Starting phenix.real_space_refine
on Tue Feb 11 03:35:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p9u_13266/02_2025/7p9u_13266.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p9u_13266/02_2025/7p9u_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_13266/02_2025/7p9u_13266.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p9u_13266/02_2025/7p9u_13266.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p9u_13266/02_2025/7p9u_13266.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p9u_13266/02_2025/7p9u_13266.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 3.05, per 1000 atoms: 0.77
  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: 0.98
  Conformation dependent library (CDL) restraints added in 483.0 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: 0.43
  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: 1.14

  Time building geometry restraints manager: 1.15 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:             1.740
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.830
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.840
-------------------------------------------------------------------------------
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   4045  Z= 0.206
  Angle     :  0.678   7.320   5511  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 : 11.55
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (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
 TRP   0.064   0.003   TRP B 249 
 HIS   0.002   0.001   HIS B 373 
 PHE   0.023   0.002   PHE B 250 
 TYR   0.014   0.002   TYR B 251 
 ARG   0.002   0.000   ARG B 396 

*********************** 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  : 0.403 
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: 0.7918 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.1089
  time to fit residues: 17.5396
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  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 12 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0050
   overall best weight:    0.7194

-------------------------------------------------------------------------------
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 = 0.3852 r_free = 0.3852 target = 0.140659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.129312 restraints weight = 8515.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.132462 restraints weight = 4688.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.134528 restraints weight = 2895.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.1194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4045  Z= 0.204
  Angle     :  0.693   9.208   5511  Z= 0.350
  Chirality :  0.044   0.160    659
  Planarity :  0.004   0.030    666
  Dihedral  :  4.865  44.924    540
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  5.62 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 12.85 %
    Favored  : 85.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.41), residues: 498
  helix:  1.68 (0.29), residues: 356
  sheet:  None (None), residues: 0
  loop : -2.23 (0.55), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 249 
 HIS   0.004   0.001   HIS B 359 
 PHE   0.028   0.002   PHE B 391 
 TYR   0.019   0.002   TYR B 149 
 ARG   0.002   0.000   ARG A 183 

*********************** 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
  108 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.419 
Fit side-chains
REVERT: B   78 MET cc_start: 0.7711 (tpt) cc_final: 0.7190 (tpp)
REVERT: B   86 CYS cc_start: 0.8432 (m) cc_final: 0.7913 (m)
REVERT: B  270 ILE cc_start: 0.9446 (tp) cc_final: 0.9177 (tp)
  outliers start: 8
  outliers final: 7
  residues processed: 101
  average time/residue: 0.1051
  time to fit residues: 14.5761
Evaluate side-chains
  99 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   64 ILE
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
Chi-restraints excluded: chain B residue  366 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 3 optimal weight:    0.5980
   chunk 39 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 40 optimal weight:    0.2980
   chunk 20 optimal weight:    0.0770
   chunk 10 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 22 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.4538

-------------------------------------------------------------------------------
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 = 0.3870 r_free = 0.3870 target = 0.141755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.130501 restraints weight = 8385.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.133638 restraints weight = 4593.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.135613 restraints weight = 2832.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.1554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4045  Z= 0.165
  Angle     :  0.637   7.284   5511  Z= 0.321
  Chirality :  0.042   0.191    659
  Planarity :  0.004   0.029    666
  Dihedral  :  4.844  46.232    540
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  6.22 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 16.82 %
    Favored  : 81.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.41), residues: 498
  helix:  1.73 (0.29), residues: 356
  sheet:  None (None), residues: 0
  loop : -2.52 (0.53), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 249 
 HIS   0.003   0.001   HIS B 359 
 PHE   0.039   0.001   PHE B 239 
 TYR   0.015   0.001   TYR B 149 
 ARG   0.002   0.000   ARG B 478 

*********************** 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: 7
    poor density    : 106
  time to evaluate  : 0.454 
Fit side-chains
REVERT: A  172 LYS cc_start: 0.7214 (pttm) cc_final: 0.6984 (tptp)
REVERT: A  214 LEU cc_start: 0.6505 (mt) cc_final: 0.6078 (mt)
REVERT: B   78 MET cc_start: 0.7719 (tpt) cc_final: 0.7220 (tpp)
REVERT: B   86 CYS cc_start: 0.8452 (m) cc_final: 0.8012 (m)
REVERT: B  379 MET cc_start: 0.7954 (mmt) cc_final: 0.7685 (mmt)
REVERT: B  407 LEU cc_start: 0.8871 (mt) cc_final: 0.8644 (mt)
  outliers start: 7
  outliers final: 4
  residues processed: 106
  average time/residue: 0.1171
  time to fit residues: 16.7017
Evaluate side-chains
  98 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 94
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
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  321 ILE
Chi-restraints excluded: chain B residue  360 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0470
   chunk 4 optimal weight:    4.9990
   chunk 7 optimal weight:    0.8980
   chunk 32 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.6678

-------------------------------------------------------------------------------
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 = 0.3861 r_free = 0.3861 target = 0.141177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.129918 restraints weight = 8336.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.133005 restraints weight = 4586.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.134987 restraints weight = 2837.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4045  Z= 0.191
  Angle     :  0.646   8.909   5511  Z= 0.323
  Chirality :  0.043   0.181    659
  Planarity :  0.004   0.030    666
  Dihedral  :  4.844  47.086    540
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  6.22 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 21.03 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.41), residues: 498
  helix:  1.76 (0.29), residues: 356
  sheet:  None (None), residues: 0
  loop : -2.53 (0.52), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 249 
 HIS   0.003   0.001   HIS B 359 
 PHE   0.038   0.001   PHE B 239 
 TYR   0.018   0.001   TYR B 240 
 ARG   0.001   0.000   ARG B 478 

*********************** 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
  115 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 104
  time to evaluate  : 0.453 
Fit side-chains
REVERT: A  214 LEU cc_start: 0.6582 (mt) cc_final: 0.6156 (mt)
REVERT: B   78 MET cc_start: 0.7736 (tpt) cc_final: 0.7291 (tpp)
REVERT: B   86 CYS cc_start: 0.8460 (m) cc_final: 0.8027 (m)
REVERT: B   99 GLU cc_start: 0.7701 (tt0) cc_final: 0.7453 (tt0)
REVERT: B  113 TYR cc_start: 0.7382 (m-80) cc_final: 0.6906 (m-80)
REVERT: B  379 MET cc_start: 0.7832 (mmt) cc_final: 0.7581 (mmt)
REVERT: B  407 LEU cc_start: 0.8840 (mt) cc_final: 0.8223 (mt)
REVERT: B  490 ILE cc_start: 0.8325 (mm) cc_final: 0.8095 (mm)
  outliers start: 11
  outliers final: 6
  residues processed: 106
  average time/residue: 0.1211
  time to fit residues: 16.9244
Evaluate side-chains
  103 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 97
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 44 optimal weight:    0.6980
   chunk 48 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0980
   chunk 30 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3857 r_free = 0.3857 target = 0.140750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.129289 restraints weight = 8646.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.132423 restraints weight = 4736.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.134437 restraints weight = 2919.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4045  Z= 0.190
  Angle     :  0.651   7.591   5511  Z= 0.325
  Chirality :  0.043   0.175    659
  Planarity :  0.004   0.029    666
  Dihedral  :  4.852  46.992    540
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  5.82 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 22.66 %
    Favored  : 74.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.41), residues: 498
  helix:  1.75 (0.29), residues: 357
  sheet:  None (None), residues: 0
  loop : -2.72 (0.50), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 249 
 HIS   0.003   0.001   HIS B 359 
 PHE   0.039   0.001   PHE B 239 
 TYR   0.013   0.001   TYR B 149 
 ARG   0.002   0.000   ARG B 148 

*********************** 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
  114 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.460 
Fit side-chains
REVERT: A  214 LEU cc_start: 0.6613 (mt) cc_final: 0.6187 (mt)
REVERT: B   78 MET cc_start: 0.7723 (tpt) cc_final: 0.7240 (tpp)
REVERT: B   86 CYS cc_start: 0.8471 (m) cc_final: 0.8034 (m)
REVERT: B   99 GLU cc_start: 0.7687 (tt0) cc_final: 0.7442 (tt0)
REVERT: B  113 TYR cc_start: 0.7426 (m-80) cc_final: 0.6974 (m-80)
REVERT: B  379 MET cc_start: 0.7782 (mmt) cc_final: 0.7569 (mmt)
REVERT: B  407 LEU cc_start: 0.8841 (mt) cc_final: 0.8219 (mt)
REVERT: B  490 ILE cc_start: 0.8338 (mm) cc_final: 0.8115 (mm)
  outliers start: 13
  outliers final: 8
  residues processed: 104
  average time/residue: 0.1213
  time to fit residues: 16.8820
Evaluate side-chains
  104 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
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  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 45 optimal weight:    1.9990
   chunk 25 optimal weight:    0.1980
   chunk 13 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0980
   chunk 0 optimal weight:    6.9990
   chunk 47 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3862 r_free = 0.3862 target = 0.141330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.130043 restraints weight = 8399.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.133119 restraints weight = 4592.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.135098 restraints weight = 2836.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4045  Z= 0.178
  Angle     :  0.636   6.968   5511  Z= 0.319
  Chirality :  0.042   0.172    659
  Planarity :  0.004   0.030    666
  Dihedral  :  4.824  46.496    540
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.22 %
    Favored  : 93.57 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.40), residues: 498
  helix:  1.72 (0.29), residues: 358
  sheet:  None (None), residues: 0
  loop : -2.69 (0.50), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 249 
 HIS   0.003   0.001   HIS B 359 
 PHE   0.040   0.001   PHE B 239 
 TYR   0.014   0.001   TYR B 149 
 ARG   0.001   0.000   ARG B  48 

*********************** 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
  121 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.381 
Fit side-chains
REVERT: A  214 LEU cc_start: 0.6593 (mt) cc_final: 0.6185 (mt)
REVERT: B   78 MET cc_start: 0.7680 (tpt) cc_final: 0.7270 (tpp)
REVERT: B   86 CYS cc_start: 0.8475 (m) cc_final: 0.8057 (m)
REVERT: B  113 TYR cc_start: 0.7395 (m-80) cc_final: 0.6932 (m-80)
REVERT: B  407 LEU cc_start: 0.8831 (mt) cc_final: 0.8521 (mt)
REVERT: B  490 ILE cc_start: 0.8317 (mm) cc_final: 0.8089 (mm)
  outliers start: 15
  outliers final: 9
  residues processed: 111
  average time/residue: 0.1124
  time to fit residues: 16.6902
Evaluate side-chains
  106 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  197 MET
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 34 optimal weight:    8.9990
   chunk 5 optimal weight:    0.0670
   chunk 30 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   overall best weight:    0.7518

-------------------------------------------------------------------------------
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 = 0.3853 r_free = 0.3853 target = 0.140528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.129292 restraints weight = 8534.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.132309 restraints weight = 4706.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.134318 restraints weight = 2907.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.2107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4045  Z= 0.194
  Angle     :  0.691  14.509   5511  Z= 0.334
  Chirality :  0.043   0.166    659
  Planarity :  0.004   0.033    666
  Dihedral  :  4.839  46.563    540
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.63 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 25.00 %
    Favored  : 71.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.40), residues: 498
  helix:  1.70 (0.29), residues: 359
  sheet:  None (None), residues: 0
  loop : -2.89 (0.48), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP B 249 
 HIS   0.003   0.001   HIS B 359 
 PHE   0.039   0.001   PHE B 239 
 TYR   0.012   0.001   TYR B 149 
 ARG   0.005   0.000   ARG B 148 

*********************** 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
  120 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.482 
Fit side-chains
REVERT: A  214 LEU cc_start: 0.6634 (mt) cc_final: 0.6230 (mt)
REVERT: B   78 MET cc_start: 0.7675 (tpt) cc_final: 0.7264 (tpp)
REVERT: B   86 CYS cc_start: 0.8458 (m) cc_final: 0.8066 (m)
REVERT: B   99 GLU cc_start: 0.7709 (tt0) cc_final: 0.7320 (tt0)
REVERT: B  357 MET cc_start: 0.7961 (tpp) cc_final: 0.7583 (tpp)
REVERT: B  407 LEU cc_start: 0.8803 (mt) cc_final: 0.8397 (mt)
REVERT: B  490 ILE cc_start: 0.8352 (mm) cc_final: 0.8140 (mm)
  outliers start: 15
  outliers final: 8
  residues processed: 110
  average time/residue: 0.1219
  time to fit residues: 17.8826
Evaluate side-chains
  105 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  173 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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 12 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 44 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0770
   chunk 24 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 18 optimal weight:    4.9990
   overall best weight:    0.6738

-------------------------------------------------------------------------------
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 = 0.140588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.129264 restraints weight = 8400.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.132284 restraints weight = 4645.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.134333 restraints weight = 2885.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.2204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4045  Z= 0.196
  Angle     :  0.707  13.543   5511  Z= 0.343
  Chirality :  0.044   0.165    659
  Planarity :  0.004   0.031    666
  Dihedral  :  4.839  46.705    540
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.83 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 26.17 %
    Favored  : 70.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.40), residues: 498
  helix:  1.69 (0.29), residues: 357
  sheet:  None (None), residues: 0
  loop : -2.95 (0.47), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP B 249 
 HIS   0.013   0.002   HIS B 359 
 PHE   0.038   0.001   PHE B 239 
 TYR   0.033   0.002   TYR B 240 
 ARG   0.003   0.000   ARG B 148 

*********************** 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
  114 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.462 
Fit side-chains
REVERT: A  214 LEU cc_start: 0.6633 (mt) cc_final: 0.6224 (mt)
REVERT: B   78 MET cc_start: 0.7659 (tpt) cc_final: 0.7284 (tpp)
REVERT: B   86 CYS cc_start: 0.8479 (m) cc_final: 0.8087 (m)
REVERT: B   99 GLU cc_start: 0.7696 (tt0) cc_final: 0.7407 (tt0)
REVERT: B  357 MET cc_start: 0.7962 (tpp) cc_final: 0.7689 (tpp)
REVERT: B  407 LEU cc_start: 0.8766 (mt) cc_final: 0.8326 (mt)
REVERT: B  490 ILE cc_start: 0.8320 (mm) cc_final: 0.8105 (mm)
  outliers start: 13
  outliers final: 10
  residues processed: 105
  average time/residue: 0.1184
  time to fit residues: 16.6570
Evaluate side-chains
  110 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  197 MET
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 25 optimal weight:    0.1980
   chunk 0 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3844 r_free = 0.3844 target = 0.140461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.129215 restraints weight = 8354.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.132245 restraints weight = 4572.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.134263 restraints weight = 2837.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.2317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4045  Z= 0.193
  Angle     :  0.703  13.309   5511  Z= 0.340
  Chirality :  0.044   0.181    659
  Planarity :  0.004   0.030    666
  Dihedral  :  4.832  46.717    540
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.83 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 25.47 %
    Favored  : 71.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.40), residues: 498
  helix:  1.51 (0.29), residues: 363
  sheet:  None (None), residues: 0
  loop : -2.81 (0.48), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP B 249 
 HIS   0.012   0.002   HIS B 359 
 PHE   0.038   0.001   PHE B 239 
 TYR   0.053   0.002   TYR B 240 
 ARG   0.003   0.000   ARG B 148 

*********************** 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
  118 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.432 
Fit side-chains
REVERT: A  214 LEU cc_start: 0.6625 (mt) cc_final: 0.6219 (mt)
REVERT: B   78 MET cc_start: 0.7712 (tpt) cc_final: 0.7319 (tpp)
REVERT: B   86 CYS cc_start: 0.8459 (m) cc_final: 0.8077 (m)
REVERT: B   99 GLU cc_start: 0.7790 (tt0) cc_final: 0.7505 (tt0)
REVERT: B  223 ASP cc_start: 0.6627 (m-30) cc_final: 0.6424 (m-30)
REVERT: B  240 TYR cc_start: 0.7873 (m-80) cc_final: 0.7575 (m-80)
REVERT: B  407 LEU cc_start: 0.8776 (mt) cc_final: 0.8340 (mt)
REVERT: B  490 ILE cc_start: 0.8358 (mm) cc_final: 0.8130 (mm)
  outliers start: 13
  outliers final: 10
  residues processed: 108
  average time/residue: 0.1203
  time to fit residues: 17.4677
Evaluate side-chains
  110 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  197 MET
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 1 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3834 r_free = 0.3834 target = 0.139709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.128375 restraints weight = 8443.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.131359 restraints weight = 4632.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.133410 restraints weight = 2882.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.2400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4045  Z= 0.210
  Angle     :  0.722  13.082   5511  Z= 0.351
  Chirality :  0.045   0.164    659
  Planarity :  0.004   0.029    666
  Dihedral  :  4.865  47.550    540
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.43 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 25.70 %
    Favored  : 71.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.40), residues: 498
  helix:  1.48 (0.29), residues: 365
  sheet:  None (None), residues: 0
  loop : -2.82 (0.48), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.054   0.002   TRP B 249 
 HIS   0.011   0.001   HIS B 359 
 PHE   0.038   0.001   PHE B 239 
 TYR   0.048   0.002   TYR B 240 
 ARG   0.003   0.000   ARG B 148 

********************** 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
  116 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.431 
Fit side-chains
REVERT: A  214 LEU cc_start: 0.6665 (mt) cc_final: 0.6253 (mt)
REVERT: B   78 MET cc_start: 0.7687 (tpt) cc_final: 0.7354 (tpp)
REVERT: B   86 CYS cc_start: 0.8481 (m) cc_final: 0.8099 (m)
REVERT: B   99 GLU cc_start: 0.7794 (tt0) cc_final: 0.7390 (tt0)
REVERT: B  240 TYR cc_start: 0.7888 (m-80) cc_final: 0.7617 (m-80)
REVERT: B  295 GLU cc_start: 0.8222 (mp0) cc_final: 0.7780 (tm-30)
REVERT: B  407 LEU cc_start: 0.8769 (mt) cc_final: 0.8357 (mt)
REVERT: B  490 ILE cc_start: 0.8347 (mm) cc_final: 0.8113 (mm)
  outliers start: 14
  outliers final: 10
  residues processed: 105
  average time/residue: 0.1224
  time to fit residues: 17.3687
Evaluate side-chains
  110 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  197 MET
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  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  436 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 32 optimal weight:    0.2980
   chunk 6 optimal weight:    0.9990
   chunk 44 optimal weight:    4.9990
   chunk 13 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0570
   chunk 15 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.4698

-------------------------------------------------------------------------------
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 = 0.3855 r_free = 0.3855 target = 0.141231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.130053 restraints weight = 8343.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.133083 restraints weight = 4567.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.135115 restraints weight = 2822.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.2470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4045  Z= 0.196
  Angle     :  0.712  13.166   5511  Z= 0.346
  Chirality :  0.044   0.166    659
  Planarity :  0.004   0.030    666
  Dihedral  :  4.894  50.865    540
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.83 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 26.17 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.40), residues: 498
  helix:  1.50 (0.29), residues: 365
  sheet:  None (None), residues: 0
  loop : -2.79 (0.48), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP B 249 
 HIS   0.011   0.002   HIS B 359 
 PHE   0.037   0.001   PHE B 239 
 TYR   0.047   0.002   TYR B 240 
 ARG   0.003   0.000   ARG B 148 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1488.90 seconds
wall clock time: 27 minutes 21.23 seconds (1641.23 seconds total)