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   6054  Z= 0.199
  Angle     :  0.619   7.468   8241  Z= 0.330
  Chirality :  0.046   0.173    901
  Planarity :  0.005   0.044   1064
  Dihedral  :  5.480  24.531    818
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 13.43 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.90 (0.28), residues: 735
  helix: -3.83 (1.02), residues: 15
  sheet: -0.16 (0.30), residues: 291
  loop : -2.05 (0.25), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 425 
 TYR   0.012   0.002   TYR B 355 
 PHE   0.021   0.002   PHE C 342 
 TRP   0.016   0.002   TRP A 356 
 HIS   0.003   0.001   HIS C 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 6054)
  covalent geometry    : angle       0.61883 ( 8241)
  hydrogen bonds       : bond        0.04462 (   98)
  hydrogen bonds       : angle       5.45924 (  246)

*********************** 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
  140 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 112
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A   36 ASN cc_start: 0.8269 (m-40) cc_final: 0.7942 (m110)
REVERT: A   49 ASN cc_start: 0.7912 (p0) cc_final: 0.7600 (p0)
REVERT: A  304 THR cc_start: 0.8302 (t) cc_final: 0.7896 (m)
REVERT: A  326 PHE cc_start: 0.7239 (m-80) cc_final: 0.7004 (m-10)
REVERT: A  346 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7565 (mtpp)
REVERT: A  349 SER cc_start: 0.8148 (t) cc_final: 0.7873 (p)
REVERT: B   64 LEU cc_start: 0.8358 (mt) cc_final: 0.8149 (mt)
REVERT: B  364 ASN cc_start: 0.7496 (p0) cc_final: 0.7180 (p0)
REVERT: B  367 TYR cc_start: 0.7867 (m-80) cc_final: 0.7386 (m-80)
REVERT: C  312 VAL cc_start: 0.7985 (t) cc_final: 0.7596 (m)
REVERT: C  328 PHE cc_start: 0.8065 (t80) cc_final: 0.7858 (t80)
REVERT: C  368 VAL cc_start: 0.8613 (p) cc_final: 0.8277 (t)
  outliers start: 28
  outliers final: 19
  residues processed: 122
  average time/residue: 0.0687
  time to fit residues: 11.6942
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  : 0.205 
-------------------------------------------------------------------------------
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  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  300 ASN
Chi-restraints excluded: chain B residue  375 LEU
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  432 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 40 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0980
   chunk 24 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0870
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
A 302 GLN
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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.113971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.101506 restraints weight = 10209.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.103817 restraints weight = 6424.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.105271 restraints weight = 4573.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.106434 restraints weight = 3564.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.107305 restraints weight = 2913.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.4609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6054  Z= 0.152
  Angle     :  0.563   7.322   8241  Z= 0.300
  Chirality :  0.045   0.163    901
  Planarity :  0.004   0.044   1064
  Dihedral  :  5.173  22.737    818
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 13.58 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.81 (0.28), residues: 735
  helix: -3.77 (1.03), residues: 15
  sheet:  0.04 (0.31), residues: 287
  loop : -2.09 (0.24), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 369 
 TYR   0.010   0.001   TYR B 305 
 PHE   0.017   0.002   PHE B 328 
 TRP   0.016   0.002   TRP A 356 
 HIS   0.003   0.001   HIS C 436 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 6054)
  covalent geometry    : angle       0.56334 ( 8241)
  hydrogen bonds       : bond        0.03980 (   98)
  hydrogen bonds       : angle       5.27560 (  246)

*********************** 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
  137 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 103
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A  304 THR cc_start: 0.8234 (t) cc_final: 0.7860 (m)
REVERT: A  349 SER cc_start: 0.8120 (t) cc_final: 0.7815 (p)
REVERT: A  386 ASN cc_start: 0.6957 (OUTLIER) cc_final: 0.6569 (p0)
REVERT: B  364 ASN cc_start: 0.7477 (p0) cc_final: 0.7097 (p0)
REVERT: B  367 TYR cc_start: 0.7817 (m-80) cc_final: 0.7321 (m-80)
REVERT: C  312 VAL cc_start: 0.8023 (t) cc_final: 0.7640 (m)
REVERT: C  328 PHE cc_start: 0.7998 (t80) cc_final: 0.7766 (t80)
REVERT: C  344 VAL cc_start: 0.8504 (t) cc_final: 0.8263 (p)
  outliers start: 34
  outliers final: 29
  residues processed: 122
  average time/residue: 0.0558
  time to fit residues: 9.5245
Evaluate side-chains
  130 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 100
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  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  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  472 SER
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain C residue  306 THR
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 302 GLN
A 436 HIS
** 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.112233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.099962 restraints weight = 10235.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.102269 restraints weight = 6459.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.103821 restraints weight = 4581.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.104934 restraints weight = 3532.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.105751 restraints weight = 2880.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7182
moved from start:          0.4922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   6054  Z= 0.209
  Angle     :  0.625   7.541   8241  Z= 0.331
  Chirality :  0.046   0.168    901
  Planarity :  0.004   0.044   1064
  Dihedral  :  5.526  24.465    818
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 14.81 %
    Favored  : 79.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.86 (0.28), residues: 735
  helix: -3.94 (0.92), residues: 15
  sheet:  0.06 (0.31), residues: 286
  loop : -2.16 (0.24), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 307 
 TYR   0.012   0.001   TYR B 305 
 PHE   0.023   0.002   PHE C 342 
 TRP   0.017   0.002   TRP A 356 
 HIS   0.005   0.001   HIS A 436 

Details of bonding type rmsd
  covalent geometry    : bond        0.00504 ( 6054)
  covalent geometry    : angle       0.62518 ( 8241)
  hydrogen bonds       : bond        0.04451 (   98)
  hydrogen bonds       : angle       5.36498 (  246)

*********************** 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
  159 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 125
  time to evaluate  : 0.242 
Fit side-chains
REVERT: A  304 THR cc_start: 0.8252 (t) cc_final: 0.7890 (m)
REVERT: A  349 SER cc_start: 0.8122 (t) cc_final: 0.7851 (p)
REVERT: A  369 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.7228 (mtp85)
REVERT: A  386 ASN cc_start: 0.6984 (OUTLIER) cc_final: 0.6584 (p0)
REVERT: B  364 ASN cc_start: 0.7588 (p0) cc_final: 0.7152 (p0)
REVERT: B  367 TYR cc_start: 0.7858 (m-80) cc_final: 0.7430 (m-80)
REVERT: B  472 SER cc_start: 0.8244 (OUTLIER) cc_final: 0.7929 (p)
REVERT: C  312 VAL cc_start: 0.8014 (t) cc_final: 0.7647 (m)
REVERT: C  348 ASN cc_start: 0.7219 (t0) cc_final: 0.6907 (p0)
REVERT: C  349 SER cc_start: 0.7947 (t) cc_final: 0.7658 (p)
REVERT: C  412 SER cc_start: 0.7853 (t) cc_final: 0.7497 (p)
  outliers start: 34
  outliers final: 29
  residues processed: 145
  average time/residue: 0.0747
  time to fit residues: 14.5108
Evaluate side-chains
  148 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 116
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
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  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  336 ASP
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  472 SER
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain C residue  306 THR
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 12 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 34 optimal weight:    0.3980
   chunk 10 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 57 optimal weight:    0.6980
   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
C 266 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.112152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.099799 restraints weight = 10109.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.102068 restraints weight = 6439.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.103660 restraints weight = 4574.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.104650 restraints weight = 3533.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.105494 restraints weight = 2930.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7178
moved from start:          0.5115

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= 0.180
  Angle     :  0.600   7.394   8241  Z= 0.316
  Chirality :  0.045   0.165    901
  Planarity :  0.004   0.044   1064
  Dihedral  :  5.344  23.463    818
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  5.86 %
    Allowed  : 16.36 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.88 (0.29), residues: 735
  helix: -3.88 (0.95), residues: 15
  sheet:  0.01 (0.32), residues: 280
  loop : -2.12 (0.24), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 425 
 TYR   0.011   0.001   TYR B 305 
 PHE   0.019   0.002   PHE C 342 
 TRP   0.016   0.002   TRP A 356 
 HIS   0.003   0.001   HIS C 436 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 6054)
  covalent geometry    : angle       0.60033 ( 8241)
  hydrogen bonds       : bond        0.04094 (   98)
  hydrogen bonds       : angle       5.27128 (  246)

*********************** 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
  147 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 109
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A  280 THR cc_start: 0.7361 (m) cc_final: 0.7072 (t)
REVERT: A  304 THR cc_start: 0.8263 (t) cc_final: 0.7893 (m)
REVERT: A  349 SER cc_start: 0.8142 (t) cc_final: 0.7791 (p)
REVERT: A  369 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.7237 (mtp85)
REVERT: A  386 ASN cc_start: 0.6959 (OUTLIER) cc_final: 0.6584 (p0)
REVERT: B  336 ASP cc_start: 0.6471 (OUTLIER) cc_final: 0.6268 (m-30)
REVERT: B  364 ASN cc_start: 0.7497 (p0) cc_final: 0.7029 (p0)
REVERT: B  367 TYR cc_start: 0.7854 (m-80) cc_final: 0.7407 (m-80)
REVERT: B  472 SER cc_start: 0.8205 (OUTLIER) cc_final: 0.7899 (p)
REVERT: C  300 ASN cc_start: 0.7719 (m-40) cc_final: 0.7479 (m110)
REVERT: C  312 VAL cc_start: 0.8026 (t) cc_final: 0.7653 (m)
REVERT: C  348 ASN cc_start: 0.7253 (t0) cc_final: 0.6968 (p0)
REVERT: C  349 SER cc_start: 0.8022 (t) cc_final: 0.7710 (p)
REVERT: C  412 SER cc_start: 0.7883 (t) cc_final: 0.7550 (p)
  outliers start: 38
  outliers final: 29
  residues processed: 132
  average time/residue: 0.0751
  time to fit residues: 13.0705
Evaluate side-chains
  142 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 109
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
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  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  336 ASP
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  471 ILE
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  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 50 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 302 GLN
C 266 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.110571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.098739 restraints weight = 10217.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.100883 restraints weight = 6517.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.102459 restraints weight = 4650.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.103602 restraints weight = 3571.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.104354 restraints weight = 2903.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7204
moved from start:          0.5323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   6054  Z= 0.243
  Angle     :  0.657   8.216   8241  Z= 0.346
  Chirality :  0.047   0.167    901
  Planarity :  0.005   0.045   1064
  Dihedral  :  5.748  25.802    818
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  6.17 %
    Allowed  : 16.05 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.96 (0.29), residues: 735
  helix: -3.76 (1.15), residues: 9
  sheet: -0.11 (0.31), residues: 314
  loop : -2.33 (0.25), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 427 
 TYR   0.015   0.002   TYR B 305 
 PHE   0.030   0.002   PHE B 468 
 TRP   0.017   0.002   TRP A 356 
 HIS   0.004   0.001   HIS C 436 

Details of bonding type rmsd
  covalent geometry    : bond        0.00586 ( 6054)
  covalent geometry    : angle       0.65729 ( 8241)
  hydrogen bonds       : bond        0.04620 (   98)
  hydrogen bonds       : angle       5.39203 (  246)

*********************** 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
  153 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 113
  time to evaluate  : 0.256 
Fit side-chains
REVERT: A  304 THR cc_start: 0.8263 (t) cc_final: 0.7928 (m)
REVERT: A  349 SER cc_start: 0.8092 (t) cc_final: 0.7791 (p)
REVERT: A  386 ASN cc_start: 0.7010 (OUTLIER) cc_final: 0.6638 (p0)
REVERT: B  364 ASN cc_start: 0.7583 (p0) cc_final: 0.7129 (p0)
REVERT: B  367 TYR cc_start: 0.7905 (m-80) cc_final: 0.7508 (m-80)
REVERT: B  472 SER cc_start: 0.8160 (OUTLIER) cc_final: 0.7856 (p)
REVERT: C  300 ASN cc_start: 0.7751 (m-40) cc_final: 0.7535 (m110)
REVERT: C  312 VAL cc_start: 0.8034 (t) cc_final: 0.7675 (m)
REVERT: C  348 ASN cc_start: 0.7245 (t0) cc_final: 0.6969 (p0)
REVERT: C  349 SER cc_start: 0.7966 (t) cc_final: 0.7659 (p)
REVERT: C  412 SER cc_start: 0.7875 (t) cc_final: 0.7560 (p)
  outliers start: 40
  outliers final: 33
  residues processed: 135
  average time/residue: 0.0739
  time to fit residues: 13.3429
Evaluate side-chains
  144 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 109
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
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  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  336 ASP
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  463 GLU
Chi-restraints excluded: chain B residue  472 SER
Chi-restraints excluded: chain B residue  474 VAL
Chi-restraints excluded: chain C residue  295 SER
Chi-restraints excluded: chain C residue  306 THR
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
Chi-restraints excluded: chain C residue  456 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 51 optimal weight:    0.5980
   chunk 73 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 66 optimal weight:    0.4980
   chunk 22 optimal weight:    1.9990
   chunk 21 optimal weight:    0.1980
   chunk 36 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   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
B 329 ASN
C 266 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.112872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.101146 restraints weight = 10190.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.103344 restraints weight = 6472.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.104840 restraints weight = 4580.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.106047 restraints weight = 3531.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.106922 restraints weight = 2841.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7175
moved from start:          0.5385

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= 0.160
  Angle     :  0.605   9.642   8241  Z= 0.315
  Chirality :  0.045   0.176    901
  Planarity :  0.004   0.045   1064
  Dihedral  :  5.318  23.123    818
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  5.40 %
    Allowed  : 16.82 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.88 (0.29), residues: 735
  helix: -4.25 (0.79), residues: 15
  sheet: -0.10 (0.31), residues: 312
  loop : -2.16 (0.26), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 425 
 TYR   0.010   0.001   TYR B 305 
 PHE   0.019   0.002   PHE B 328 
 TRP   0.016   0.002   TRP A 356 
 HIS   0.003   0.001   HIS C 436 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 6054)
  covalent geometry    : angle       0.60548 ( 8241)
  hydrogen bonds       : bond        0.03983 (   98)
  hydrogen bonds       : angle       5.26533 (  246)

*********************** 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
  149 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 114
  time to evaluate  : 0.187 
Fit side-chains
REVERT: A  304 THR cc_start: 0.8261 (t) cc_final: 0.7874 (m)
REVERT: A  349 SER cc_start: 0.8146 (t) cc_final: 0.7757 (p)
REVERT: A  386 ASN cc_start: 0.6967 (OUTLIER) cc_final: 0.6578 (p0)
REVERT: B  364 ASN cc_start: 0.7445 (p0) cc_final: 0.6954 (p0)
REVERT: B  367 TYR cc_start: 0.7864 (m-80) cc_final: 0.7417 (m-80)
REVERT: B  472 SER cc_start: 0.8173 (OUTLIER) cc_final: 0.7876 (p)
REVERT: C  312 VAL cc_start: 0.8029 (t) cc_final: 0.7652 (m)
REVERT: C  344 VAL cc_start: 0.8464 (t) cc_final: 0.8185 (p)
REVERT: C  348 ASN cc_start: 0.7248 (t0) cc_final: 0.7033 (p0)
REVERT: C  349 SER cc_start: 0.7965 (t) cc_final: 0.7707 (p)
REVERT: C  412 SER cc_start: 0.7842 (t) cc_final: 0.7526 (p)
  outliers start: 35
  outliers final: 26
  residues processed: 137
  average time/residue: 0.0837
  time to fit residues: 14.6927
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  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  329 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  394 TRP
Chi-restraints excluded: chain B residue  413 THR
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  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 60 optimal weight:    0.4980
   chunk 29 optimal weight:    2.9990
   chunk 41 optimal weight:    0.3980
   chunk 62 optimal weight:    0.2980
   chunk 65 optimal weight:    0.3980
   chunk 40 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.4380

-------------------------------------------------------------------------------
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 = 0.3367 r_free = 0.3367 target = 0.112428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.100602 restraints weight = 10321.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.102786 restraints weight = 6554.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.104431 restraints weight = 4645.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.105298 restraints weight = 3538.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.106248 restraints weight = 2954.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7166
moved from start:          0.5430

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= 0.137
  Angle     :  0.585  10.092   8241  Z= 0.306
  Chirality :  0.045   0.167    901
  Planarity :  0.004   0.045   1064
  Dihedral  :  5.098  22.322    818
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 17.90 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.73 (0.30), residues: 735
  helix: -4.27 (0.80), residues: 15
  sheet:  0.03 (0.29), residues: 351
  loop : -2.28 (0.27), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 425 
 TYR   0.009   0.001   TYR B 305 
 PHE   0.022   0.002   PHE B 328 
 TRP   0.015   0.002   TRP A 356 
 HIS   0.002   0.001   HIS C 436 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 6054)
  covalent geometry    : angle       0.58540 ( 8241)
  hydrogen bonds       : bond        0.03853 (   98)
  hydrogen bonds       : angle       5.20890 (  246)

********************** 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
  132 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 107
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A  304 THR cc_start: 0.8260 (t) cc_final: 0.7866 (m)
REVERT: A  349 SER cc_start: 0.8149 (t) cc_final: 0.7825 (p)
REVERT: B  364 ASN cc_start: 0.7386 (p0) cc_final: 0.6921 (p0)
REVERT: B  367 TYR cc_start: 0.7833 (m-80) cc_final: 0.7406 (m-80)
REVERT: B  472 SER cc_start: 0.8191 (OUTLIER) cc_final: 0.7870 (p)
REVERT: C  312 VAL cc_start: 0.8039 (t) cc_final: 0.7654 (m)
REVERT: C  344 VAL cc_start: 0.8466 (t) cc_final: 0.8210 (p)
REVERT: C  348 ASN cc_start: 0.7250 (t0) cc_final: 0.7028 (p0)
REVERT: C  349 SER cc_start: 0.7969 (t) cc_final: 0.7717 (p)
REVERT: C  412 SER cc_start: 0.7810 (t) cc_final: 0.7505 (p)
  outliers start: 25
  outliers final: 23
  residues processed: 122
  average time/residue: 0.0729
  time to fit residues: 11.8463
Evaluate side-chains
  130 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 106
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  271 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  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  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  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  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 8 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 48 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 62 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 55 optimal weight:    0.0170
   chunk 2 optimal weight:    0.5980
   chunk 56 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.5018

-------------------------------------------------------------------------------
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 = 0.3365 r_free = 0.3365 target = 0.112934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.101179 restraints weight = 10175.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.103371 restraints weight = 6426.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.104783 restraints weight = 4525.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.106016 restraints weight = 3499.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.106716 restraints weight = 2822.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7168
moved from start:          0.5473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6054  Z= 0.150
  Angle     :  0.608  10.603   8241  Z= 0.315
  Chirality :  0.045   0.196    901
  Planarity :  0.004   0.044   1064
  Dihedral  :  5.103  22.716    818
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 17.90 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.72 (0.30), residues: 735
  helix: -4.29 (0.77), residues: 15
  sheet:  0.02 (0.29), residues: 351
  loop : -2.26 (0.27), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 427 
 TYR   0.010   0.001   TYR B 305 
 PHE   0.020   0.002   PHE B 328 
 TRP   0.016   0.002   TRP A 356 
 HIS   0.003   0.001   HIS C 436 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 6054)
  covalent geometry    : angle       0.60840 ( 8241)
  hydrogen bonds       : bond        0.03909 (   98)
  hydrogen bonds       : angle       5.18657 (  246)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1144.35 seconds
wall clock time: 20 minutes 27.99 seconds (1227.99 seconds total)