Starting phenix.real_space_refine
on Tue Mar  3 12:12:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p9u_13266/03_2026/7p9u_13266.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p9u_13266/03_2026/7p9u_13266.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p9u_13266/03_2026/7p9u_13266.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p9u_13266/03_2026/7p9u_13266.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p9u_13266/03_2026/7p9u_13266.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p9u_13266/03_2026/7p9u_13266.cif"
  }
  resolution = 3.7
  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=  -0.002 sd=   0.041
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      22      5.16       5
     C    2631      2.51       5
     N     625      2.21       5
     O     665      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3943
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 375
          Classifications: {'peptide': 47}
          Link IDs: {'PTRANS': 2, 'TRANS': 44}
    Chain: "B"
      Number of atoms: 3568
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 456, 3568
          Classifications: {'peptide': 456}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 23, 'TRANS': 432}
          Chain breaks: 1
  Time building chain proxies: 0.81, per 1000 atoms: 0.21
  Number of scatterers: 3943
  At special positions: 0
  Unit cell: (68.224, 81.536, 89.856, 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      22     16.00
     O     665      8.00
     N     625      7.00
     C    2631      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 211 " - pdb=" SG  CYS B 158 " distance=2.03

  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: 0.19
  Conformation dependent library (CDL) restraints added in 96.8 milliseconds
  

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  932

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 1 sheets defined
      77.3% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 178 through 208
    Processing helix  chain 'B' and resid 46 through 58
    Processing helix  chain 'B' and resid 60 through 63
    Processing helix  chain 'B' and resid 64 through 74
      removed outlier: 4.132A  pdb=" N   GLY B  68 " --> pdb=" O   ILE B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 105
    Processing helix  chain 'B' and resid 109 through 118
      removed outlier: 3.718A  pdb=" N   TYR B 113 " --> pdb=" O   GLY B 109 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ILE B 114 " --> pdb=" O   HIS B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 133
      removed outlier: 3.814A  pdb=" N   ALA B 123 " --> pdb=" O   GLY B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 133 through 152
    Processing helix  chain 'B' and resid 162 through 183
    Processing helix  chain 'B' and resid 184 through 190
      removed outlier: 3.597A  pdb=" N   ILE B 190 " --> pdb=" O   TRP B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 216
      removed outlier: 3.523A  pdb=" N   ILE B 202 " --> pdb=" O   LYS B 198 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LEU B 203 " --> pdb=" O   LEU B 199 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ILE B 205 " --> pdb=" O   ALA B 201 " (cutoff:3.500A)
      Proline residue:  B 208  - end of helix
    Processing helix  chain 'B' and resid 231 through 233
      No H-bonds generated for 'chain 'B' and resid 231 through 233'
    Processing helix  chain 'B' and resid 234 through 246
      removed outlier: 3.547A  pdb=" N   TYR B 244 " --> pdb=" O   TYR B 240 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   ALA B 245 " --> pdb=" O   TYR B 241 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   TYR B 246 " --> pdb=" O   GLY B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 264 through 292
      removed outlier: 3.941A  pdb=" N   THR B 291 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 293 through 299
    Processing helix  chain 'B' and resid 302 through 312
    Processing helix  chain 'B' and resid 318 through 349
      removed outlier: 3.738A  pdb=" N   SER B 330 " --> pdb=" O   SER B 326 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   MET B 331 " --> pdb=" O   CYS B 327 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ASN B 332 " --> pdb=" O   PHE B 328 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   GLY B 333 " --> pdb=" O   GLY B 329 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   GLY B 334 " --> pdb=" O   SER B 330 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   VAL B 335 " --> pdb=" O   MET B 331 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   PHE B 336 " --> pdb=" O   ASN B 332 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   PHE B 342 " --> pdb=" O   VAL B 338 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   TYR B 343 " --> pdb=" O   SER B 339 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   VAL B 344 " --> pdb=" O   ARG B 340 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   ARG B 347 " --> pdb=" O   TYR B 343 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   GLU B 348 " --> pdb=" O   VAL B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 352 through 357
    Processing helix  chain 'B' and resid 372 through 382
    Processing helix  chain 'B' and resid 384 through 413
      removed outlier: 3.930A  pdb=" N   ASN B 390 " --> pdb=" O   ASP B 386 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   ALA B 395 " --> pdb=" O   PHE B 391 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   LEU B 407 " --> pdb=" O   ALA B 403 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   ILE B 408 " --> pdb=" O   VAL B 404 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   TYR B 409 " --> pdb=" O   ALA B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 442
      removed outlier: 3.626A  pdb=" N   ALA B 429 " --> pdb=" O   LEU B 425 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 460
      removed outlier: 3.573A  pdb=" N   THR B 450 " --> pdb=" O   ASP B 446 " (cutoff:3.500A)
      removed outlier: 4.876A  pdb=" N   ILE B 452 " --> pdb=" O   PHE B 448 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   GLY B 453 " --> pdb=" O   SER B 449 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 461 through 467
    Processing helix  chain 'B' and resid 478 through 493
    Processing sheet with id=AA1, first strand: chain 'B' and resid 358 through 359

    263 hydrogen bonds defined for protein.
    762 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: 0.46

  Time building geometry restraints manager: 0.28 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1179
        1.34 -     1.46: 916
        1.46 -     1.58: 1914
        1.58 -     1.69: 0
        1.69 -     1.81: 36
  Bond restraints: 4045
  Sorted by residual:
  bond pdb=" CG  MET B 243 "
       pdb=" SD  MET B 243 "
    ideal  model  delta    sigma   weight residual
    1.803  1.760  0.043 2.50e-02 1.60e+03 2.92e+00
  bond pdb=" CG  MET B 357 "
       pdb=" SD  MET B 357 "
    ideal  model  delta    sigma   weight residual
    1.803  1.772  0.031 2.50e-02 1.60e+03 1.55e+00
  bond pdb=" SD  MET B 357 "
       pdb=" CE  MET B 357 "
    ideal  model  delta    sigma   weight residual
    1.791  1.765  0.026 2.50e-02 1.60e+03 1.07e+00
  bond pdb=" CB  THR B 169 "
       pdb=" CG2 THR B 169 "
    ideal  model  delta    sigma   weight residual
    1.521  1.491  0.030 3.30e-02 9.18e+02 8.33e-01
  bond pdb=" CA  ASP B 446 "
       pdb=" CB  ASP B 446 "
    ideal  model  delta    sigma   weight residual
    1.530  1.544 -0.014 1.58e-02 4.01e+03 8.08e-01
  ... (remaining 4040 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.46: 5315
        1.46 -     2.93: 140
        2.93 -     4.39: 35
        4.39 -     5.86: 17
        5.86 -     7.32: 4
  Bond angle restraints: 5511
  Sorted by residual:
  angle pdb=" CA  LYS B 362 "
        pdb=" CB  LYS B 362 "
        pdb=" CG  LYS B 362 "
      ideal   model   delta    sigma   weight residual
     114.10  120.16   -6.06 2.00e+00 2.50e-01 9.19e+00
  angle pdb=" C   PRO B 262 "
        pdb=" N   GLU B 263 "
        pdb=" CA  GLU B 263 "
      ideal   model   delta    sigma   weight residual
     121.54  126.85   -5.31 1.91e+00 2.74e-01 7.73e+00
  angle pdb=" CG  MET B 357 "
        pdb=" SD  MET B 357 "
        pdb=" CE  MET B 357 "
      ideal   model   delta    sigma   weight residual
     100.90   95.00    5.90 2.20e+00 2.07e-01 7.19e+00
  angle pdb=" CA  PHE B 239 "
        pdb=" CB  PHE B 239 "
        pdb=" CG  PHE B 239 "
      ideal   model   delta    sigma   weight residual
     113.80  116.39   -2.59 1.00e+00 1.00e+00 6.70e+00
  angle pdb=" C   PRO B 161 "
        pdb=" N   GLU B 162 "
        pdb=" CA  GLU B 162 "
      ideal   model   delta    sigma   weight residual
     121.54  126.45   -4.91 1.91e+00 2.74e-01 6.61e+00
  ... (remaining 5506 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.16: 2090
       17.16 -    34.32: 222
       34.32 -    51.47: 37
       51.47 -    68.63: 5
       68.63 -    85.79: 4
  Dihedral angle restraints: 2358
    sinusoidal: 909
      harmonic: 1449
  Sorted by residual:
  dihedral pdb=" CB  CYS A 211 "
           pdb=" SG  CYS A 211 "
           pdb=" SG  CYS B 158 "
           pdb=" CB  CYS B 158 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -171.79   85.79     1      1.00e+01 1.00e-02 8.90e+01
  dihedral pdb=" CA  ARG A 212 "
           pdb=" C   ARG A 212 "
           pdb=" N   GLU A 213 "
           pdb=" CA  GLU A 213 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.84  -18.16     0      5.00e+00 4.00e-02 1.32e+01
  dihedral pdb=" CA  LYS B 362 "
           pdb=" C   LYS B 362 "
           pdb=" N   HIS B 363 "
           pdb=" CA  HIS B 363 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.97  -18.03     0      5.00e+00 4.00e-02 1.30e+01
  ... (remaining 2355 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 375
       0.030 -    0.060: 181
       0.060 -    0.090: 67
       0.090 -    0.120: 31
       0.120 -    0.150: 5
  Chirality restraints: 659
  Sorted by residual:
  chirality pdb=" CB  THR B 169 "
            pdb=" CA  THR B 169 "
            pdb=" OG1 THR B 169 "
            pdb=" CG2 THR B 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.15 2.00e-01 2.50e+01 5.65e-01
  chirality pdb=" CA  ASP B 446 "
            pdb=" N   ASP B 446 "
            pdb=" C   ASP B 446 "
            pdb=" CB  ASP B 446 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.42e-01
  chirality pdb=" CA  VAL B 495 "
            pdb=" N   VAL B 495 "
            pdb=" C   VAL B 495 "
            pdb=" CB  VAL B 495 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.88e-01
  ... (remaining 656 not shown)

  Planarity restraints: 666
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 249 "    0.020 2.00e-02 2.50e+03   2.45e-02 1.50e+01
        pdb=" CG  TRP B 249 "   -0.064 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 249 "    0.038 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 249 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 249 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 249 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 249 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 249 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 249 "    0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 249 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 239 "   -0.020 2.00e-02 2.50e+03   1.30e-02 2.95e+00
        pdb=" CG  PHE B 239 "    0.020 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 239 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 239 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 239 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 239 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 239 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 366 "   -0.028 5.00e-02 4.00e+02   4.25e-02 2.89e+00
        pdb=" N   PRO B 367 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO B 367 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 367 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 663 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 261
        2.73 -     3.27: 4305
        3.27 -     3.82: 6575
        3.82 -     4.36: 7277
        4.36 -     4.90: 12570
  Nonbonded interactions: 30988
  Sorted by model distance:
  nonbonded pdb=" O   PRO B 161 "
            pdb=" N   LEU B 163 "
     model   vdw
     2.188 3.120
  nonbonded pdb=" O   VAL B 455 "
            pdb=" OG1 THR B 459 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" NH2 ARG A 183 "
            pdb=" O   ILE B 490 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" O   TRP A 179 "
            pdb=" OG1 THR A 182 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   ILE B 378 "
            pdb=" OG  SER B 382 "
     model   vdw
     2.250 3.040
  ... (remaining 30983 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.680
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
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      :  0.003   0.043   4046  Z= 0.144
  Angle     :  0.679   7.320   5513  Z= 0.350
  Chirality :  0.043   0.150    659
  Planarity :  0.004   0.042    666
  Dihedral  : 14.105  80.165   1423
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  6.83 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.41), residues: 498
  helix:  1.76 (0.30), residues: 346
  sheet:  None (None), residues: 0
  loop : -1.99 (0.53), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 396 
 TYR   0.014   0.002   TYR B 251 
 PHE   0.023   0.002   PHE B 250 
 TRP   0.064   0.003   TRP B 249 
 HIS   0.002   0.001   HIS B 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 4045)
  covalent geometry    : angle       0.67835 ( 5511)
  SS BOND              : bond        0.00361 (    1)
  SS BOND              : angle       1.53623 (    2)
  hydrogen bonds       : bond        0.15253 (  263)
  hydrogen bonds       : angle       5.45058 (  762)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.154 
Fit side-chains
REVERT: B   78 MET cc_start: 0.7635 (tpt) cc_final: 0.7138 (tpp)
REVERT: B   86 CYS cc_start: 0.8361 (m) cc_final: 0.7917 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.0454
  time to fit residues: 7.4269
Evaluate side-chains
  97 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.8980
   chunk 22 optimal weight:    6.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B 489 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.140192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.128746 restraints weight = 8514.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.131942 restraints weight = 4682.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.134026 restraints weight = 2879.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.135458 restraints weight = 1919.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.136554 restraints weight = 1366.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.1315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4046  Z= 0.152
  Angle     :  0.694   9.154   5513  Z= 0.351
  Chirality :  0.044   0.160    659
  Planarity :  0.004   0.028    666
  Dihedral  :  4.925  45.949    540
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  5.42 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 14.72 %
    Favored  : 83.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.41), residues: 498
  helix:  1.65 (0.29), residues: 357
  sheet:  None (None), residues: 0
  loop : -2.46 (0.52), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  48 
 TYR   0.018   0.001   TYR B 149 
 PHE   0.029   0.002   PHE B 239 
 TRP   0.028   0.002   TRP B 249 
 HIS   0.005   0.001   HIS B 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 4045)
  covalent geometry    : angle       0.69400 ( 5511)
  SS BOND              : bond        0.00343 (    1)
  SS BOND              : angle       1.14678 (    2)
  hydrogen bonds       : bond        0.03981 (  263)
  hydrogen bonds       : angle       4.58972 (  762)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 0.143 
Fit side-chains
REVERT: B   78 MET cc_start: 0.7662 (tpt) cc_final: 0.7186 (tpp)
REVERT: B  270 ILE cc_start: 0.9446 (tp) cc_final: 0.9148 (tp)
  outliers start: 6
  outliers final: 5
  residues processed: 101
  average time/residue: 0.0422
  time to fit residues: 6.0340
Evaluate side-chains
  96 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 91
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  156 ILE
Chi-restraints excluded: chain B residue  168 ILE
Chi-restraints excluded: chain B residue  173 ILE
Chi-restraints excluded: chain B residue  202 ILE
Chi-restraints excluded: chain B residue  360 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 44 optimal weight:    0.1980
   chunk 10 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0040
   chunk 7 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.5592

-------------------------------------------------------------------------------
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 = 0.3863 r_free = 0.3863 target = 0.141304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.129945 restraints weight = 8483.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.133048 restraints weight = 4677.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.135076 restraints weight = 2899.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.136395 restraints weight = 1955.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.137494 restraints weight = 1427.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.1590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4046  Z= 0.128
  Angle     :  0.639   7.269   5513  Z= 0.323
  Chirality :  0.043   0.189    659
  Planarity :  0.004   0.027    666
  Dihedral  :  4.862  46.136    540
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  6.02 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 16.59 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.41), residues: 498
  helix:  1.73 (0.29), residues: 355
  sheet:  None (None), residues: 0
  loop : -2.53 (0.52), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 478 
 TYR   0.016   0.002   TYR B 240 
 PHE   0.037   0.001   PHE B 239 
 TRP   0.016   0.002   TRP B 249 
 HIS   0.003   0.001   HIS B 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 4045)
  covalent geometry    : angle       0.63850 ( 5511)
  SS BOND              : bond        0.00306 (    1)
  SS BOND              : angle       1.03849 (    2)
  hydrogen bonds       : bond        0.03651 (  263)
  hydrogen bonds       : angle       4.39392 (  762)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.135 
Fit side-chains
REVERT: B   78 MET cc_start: 0.7701 (tpt) cc_final: 0.7181 (tpp)
REVERT: B   86 CYS cc_start: 0.8498 (m) cc_final: 0.8052 (m)
REVERT: B  113 TYR cc_start: 0.7320 (m-80) cc_final: 0.6822 (m-80)
REVERT: B  379 MET cc_start: 0.7930 (mmt) cc_final: 0.7648 (mmt)
REVERT: B  407 LEU cc_start: 0.8855 (mt) cc_final: 0.8641 (mt)
  outliers start: 11
  outliers final: 6
  residues processed: 104
  average time/residue: 0.0447
  time to fit residues: 6.2810
Evaluate side-chains
  100 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain B residue  173 ILE
Chi-restraints excluded: chain B residue  202 ILE
Chi-restraints excluded: chain B residue  321 ILE
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  366 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0770
   chunk 13 optimal weight:    0.8980
   chunk 22 optimal weight:    6.9990
   chunk 14 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0970
   chunk 40 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.4336

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

Flipped N/Q/H residues before XYZ refinement:
B 390 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.142081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.130732 restraints weight = 8424.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.133838 restraints weight = 4647.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.135847 restraints weight = 2884.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.137274 restraints weight = 1961.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.138325 restraints weight = 1405.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4046  Z= 0.120
  Angle     :  0.638   9.010   5513  Z= 0.318
  Chirality :  0.042   0.181    659
  Planarity :  0.004   0.026    666
  Dihedral  :  4.803  46.075    540
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  5.82 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 19.86 %
    Favored  : 77.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.41), residues: 498
  helix:  1.78 (0.29), residues: 356
  sheet:  None (None), residues: 0
  loop : -2.61 (0.51), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 478 
 TYR   0.012   0.001   TYR B 149 
 PHE   0.037   0.001   PHE B 239 
 TRP   0.021   0.001   TRP B 249 
 HIS   0.003   0.001   HIS B 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 4045)
  covalent geometry    : angle       0.63827 ( 5511)
  SS BOND              : bond        0.00277 (    1)
  SS BOND              : angle       1.07447 (    2)
  hydrogen bonds       : bond        0.03428 (  263)
  hydrogen bonds       : angle       4.30974 (  762)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.136 
Fit side-chains
REVERT: B   78 MET cc_start: 0.7684 (tpt) cc_final: 0.7234 (tpp)
REVERT: B   86 CYS cc_start: 0.8501 (m) cc_final: 0.8064 (m)
REVERT: B   99 GLU cc_start: 0.7639 (tt0) cc_final: 0.7405 (tt0)
REVERT: B  113 TYR cc_start: 0.7315 (m-80) cc_final: 0.6838 (m-80)
REVERT: B  379 MET cc_start: 0.7735 (mmt) cc_final: 0.7511 (mmt)
REVERT: B  407 LEU cc_start: 0.8823 (mt) cc_final: 0.8203 (mt)
REVERT: B  490 ILE cc_start: 0.8283 (mm) cc_final: 0.8043 (mm)
  outliers start: 12
  outliers final: 10
  residues processed: 109
  average time/residue: 0.0452
  time to fit residues: 6.8093
Evaluate side-chains
  111 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  173 ILE
Chi-restraints excluded: chain B residue  202 ILE
Chi-restraints excluded: chain B residue  243 MET
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  321 ILE
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  366 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 4 optimal weight:    0.0000
   chunk 38 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 48 optimal weight:    0.3980
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.5784

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

Flipped N/Q/H residues before XYZ refinement:
B 363 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.141420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.130154 restraints weight = 8458.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.133182 restraints weight = 4656.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.135146 restraints weight = 2899.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.136522 restraints weight = 1950.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.137568 restraints weight = 1404.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4046  Z= 0.125
  Angle     :  0.639   7.398   5513  Z= 0.318
  Chirality :  0.042   0.174    659
  Planarity :  0.004   0.028    666
  Dihedral  :  4.804  46.309    540
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  5.82 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 22.66 %
    Favored  : 74.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.89 (0.40), residues: 498
  helix:  1.77 (0.29), residues: 357
  sheet:  None (None), residues: 0
  loop : -2.68 (0.50), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 148 
 TYR   0.012   0.001   TYR B 149 
 PHE   0.036   0.001   PHE B 239 
 TRP   0.025   0.001   TRP B 249 
 HIS   0.003   0.001   HIS B 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 4045)
  covalent geometry    : angle       0.63864 ( 5511)
  SS BOND              : bond        0.00320 (    1)
  SS BOND              : angle       1.05450 (    2)
  hydrogen bonds       : bond        0.03355 (  263)
  hydrogen bonds       : angle       4.29650 (  762)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.154 
Fit side-chains
REVERT: B   78 MET cc_start: 0.7671 (tpt) cc_final: 0.7186 (tpp)
REVERT: B   86 CYS cc_start: 0.8474 (m) cc_final: 0.8053 (m)
REVERT: B   99 GLU cc_start: 0.7597 (tt0) cc_final: 0.7359 (tt0)
REVERT: B  113 TYR cc_start: 0.7324 (m-80) cc_final: 0.7086 (m-80)
REVERT: B  211 MET cc_start: 0.6676 (mtp) cc_final: 0.6434 (mtt)
REVERT: B  357 MET cc_start: 0.7863 (tpp) cc_final: 0.7619 (tpp)
REVERT: B  407 LEU cc_start: 0.8834 (mt) cc_final: 0.8207 (mt)
REVERT: B  490 ILE cc_start: 0.8323 (mm) cc_final: 0.8107 (mm)
  outliers start: 14
  outliers final: 9
  residues processed: 109
  average time/residue: 0.0430
  time to fit residues: 6.4345
Evaluate side-chains
  105 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  173 ILE
Chi-restraints excluded: chain B residue  202 ILE
Chi-restraints excluded: chain B residue  243 MET
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  321 ILE
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  366 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 35 optimal weight:    4.9990
   chunk 6 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 34 optimal weight:   10.0000
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 390 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.139943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.128639 restraints weight = 8511.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.131697 restraints weight = 4658.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.133709 restraints weight = 2885.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.135128 restraints weight = 1943.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.136109 restraints weight = 1389.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.2097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4046  Z= 0.138
  Angle     :  0.650   7.222   5513  Z= 0.327
  Chirality :  0.043   0.167    659
  Planarity :  0.004   0.028    666
  Dihedral  :  4.870  46.429    540
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.63 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 22.66 %
    Favored  : 73.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.40), residues: 498
  helix:  1.71 (0.29), residues: 357
  sheet:  None (None), residues: 0
  loop : -2.97 (0.46), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  48 
 TYR   0.031   0.002   TYR B 240 
 PHE   0.037   0.002   PHE B 239 
 TRP   0.030   0.002   TRP B 249 
 HIS   0.003   0.001   HIS B 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 4045)
  covalent geometry    : angle       0.65009 ( 5511)
  SS BOND              : bond        0.00426 (    1)
  SS BOND              : angle       1.20299 (    2)
  hydrogen bonds       : bond        0.03375 (  263)
  hydrogen bonds       : angle       4.34549 (  762)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.154 
Fit side-chains
REVERT: B   78 MET cc_start: 0.7627 (tpt) cc_final: 0.7232 (tpp)
REVERT: B  407 LEU cc_start: 0.8805 (mt) cc_final: 0.8494 (mt)
REVERT: B  490 ILE cc_start: 0.8319 (mm) cc_final: 0.8111 (mm)
  outliers start: 18
  outliers final: 12
  residues processed: 110
  average time/residue: 0.0456
  time to fit residues: 6.8142
Evaluate side-chains
  110 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  156 ILE
Chi-restraints excluded: chain B residue  168 ILE
Chi-restraints excluded: chain B residue  173 ILE
Chi-restraints excluded: chain B residue  202 ILE
Chi-restraints excluded: chain B residue  243 MET
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  321 ILE
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  366 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0000
   chunk 36 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 22 optimal weight:    6.9990
   chunk 4 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.5984

-------------------------------------------------------------------------------
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 = 0.3850 r_free = 0.3850 target = 0.140497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.129188 restraints weight = 8610.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.132228 restraints weight = 4728.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.134233 restraints weight = 2920.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.135673 restraints weight = 1967.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.136608 restraints weight = 1408.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.2192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4046  Z= 0.127
  Angle     :  0.685  14.222   5513  Z= 0.330
  Chirality :  0.043   0.167    659
  Planarity :  0.004   0.033    666
  Dihedral  :  4.832  45.400    540
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.43 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 23.83 %
    Favored  : 72.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.40), residues: 498
  helix:  1.62 (0.29), residues: 359
  sheet:  None (None), residues: 0
  loop : -2.85 (0.48), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 148 
 TYR   0.050   0.002   TYR B 240 
 PHE   0.038   0.001   PHE B 239 
 TRP   0.034   0.002   TRP B 249 
 HIS   0.003   0.001   HIS B 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 4045)
  covalent geometry    : angle       0.68443 ( 5511)
  SS BOND              : bond        0.00364 (    1)
  SS BOND              : angle       1.07304 (    2)
  hydrogen bonds       : bond        0.03336 (  263)
  hydrogen bonds       : angle       4.32475 (  762)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.130 
Fit side-chains
REVERT: B   78 MET cc_start: 0.7630 (tpt) cc_final: 0.7219 (tpp)
REVERT: B   86 CYS cc_start: 0.8472 (m) cc_final: 0.8068 (m)
REVERT: B  113 TYR cc_start: 0.7318 (m-80) cc_final: 0.6780 (m-80)
REVERT: B  240 TYR cc_start: 0.7887 (m-80) cc_final: 0.7622 (m-80)
REVERT: B  407 LEU cc_start: 0.8768 (mt) cc_final: 0.8419 (mt)
REVERT: B  490 ILE cc_start: 0.8332 (mm) cc_final: 0.8120 (mm)
  outliers start: 15
  outliers final: 11
  residues processed: 106
  average time/residue: 0.0405
  time to fit residues: 5.9868
Evaluate side-chains
  108 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  156 ILE
Chi-restraints excluded: chain B residue  173 ILE
Chi-restraints excluded: chain B residue  202 ILE
Chi-restraints excluded: chain B residue  243 MET
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  321 ILE
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  366 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0570
   chunk 17 optimal weight:    0.9990
   chunk 8 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 32 optimal weight:    0.4980
   chunk 6 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.6702

-------------------------------------------------------------------------------
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 = 0.3850 r_free = 0.3850 target = 0.140426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.128989 restraints weight = 8410.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.132058 restraints weight = 4603.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.134095 restraints weight = 2844.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.135511 restraints weight = 1906.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.136561 restraints weight = 1369.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4046  Z= 0.134
  Angle     :  0.699  13.329   5513  Z= 0.342
  Chirality :  0.044   0.165    659
  Planarity :  0.004   0.027    666
  Dihedral  :  4.796  45.234    540
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.43 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 25.47 %
    Favored  : 71.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.40), residues: 498
  helix:  1.63 (0.29), residues: 359
  sheet:  None (None), residues: 0
  loop : -2.83 (0.48), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  48 
 TYR   0.042   0.002   TYR B 240 
 PHE   0.037   0.001   PHE B 239 
 TRP   0.033   0.002   TRP B 249 
 HIS   0.003   0.001   HIS B 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 4045)
  covalent geometry    : angle       0.69833 ( 5511)
  SS BOND              : bond        0.00381 (    1)
  SS BOND              : angle       1.09484 (    2)
  hydrogen bonds       : bond        0.03374 (  263)
  hydrogen bonds       : angle       4.32599 (  762)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.100 
Fit side-chains
REVERT: B   78 MET cc_start: 0.7602 (tpt) cc_final: 0.7216 (tpp)
REVERT: B   86 CYS cc_start: 0.8485 (m) cc_final: 0.8070 (m)
REVERT: B  240 TYR cc_start: 0.7971 (m-80) cc_final: 0.7707 (m-80)
REVERT: B  490 ILE cc_start: 0.8329 (mm) cc_final: 0.8105 (mm)
  outliers start: 14
  outliers final: 10
  residues processed: 103
  average time/residue: 0.0441
  time to fit residues: 6.2904
Evaluate side-chains
  109 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  173 ILE
Chi-restraints excluded: chain B residue  202 ILE
Chi-restraints excluded: chain B residue  243 MET
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  436 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9980
   chunk 30 optimal weight:    0.0470
   chunk 13 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.6478

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

Flipped N/Q/H residues before XYZ refinement:
B 390 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.140368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.128898 restraints weight = 8585.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.131969 restraints weight = 4659.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.133994 restraints weight = 2884.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.135417 restraints weight = 1933.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.136386 restraints weight = 1376.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.2360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4046  Z= 0.136
  Angle     :  0.707  13.439   5513  Z= 0.345
  Chirality :  0.044   0.164    659
  Planarity :  0.004   0.027    666
  Dihedral  :  4.854  47.127    540
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.43 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 25.23 %
    Favored  : 71.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.40), residues: 498
  helix:  1.47 (0.29), residues: 365
  sheet:  None (None), residues: 0
  loop : -2.68 (0.50), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 148 
 TYR   0.040   0.002   TYR B 240 
 PHE   0.036   0.001   PHE B 239 
 TRP   0.044   0.002   TRP B 249 
 HIS   0.003   0.001   HIS B 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 4045)
  covalent geometry    : angle       0.70658 ( 5511)
  SS BOND              : bond        0.00368 (    1)
  SS BOND              : angle       1.06097 (    2)
  hydrogen bonds       : bond        0.03399 (  263)
  hydrogen bonds       : angle       4.36032 (  762)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.138 
Fit side-chains
REVERT: B   78 MET cc_start: 0.7646 (tpt) cc_final: 0.7241 (tpp)
REVERT: B   86 CYS cc_start: 0.8478 (m) cc_final: 0.8085 (m)
REVERT: B  113 TYR cc_start: 0.7355 (m-80) cc_final: 0.6850 (m-80)
REVERT: B  240 TYR cc_start: 0.7975 (m-80) cc_final: 0.7753 (m-80)
  outliers start: 15
  outliers final: 11
  residues processed: 105
  average time/residue: 0.0421
  time to fit residues: 6.1702
Evaluate side-chains
  112 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  156 ILE
Chi-restraints excluded: chain B residue  173 ILE
Chi-restraints excluded: chain B residue  202 ILE
Chi-restraints excluded: chain B residue  243 MET
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  436 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 39 optimal weight:    0.0670
   chunk 2 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 36 optimal weight:    0.2980
   chunk 45 optimal weight:    0.2980
   overall best weight:    0.4920

-------------------------------------------------------------------------------
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 = 0.3854 r_free = 0.3854 target = 0.141131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.129661 restraints weight = 8435.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.132685 restraints weight = 4630.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.134721 restraints weight = 2883.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.136117 restraints weight = 1952.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.137102 restraints weight = 1406.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.2395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4046  Z= 0.128
  Angle     :  0.705  13.362   5513  Z= 0.343
  Chirality :  0.044   0.166    659
  Planarity :  0.004   0.030    666
  Dihedral  :  4.860  49.278    540
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.02 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 25.00 %
    Favored  : 72.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.40), residues: 498
  helix:  1.51 (0.29), residues: 365
  sheet:  None (None), residues: 0
  loop : -2.60 (0.51), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 396 
 TYR   0.039   0.002   TYR B 240 
 PHE   0.036   0.001   PHE B 239 
 TRP   0.051   0.002   TRP B 249 
 HIS   0.002   0.001   HIS B 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 4045)
  covalent geometry    : angle       0.70476 ( 5511)
  SS BOND              : bond        0.00301 (    1)
  SS BOND              : angle       1.05014 (    2)
  hydrogen bonds       : bond        0.03332 (  263)
  hydrogen bonds       : angle       4.32815 (  762)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.164 
Fit side-chains
REVERT: B   78 MET cc_start: 0.7645 (tpt) cc_final: 0.7283 (tpp)
REVERT: B   86 CYS cc_start: 0.8478 (m) cc_final: 0.8098 (m)
REVERT: B  113 TYR cc_start: 0.7320 (m-80) cc_final: 0.6778 (m-80)
REVERT: B  295 GLU cc_start: 0.8241 (mp0) cc_final: 0.7864 (tm-30)
REVERT: B  438 MET cc_start: 0.6405 (ttm) cc_final: 0.6169 (ppp)
  outliers start: 12
  outliers final: 10
  residues processed: 108
  average time/residue: 0.0395
  time to fit residues: 5.9773
Evaluate side-chains
  109 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  156 ILE
Chi-restraints excluded: chain B residue  173 ILE
Chi-restraints excluded: chain B residue  202 ILE
Chi-restraints excluded: chain B residue  243 MET
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  436 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 22 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 24 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3840 r_free = 0.3840 target = 0.140066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.128556 restraints weight = 8434.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.131628 restraints weight = 4639.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.133674 restraints weight = 2871.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.135102 restraints weight = 1934.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.136031 restraints weight = 1389.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.3782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.2443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4046  Z= 0.147
  Angle     :  0.728  12.639   5513  Z= 0.358
  Chirality :  0.045   0.163    659
  Planarity :  0.004   0.031    666
  Dihedral  :  4.968  50.983    540
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.22 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 25.00 %
    Favored  : 71.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.40), residues: 498
  helix:  1.40 (0.28), residues: 366
  sheet:  None (None), residues: 0
  loop : -2.66 (0.51), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 148 
 TYR   0.055   0.002   TYR B 240 
 PHE   0.037   0.002   PHE B 239 
 TRP   0.064   0.002   TRP B 249 
 HIS   0.003   0.001   HIS B 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 4045)
  covalent geometry    : angle       0.72734 ( 5511)
  SS BOND              : bond        0.00429 (    1)
  SS BOND              : angle       1.14116 (    2)
  hydrogen bonds       : bond        0.03402 (  263)
  hydrogen bonds       : angle       4.43515 (  762)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 742.14 seconds
wall clock time: 13 minutes 27.90 seconds (807.90 seconds total)