Starting phenix.real_space_refine
on Tue Mar  3 16:44:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xja_33223/03_2026/7xja_33223.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xja_33223/03_2026/7xja_33223.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xja_33223/03_2026/7xja_33223.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xja_33223/03_2026/7xja_33223.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xja_33223/03_2026/7xja_33223.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xja_33223/03_2026/7xja_33223.cif"
  }
  resolution = 3.5
  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=   0.000 sd=   0.003
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      44      5.16       5
     C    4808      2.51       5
     N    1184      2.21       5
     O    1240      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 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: 7276
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 472, 3638
          Classifications: {'peptide': 472}
          Link IDs: {'PTRANS': 22, 'TRANS': 449}
    Chain: "B"
      Number of atoms: 3638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 472, 3638
          Classifications: {'peptide': 472}
          Link IDs: {'PTRANS': 22, 'TRANS': 449}
  Time building chain proxies: 1.53, per 1000 atoms: 0.21
  Number of scatterers: 7276
  At special positions: 0
  Unit cell: (80.413, 113.573, 79.584, 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      44     16.00
     O    1240      8.00
     N    1184      7.00
     C    4808      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 229.8 milliseconds
  

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1744

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 3 sheets defined
      81.5% alpha, 1.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 89 through 126
    Processing helix  chain 'A' and resid 129 through 156
      Proline residue:  A 141  - end of helix
    Processing helix  chain 'A' and resid 157 through 160
    Processing helix  chain 'A' and resid 163 through 172
    Processing helix  chain 'A' and resid 176 through 180
    Processing helix  chain 'A' and resid 181 through 198
    Processing helix  chain 'A' and resid 204 through 225
    Processing helix  chain 'A' and resid 226 through 231
      removed outlier: 6.910A  pdb=" N   ILE A 229 " --> pdb=" O   PHE A 226 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   TYR A 230 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 253
      removed outlier: 3.609A  pdb=" N   PHE A 252 " --> pdb=" O   VAL A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 267
      removed outlier: 3.614A  pdb=" N   SER A 267 " --> pdb=" O   ILE A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 296
    Processing helix  chain 'A' and resid 317 through 319
      No H-bonds generated for 'chain 'A' and resid 317 through 319'
    Processing helix  chain 'A' and resid 320 through 352
      removed outlier: 3.514A  pdb=" N   GLN A 352 " --> pdb=" O   VAL A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 362
    Processing helix  chain 'A' and resid 364 through 378
      removed outlier: 3.556A  pdb=" N   ALA A 368 " --> pdb=" O   LEU A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 386
      removed outlier: 3.726A  pdb=" N   GLN A 385 " --> pdb=" O   GLY A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 401
    Processing helix  chain 'A' and resid 419 through 425
    Processing helix  chain 'A' and resid 430 through 450
      removed outlier: 4.142A  pdb=" N   TRP A 444 " --> pdb=" O   LEU A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 481
    Processing helix  chain 'A' and resid 495 through 513
      removed outlier: 3.872A  pdb=" N   TYR A 499 " --> pdb=" O   VAL A 495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 526
      removed outlier: 4.425A  pdb=" N   VAL A 519 " --> pdb=" O   VAL A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 549
    Processing helix  chain 'A' and resid 551 through 560
    Processing helix  chain 'B' and resid 90 through 126
      removed outlier: 3.514A  pdb=" N   LEU B 126 " --> pdb=" O   MET B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 156
      Proline residue:  B 141  - end of helix
    Processing helix  chain 'B' and resid 157 through 160
    Processing helix  chain 'B' and resid 163 through 173
    Processing helix  chain 'B' and resid 176 through 180
    Processing helix  chain 'B' and resid 181 through 198
    Processing helix  chain 'B' and resid 204 through 225
      removed outlier: 3.854A  pdb=" N   LEU B 225 " --> pdb=" O   LYS B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 226 through 231
      removed outlier: 7.085A  pdb=" N   ILE B 229 " --> pdb=" O   PHE B 226 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   TYR B 230 " --> pdb=" O   GLY B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 253
      removed outlier: 3.647A  pdb=" N   PHE B 252 " --> pdb=" O   VAL B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 267
      removed outlier: 3.716A  pdb=" N   VAL B 259 " --> pdb=" O   PRO B 255 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   SER B 267 " --> pdb=" O   ILE B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 296
    Processing helix  chain 'B' and resid 317 through 319
      No H-bonds generated for 'chain 'B' and resid 317 through 319'
    Processing helix  chain 'B' and resid 320 through 352
    Processing helix  chain 'B' and resid 352 through 363
    Processing helix  chain 'B' and resid 364 through 378
      removed outlier: 3.574A  pdb=" N   ALA B 368 " --> pdb=" O   LEU B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 382 through 386
      removed outlier: 3.674A  pdb=" N   GLN B 385 " --> pdb=" O   GLY B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 392 through 401
    Processing helix  chain 'B' and resid 405 through 409
    Processing helix  chain 'B' and resid 419 through 425
    Processing helix  chain 'B' and resid 430 through 450
      removed outlier: 4.073A  pdb=" N   TRP B 444 " --> pdb=" O   LEU B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 481
    Processing helix  chain 'B' and resid 495 through 513
      removed outlier: 3.866A  pdb=" N   TYR B 499 " --> pdb=" O   VAL B 495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 516 through 526
    Processing helix  chain 'B' and resid 530 through 549
    Processing helix  chain 'B' and resid 551 through 560
    Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 271
    Processing sheet with id=AA2, first strand: chain 'A' and resid 485 through 487
    Processing sheet with id=AA3, first strand: chain 'B' and resid 485 through 487

    569 hydrogen bonds defined for protein.
    1635 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: 0.91

  Time building geometry restraints manager: 0.73 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2238
        1.35 -     1.46: 1850
        1.46 -     1.58: 3298
        1.58 -     1.70: 0
        1.70 -     1.82: 74
  Bond restraints: 7460
  Sorted by residual:
  bond pdb=" CA  VAL A 175 "
       pdb=" CB  VAL A 175 "
    ideal  model  delta    sigma   weight residual
    1.530  1.541 -0.011 1.11e-02 8.12e+03 9.56e-01
  bond pdb=" N   PRO B 453 "
       pdb=" CA  PRO B 453 "
    ideal  model  delta    sigma   weight residual
    1.469  1.481 -0.012 1.28e-02 6.10e+03 9.45e-01
  bond pdb=" N   PRO A 453 "
       pdb=" CA  PRO A 453 "
    ideal  model  delta    sigma   weight residual
    1.469  1.481 -0.012 1.28e-02 6.10e+03 9.26e-01
  bond pdb=" CA  VAL B 175 "
       pdb=" CB  VAL B 175 "
    ideal  model  delta    sigma   weight residual
    1.530  1.540 -0.011 1.11e-02 8.12e+03 8.99e-01
  bond pdb=" CB  PRO A 381 "
       pdb=" CG  PRO A 381 "
    ideal  model  delta    sigma   weight residual
    1.492  1.447  0.045 5.00e-02 4.00e+02 8.13e-01
  ... (remaining 7455 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.74: 9958
        1.74 -     3.49: 167
        3.49 -     5.23: 24
        5.23 -     6.97: 7
        6.97 -     8.72: 4
  Bond angle restraints: 10160
  Sorted by residual:
  angle pdb=" CB  MET B 167 "
        pdb=" CG  MET B 167 "
        pdb=" SD  MET B 167 "
      ideal   model   delta    sigma   weight residual
     112.70  103.98    8.72 3.00e+00 1.11e-01 8.44e+00
  angle pdb=" CB  MET A 167 "
        pdb=" CG  MET A 167 "
        pdb=" SD  MET A 167 "
      ideal   model   delta    sigma   weight residual
     112.70  104.08    8.62 3.00e+00 1.11e-01 8.26e+00
  angle pdb=" C   TYR B 230 "
        pdb=" N   GLU B 231 "
        pdb=" CA  GLU B 231 "
      ideal   model   delta    sigma   weight residual
     121.94  116.23    5.71 2.00e+00 2.50e-01 8.16e+00
  angle pdb=" CB  MET A 460 "
        pdb=" CG  MET A 460 "
        pdb=" SD  MET A 460 "
      ideal   model   delta    sigma   weight residual
     112.70  120.99   -8.29 3.00e+00 1.11e-01 7.63e+00
  angle pdb=" CB  MET B 360 "
        pdb=" CG  MET B 360 "
        pdb=" SD  MET B 360 "
      ideal   model   delta    sigma   weight residual
     112.70  120.21   -7.51 3.00e+00 1.11e-01 6.26e+00
  ... (remaining 10155 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.10: 3975
       16.10 -    32.21: 260
       32.21 -    48.31: 70
       48.31 -    64.41: 17
       64.41 -    80.52: 20
  Dihedral angle restraints: 4342
    sinusoidal: 1636
      harmonic: 2706
  Sorted by residual:
  dihedral pdb=" CG  ARG A 558 "
           pdb=" CD  ARG A 558 "
           pdb=" NE  ARG A 558 "
           pdb=" CZ  ARG A 558 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -138.50  -41.50     2      1.50e+01 4.44e-03 9.37e+00
  dihedral pdb=" CG  ARG B 558 "
           pdb=" CD  ARG B 558 "
           pdb=" NE  ARG B 558 "
           pdb=" CZ  ARG B 558 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -138.57  -41.43     2      1.50e+01 4.44e-03 9.34e+00
  dihedral pdb=" CG  ARG A 350 "
           pdb=" CD  ARG A 350 "
           pdb=" NE  ARG A 350 "
           pdb=" CZ  ARG A 350 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -138.90  -41.10     2      1.50e+01 4.44e-03 9.22e+00
  ... (remaining 4339 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 734
       0.029 -    0.057: 286
       0.057 -    0.086: 125
       0.086 -    0.114: 44
       0.114 -    0.143: 11
  Chirality restraints: 1200
  Sorted by residual:
  chirality pdb=" CA  GLU B 231 "
            pdb=" N   GLU B 231 "
            pdb=" C   GLU B 231 "
            pdb=" CB  GLU B 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.10e-01
  chirality pdb=" CA  PHE B 284 "
            pdb=" N   PHE B 284 "
            pdb=" C   PHE B 284 "
            pdb=" CB  PHE B 284 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.52e-01
  chirality pdb=" CA  VAL B 454 "
            pdb=" N   VAL B 454 "
            pdb=" C   VAL B 454 "
            pdb=" CB  VAL B 454 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.19e-01
  ... (remaining 1197 not shown)

  Planarity restraints: 1256
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 444 "   -0.019 2.00e-02 2.50e+03   1.45e-02 5.28e+00
        pdb=" CG  TRP A 444 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 444 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 444 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 444 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 444 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 444 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 444 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 444 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 444 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 444 "    0.012 2.00e-02 2.50e+03   1.25e-02 3.89e+00
        pdb=" CG  TRP B 444 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 444 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 444 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 444 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 444 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 444 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 444 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 444 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 444 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 379 "   -0.026 5.00e-02 4.00e+02   4.00e-02 2.56e+00
        pdb=" N   PRO B 380 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B 380 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 380 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1253 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 271
        2.73 -     3.27: 7852
        3.27 -     3.81: 12578
        3.81 -     4.36: 13994
        4.36 -     4.90: 24526
  Nonbonded interactions: 59221
  Sorted by model distance:
  nonbonded pdb=" O   GLU B 166 "
            pdb=" OG1 THR B 169 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" OE2 GLU A 320 "
            pdb=" OH  TYR A 499 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" OE2 GLU B 320 "
            pdb=" OH  TYR B 499 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   GLU A 166 "
            pdb=" OG1 THR A 169 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" O   ASP A 402 "
            pdb=" NH1 ARG A 471 "
     model   vdw
     2.284 3.120
  ... (remaining 59216 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             1.170
  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:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     7.230
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  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:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7075
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   0.045   7460  Z= 0.137
  Angle     :  0.596   8.715  10160  Z= 0.332
  Chirality :  0.039   0.143   1200
  Planarity :  0.004   0.040   1256
  Dihedral  : 13.731  80.517   2598
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  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:  1.81 (0.28), residues: 940
  helix:  1.78 (0.20), residues: 692
  sheet:  None (None), residues: 0
  loop : -0.40 (0.41), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 277 
 TYR   0.016   0.001   TYR A 140 
 PHE   0.021   0.001   PHE B 147 
 TRP   0.040   0.002   TRP A 444 
 HIS   0.012   0.002   HIS B 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 7460)
  covalent geometry    : angle       0.59650 (10160)
  hydrogen bonds       : bond        0.14270 (  569)
  hydrogen bonds       : angle       5.67719 ( 1635)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 279
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 LEU cc_start: 0.7115 (tt) cc_final: 0.6625 (pt)
REVERT: A  170 ILE cc_start: 0.9021 (mm) cc_final: 0.8767 (mm)
REVERT: A  288 ILE cc_start: 0.7953 (mm) cc_final: 0.7741 (mt)
REVERT: A  309 ARG cc_start: 0.6200 (ttp-170) cc_final: 0.5059 (mmt-90)
REVERT: A  374 ILE cc_start: 0.7585 (tt) cc_final: 0.7118 (mt)
REVERT: A  433 LEU cc_start: 0.7917 (tp) cc_final: 0.7463 (mt)
REVERT: A  515 VAL cc_start: 0.8225 (t) cc_final: 0.7966 (t)
REVERT: B  153 GLN cc_start: 0.7612 (tp40) cc_final: 0.7343 (tm-30)
REVERT: B  309 ARG cc_start: 0.5313 (mtm180) cc_final: 0.4758 (mmt-90)
REVERT: B  320 GLU cc_start: 0.6377 (mt-10) cc_final: 0.5887 (mt-10)
REVERT: B  433 LEU cc_start: 0.8048 (tp) cc_final: 0.7663 (mt)
REVERT: B  477 MET cc_start: 0.7559 (ttm) cc_final: 0.7334 (ttt)
REVERT: B  540 LEU cc_start: 0.8498 (mt) cc_final: 0.8255 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 279
  average time/residue: 0.0793
  time to fit residues: 29.6170
Evaluate side-chains
  181 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 425 ASN
A 542 ASN
A 546 GLN
** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 542 ASN
B 546 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.182586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.151979 restraints weight = 9920.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.155526 restraints weight = 6498.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.157894 restraints weight = 4973.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.159475 restraints weight = 4208.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.160545 restraints weight = 3760.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.3334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7460  Z= 0.162
  Angle     :  0.605   8.117  10160  Z= 0.316
  Chirality :  0.043   0.202   1200
  Planarity :  0.005   0.040   1256
  Dihedral  :  3.626  14.588   1002
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 10.44 %
    Favored  : 86.55 %
  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:  2.33 (0.28), residues: 940
  helix:  2.18 (0.19), residues: 698
  sheet:  None (None), residues: 0
  loop : -0.32 (0.46), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 273 
 TYR   0.016   0.002   TYR B 340 
 PHE   0.021   0.002   PHE A 185 
 TRP   0.022   0.001   TRP A 444 
 HIS   0.007   0.002   HIS A 513 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 7460)
  covalent geometry    : angle       0.60460 (10160)
  hydrogen bonds       : bond        0.04433 (  569)
  hydrogen bonds       : angle       3.87571 ( 1635)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 195
  time to evaluate  : 0.287 
Fit side-chains
REVERT: A  131 LEU cc_start: 0.7669 (tt) cc_final: 0.7203 (pt)
REVERT: A  305 LEU cc_start: 0.7873 (tp) cc_final: 0.7663 (tp)
REVERT: A  309 ARG cc_start: 0.6610 (ttp-170) cc_final: 0.5307 (mmt-90)
REVERT: A  408 ARG cc_start: 0.4888 (mmp-170) cc_final: 0.4366 (tpp-160)
REVERT: B  108 MET cc_start: 0.7600 (mtt) cc_final: 0.7322 (mtp)
REVERT: B  170 ILE cc_start: 0.9087 (mm) cc_final: 0.8878 (mm)
REVERT: B  222 PHE cc_start: 0.6834 (t80) cc_final: 0.5078 (m-80)
REVERT: B  309 ARG cc_start: 0.5625 (mtm180) cc_final: 0.5097 (mmt-90)
REVERT: B  320 GLU cc_start: 0.6387 (mt-10) cc_final: 0.6181 (mt-10)
REVERT: B  408 ARG cc_start: 0.4054 (mmm160) cc_final: 0.3620 (tpp-160)
REVERT: B  433 LEU cc_start: 0.8094 (tp) cc_final: 0.7874 (mt)
REVERT: B  483 ASP cc_start: 0.6424 (t70) cc_final: 0.6187 (t0)
  outliers start: 23
  outliers final: 14
  residues processed: 210
  average time/residue: 0.0736
  time to fit residues: 21.3552
Evaluate side-chains
  170 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 156
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  557 ILE
Chi-restraints excluded: chain B residue   92 ILE
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  215 CYS
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  516 SER
Chi-restraints excluded: chain B residue  555 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 52 optimal weight:    0.7980
   chunk 85 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 46 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 542 ASN
B 425 ASN
B 542 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.176343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.145770 restraints weight = 9833.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.149120 restraints weight = 6500.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.151359 restraints weight = 5030.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.152664 restraints weight = 4301.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.153578 restraints weight = 3912.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.4027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7460  Z= 0.152
  Angle     :  0.577   7.769  10160  Z= 0.300
  Chirality :  0.042   0.166   1200
  Planarity :  0.004   0.040   1256
  Dihedral  :  3.474  13.273   1002
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 13.58 %
    Favored  : 84.07 %
  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:  2.35 (0.28), residues: 940
  helix:  2.21 (0.19), residues: 704
  sheet:  None (None), residues: 0
  loop : -0.47 (0.44), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 290 
 TYR   0.022   0.002   TYR B 134 
 PHE   0.028   0.002   PHE B 289 
 TRP   0.019   0.001   TRP A 444 
 HIS   0.005   0.002   HIS A 513 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 7460)
  covalent geometry    : angle       0.57704 (10160)
  hydrogen bonds       : bond        0.04317 (  569)
  hydrogen bonds       : angle       3.77742 ( 1635)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 169
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 MET cc_start: 0.7692 (mtp) cc_final: 0.7444 (mtp)
REVERT: A  222 PHE cc_start: 0.7115 (t80) cc_final: 0.5012 (m-10)
REVERT: A  305 LEU cc_start: 0.7813 (tp) cc_final: 0.7602 (tp)
REVERT: A  309 ARG cc_start: 0.6630 (ttp-170) cc_final: 0.5264 (mmt-90)
REVERT: A  408 ARG cc_start: 0.5089 (mmp-170) cc_final: 0.4577 (tpp-160)
REVERT: A  439 ILE cc_start: 0.7808 (mm) cc_final: 0.7402 (mt)
REVERT: B  108 MET cc_start: 0.7779 (mtt) cc_final: 0.7477 (mtp)
REVERT: B  222 PHE cc_start: 0.6729 (t80) cc_final: 0.5018 (m-80)
REVERT: B  309 ARG cc_start: 0.5570 (mtm180) cc_final: 0.4875 (mmt-90)
REVERT: B  408 ARG cc_start: 0.4075 (mmm160) cc_final: 0.3603 (tpp-160)
REVERT: B  483 ASP cc_start: 0.6572 (t70) cc_final: 0.6305 (t0)
  outliers start: 18
  outliers final: 13
  residues processed: 181
  average time/residue: 0.0766
  time to fit residues: 19.3194
Evaluate side-chains
  171 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 158
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  516 SER
Chi-restraints excluded: chain A residue  542 ASN
Chi-restraints excluded: chain A residue  557 ILE
Chi-restraints excluded: chain B residue   92 ILE
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  215 CYS
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  516 SER
Chi-restraints excluded: chain B residue  555 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 61 optimal weight:    7.9990
   chunk 79 optimal weight:    0.8980
   chunk 88 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0970
   chunk 93 optimal weight:    0.0570
   chunk 90 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 29 optimal weight:    0.0870
   overall best weight:    0.4276

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

Flipped N/Q/H residues before XYZ refinement:
A 542 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.176326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.145793 restraints weight = 9930.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.149180 restraints weight = 6508.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.151366 restraints weight = 5046.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.152759 restraints weight = 4320.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.153607 restraints weight = 3916.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.4400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7460  Z= 0.123
  Angle     :  0.543   7.900  10160  Z= 0.279
  Chirality :  0.040   0.146   1200
  Planarity :  0.004   0.039   1256
  Dihedral  :  3.373  12.569   1002
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 14.88 %
    Favored  : 83.29 %
  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:  2.54 (0.28), residues: 940
  helix:  2.39 (0.19), residues: 704
  sheet:  None (None), residues: 0
  loop : -0.53 (0.44), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 343 
 TYR   0.020   0.002   TYR A 492 
 PHE   0.023   0.001   PHE A 314 
 TRP   0.012   0.001   TRP A 444 
 HIS   0.006   0.002   HIS B 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 7460)
  covalent geometry    : angle       0.54307 (10160)
  hydrogen bonds       : bond        0.04006 (  569)
  hydrogen bonds       : angle       3.75147 ( 1635)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 167
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 MET cc_start: 0.7673 (mtp) cc_final: 0.7456 (mtp)
REVERT: A  309 ARG cc_start: 0.6638 (ttp-170) cc_final: 0.5225 (mmt-90)
REVERT: A  408 ARG cc_start: 0.5264 (mmp-170) cc_final: 0.4726 (tpp-160)
REVERT: A  439 ILE cc_start: 0.7867 (mm) cc_final: 0.7587 (mt)
REVERT: B  108 MET cc_start: 0.7751 (mtt) cc_final: 0.7515 (mtp)
REVERT: B  222 PHE cc_start: 0.6624 (t80) cc_final: 0.4954 (m-80)
REVERT: B  264 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7004 (mm-30)
REVERT: B  309 ARG cc_start: 0.5561 (mtm180) cc_final: 0.4931 (mmt-90)
REVERT: B  408 ARG cc_start: 0.4085 (mmm160) cc_final: 0.3536 (tpp-160)
REVERT: B  483 ASP cc_start: 0.6581 (t70) cc_final: 0.5935 (m-30)
  outliers start: 14
  outliers final: 10
  residues processed: 177
  average time/residue: 0.0773
  time to fit residues: 18.8057
Evaluate side-chains
  167 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 157
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  516 SER
Chi-restraints excluded: chain A residue  557 ILE
Chi-restraints excluded: chain B residue   92 ILE
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  431 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 74 optimal weight:    0.4980
   chunk 76 optimal weight:    0.6980
   chunk 72 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 82 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.167932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.137171 restraints weight = 9911.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.140620 restraints weight = 6379.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.142794 restraints weight = 4890.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.144321 restraints weight = 4148.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.145057 restraints weight = 3744.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.5116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7460  Z= 0.157
  Angle     :  0.566   6.590  10160  Z= 0.299
  Chirality :  0.042   0.154   1200
  Planarity :  0.005   0.041   1256
  Dihedral  :  3.410  11.837   1002
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 14.23 %
    Favored  : 82.51 %
  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:  2.47 (0.28), residues: 940
  helix:  2.36 (0.19), residues: 706
  sheet:  None (None), residues: 0
  loop : -0.66 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 273 
 TYR   0.027   0.002   TYR B 134 
 PHE   0.018   0.002   PHE A 280 
 TRP   0.011   0.001   TRP B 444 
 HIS   0.005   0.002   HIS A 513 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 7460)
  covalent geometry    : angle       0.56593 (10160)
  hydrogen bonds       : bond        0.04401 (  569)
  hydrogen bonds       : angle       3.74292 ( 1635)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 159
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 MET cc_start: 0.7818 (mtp) cc_final: 0.7609 (mtp)
REVERT: A  309 ARG cc_start: 0.6705 (ttp-170) cc_final: 0.5180 (mmt-90)
REVERT: A  349 MET cc_start: 0.6866 (tpp) cc_final: 0.6249 (ttp)
REVERT: A  408 ARG cc_start: 0.5459 (mmp-170) cc_final: 0.4954 (tpp-160)
REVERT: A  425 ASN cc_start: 0.7779 (t0) cc_final: 0.7480 (m-40)
REVERT: A  460 MET cc_start: 0.7738 (tpp) cc_final: 0.7440 (tpp)
REVERT: B  222 PHE cc_start: 0.6656 (t80) cc_final: 0.4941 (m-80)
REVERT: B  264 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7159 (mm-30)
REVERT: B  309 ARG cc_start: 0.5712 (mtm180) cc_final: 0.4655 (mmt-90)
REVERT: B  408 ARG cc_start: 0.4213 (mmm160) cc_final: 0.3659 (tpp-160)
REVERT: B  483 ASP cc_start: 0.6763 (t70) cc_final: 0.6155 (m-30)
REVERT: B  557 ILE cc_start: 0.8167 (tp) cc_final: 0.7894 (tp)
  outliers start: 25
  outliers final: 19
  residues processed: 176
  average time/residue: 0.0751
  time to fit residues: 18.3221
Evaluate side-chains
  163 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 144
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  516 SER
Chi-restraints excluded: chain A residue  557 ILE
Chi-restraints excluded: chain B residue   92 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  215 CYS
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  516 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 70 optimal weight:    0.8980
   chunk 75 optimal weight:    0.1980
   chunk 17 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9980
   chunk 60 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 92 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0770
   chunk 28 optimal weight:    0.7980
   chunk 64 optimal weight:    0.0970
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.4136

-------------------------------------------------------------------------------
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 = 0.3862 r_free = 0.3862 target = 0.169938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.139437 restraints weight = 9892.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.142730 restraints weight = 6511.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.144965 restraints weight = 5068.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.146336 restraints weight = 4331.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.146838 restraints weight = 3926.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.5292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7460  Z= 0.121
  Angle     :  0.534   6.625  10160  Z= 0.276
  Chirality :  0.040   0.181   1200
  Planarity :  0.004   0.039   1256
  Dihedral  :  3.276  11.560   1002
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 16.19 %
    Favored  : 81.46 %
  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:  2.59 (0.28), residues: 940
  helix:  2.46 (0.19), residues: 706
  sheet:  None (None), residues: 0
  loop : -0.65 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 350 
 TYR   0.017   0.001   TYR A 499 
 PHE   0.030   0.001   PHE A 147 
 TRP   0.013   0.001   TRP A 444 
 HIS   0.004   0.001   HIS A 513 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 7460)
  covalent geometry    : angle       0.53403 (10160)
  hydrogen bonds       : bond        0.03932 (  569)
  hydrogen bonds       : angle       3.71339 ( 1635)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 164
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 MET cc_start: 0.7796 (mtp) cc_final: 0.7586 (mtp)
REVERT: A  309 ARG cc_start: 0.6520 (ttp-170) cc_final: 0.5108 (mmt-90)
REVERT: A  349 MET cc_start: 0.6859 (tpp) cc_final: 0.6239 (ttp)
REVERT: A  408 ARG cc_start: 0.5304 (mmp-170) cc_final: 0.4894 (tpp-160)
REVERT: A  425 ASN cc_start: 0.7700 (t0) cc_final: 0.7449 (m-40)
REVERT: A  460 MET cc_start: 0.7762 (tpp) cc_final: 0.7474 (tpp)
REVERT: B  134 TYR cc_start: 0.7838 (t80) cc_final: 0.7605 (t80)
REVERT: B  222 PHE cc_start: 0.6515 (t80) cc_final: 0.4979 (m-10)
REVERT: B  264 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7098 (mm-30)
REVERT: B  309 ARG cc_start: 0.5591 (mtm180) cc_final: 0.4532 (mmt-90)
REVERT: B  320 GLU cc_start: 0.6816 (mt-10) cc_final: 0.5992 (mt-10)
REVERT: B  348 VAL cc_start: 0.8714 (OUTLIER) cc_final: 0.8266 (m)
REVERT: B  408 ARG cc_start: 0.4205 (mmm160) cc_final: 0.3703 (tpp-160)
REVERT: B  483 ASP cc_start: 0.6710 (t70) cc_final: 0.6208 (m-30)
REVERT: B  557 ILE cc_start: 0.8127 (tp) cc_final: 0.7840 (tp)
  outliers start: 18
  outliers final: 11
  residues processed: 176
  average time/residue: 0.0761
  time to fit residues: 18.5862
Evaluate side-chains
  162 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 150
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  516 SER
Chi-restraints excluded: chain A residue  557 ILE
Chi-restraints excluded: chain B residue   92 ILE
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  231 GLU
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  431 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 13 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 91 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 75 optimal weight:    0.6980
   chunk 61 optimal weight:    0.3980
   chunk 7 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.3825 r_free = 0.3825 target = 0.166727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.136296 restraints weight = 9870.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.139528 restraints weight = 6531.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.141653 restraints weight = 5090.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.142936 restraints weight = 4361.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.143836 restraints weight = 3974.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.5561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7460  Z= 0.133
  Angle     :  0.540   6.129  10160  Z= 0.280
  Chirality :  0.041   0.161   1200
  Planarity :  0.004   0.040   1256
  Dihedral  :  3.291  11.312   1002
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 15.93 %
    Favored  : 81.46 %
  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:  2.68 (0.28), residues: 940
  helix:  2.60 (0.19), residues: 692
  sheet:  None (None), residues: 0
  loop : -0.70 (0.43), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 350 
 TYR   0.018   0.001   TYR B 499 
 PHE   0.020   0.002   PHE A 279 
 TRP   0.010   0.001   TRP A 444 
 HIS   0.004   0.001   HIS A 513 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 7460)
  covalent geometry    : angle       0.53996 (10160)
  hydrogen bonds       : bond        0.04089 (  569)
  hydrogen bonds       : angle       3.69708 ( 1635)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 153
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 ARG cc_start: 0.6546 (ttp-170) cc_final: 0.5037 (mmt-90)
REVERT: A  349 MET cc_start: 0.6896 (tpp) cc_final: 0.6340 (ttp)
REVERT: A  408 ARG cc_start: 0.5455 (mmp-170) cc_final: 0.4774 (tpp-160)
REVERT: A  425 ASN cc_start: 0.7707 (t0) cc_final: 0.7465 (m-40)
REVERT: A  460 MET cc_start: 0.7824 (tpp) cc_final: 0.7545 (tpp)
REVERT: B  222 PHE cc_start: 0.6310 (t80) cc_final: 0.5191 (m-10)
REVERT: B  264 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7130 (mm-30)
REVERT: B  309 ARG cc_start: 0.5751 (mtm180) cc_final: 0.4729 (mmt-90)
REVERT: B  348 VAL cc_start: 0.8698 (t) cc_final: 0.8235 (m)
REVERT: B  408 ARG cc_start: 0.4184 (mmm160) cc_final: 0.3693 (tpp-160)
REVERT: B  483 ASP cc_start: 0.6753 (t70) cc_final: 0.6267 (m-30)
REVERT: B  557 ILE cc_start: 0.8190 (tp) cc_final: 0.7926 (tp)
  outliers start: 20
  outliers final: 13
  residues processed: 169
  average time/residue: 0.0841
  time to fit residues: 19.5761
Evaluate side-chains
  159 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 146
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  557 ILE
Chi-restraints excluded: chain B residue   92 ILE
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  215 CYS
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  515 VAL
Chi-restraints excluded: chain B residue  516 SER
Chi-restraints excluded: chain B residue  555 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 71 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 80 optimal weight:    5.9990
   chunk 88 optimal weight:    5.9990
   chunk 75 optimal weight:    0.7980
   chunk 77 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B 527 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.166606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.135374 restraints weight = 9954.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.138837 restraints weight = 6406.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.141019 restraints weight = 4937.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.142434 restraints weight = 4224.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.143106 restraints weight = 3842.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.5898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7460  Z= 0.143
  Angle     :  0.575   6.992  10160  Z= 0.295
  Chirality :  0.042   0.203   1200
  Planarity :  0.004   0.042   1256
  Dihedral  :  3.335  11.186   1002
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 17.23 %
    Favored  : 80.16 %
  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:  2.62 (0.28), residues: 940
  helix:  2.56 (0.19), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.77 (0.43), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 273 
 TYR   0.027   0.002   TYR B 134 
 PHE   0.022   0.002   PHE A 279 
 TRP   0.011   0.001   TRP A 444 
 HIS   0.004   0.002   HIS A 513 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 7460)
  covalent geometry    : angle       0.57454 (10160)
  hydrogen bonds       : bond        0.04135 (  569)
  hydrogen bonds       : angle       3.75067 ( 1635)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 153
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 ARG cc_start: 0.6613 (ttp-170) cc_final: 0.5179 (mmt-90)
REVERT: A  349 MET cc_start: 0.6981 (tpp) cc_final: 0.6452 (ttp)
REVERT: A  385 GLN cc_start: 0.8207 (pp30) cc_final: 0.7973 (pt0)
REVERT: A  408 ARG cc_start: 0.5611 (mmp-170) cc_final: 0.4891 (tpp-160)
REVERT: A  425 ASN cc_start: 0.7750 (t0) cc_final: 0.7450 (m-40)
REVERT: A  460 MET cc_start: 0.7856 (tpp) cc_final: 0.7592 (tpp)
REVERT: B  108 MET cc_start: 0.7684 (mtp) cc_final: 0.7394 (mtp)
REVERT: B  222 PHE cc_start: 0.6689 (t80) cc_final: 0.5035 (m-80)
REVERT: B  264 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7232 (mm-30)
REVERT: B  309 ARG cc_start: 0.5788 (mtm180) cc_final: 0.4710 (mmt-90)
REVERT: B  348 VAL cc_start: 0.8686 (t) cc_final: 0.8254 (m)
REVERT: B  408 ARG cc_start: 0.4333 (mmm160) cc_final: 0.3781 (tpp-160)
REVERT: B  450 THR cc_start: 0.8262 (m) cc_final: 0.7907 (p)
REVERT: B  483 ASP cc_start: 0.6741 (t70) cc_final: 0.6307 (m-30)
REVERT: B  557 ILE cc_start: 0.8189 (tp) cc_final: 0.7919 (tp)
  outliers start: 20
  outliers final: 16
  residues processed: 168
  average time/residue: 0.0779
  time to fit residues: 17.6938
Evaluate side-chains
  167 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 151
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  557 ILE
Chi-restraints excluded: chain B residue   92 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  215 CYS
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  515 VAL
Chi-restraints excluded: chain B residue  555 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 93 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 11 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9980
   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 = 0.3809 r_free = 0.3809 target = 0.165502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.135109 restraints weight = 9824.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.138516 restraints weight = 6289.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.140730 restraints weight = 4825.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.142118 restraints weight = 4116.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.142852 restraints weight = 3721.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.6160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7460  Z= 0.139
  Angle     :  0.580   8.095  10160  Z= 0.299
  Chirality :  0.042   0.241   1200
  Planarity :  0.004   0.040   1256
  Dihedral  :  3.360  11.008   1002
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 17.49 %
    Favored  : 79.77 %
  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:  2.57 (0.28), residues: 940
  helix:  2.55 (0.19), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.88 (0.43), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 124 
 TYR   0.013   0.001   TYR A 275 
 PHE   0.023   0.002   PHE A 279 
 TRP   0.010   0.001   TRP A 444 
 HIS   0.004   0.001   HIS A 513 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 7460)
  covalent geometry    : angle       0.58003 (10160)
  hydrogen bonds       : bond        0.04133 (  569)
  hydrogen bonds       : angle       3.78851 ( 1635)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 155
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 ARG cc_start: 0.6539 (ttp-170) cc_final: 0.5154 (mmt-90)
REVERT: A  349 MET cc_start: 0.6990 (tpp) cc_final: 0.6485 (ttp)
REVERT: A  385 GLN cc_start: 0.8252 (pp30) cc_final: 0.8026 (pt0)
REVERT: A  408 ARG cc_start: 0.5629 (mmp-170) cc_final: 0.4894 (tpp-160)
REVERT: A  425 ASN cc_start: 0.7779 (t0) cc_final: 0.7476 (m-40)
REVERT: A  460 MET cc_start: 0.7869 (tpp) cc_final: 0.7610 (tpp)
REVERT: B  108 MET cc_start: 0.7714 (mtp) cc_final: 0.7444 (mtp)
REVERT: B  222 PHE cc_start: 0.6800 (t80) cc_final: 0.5140 (m-10)
REVERT: B  264 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7219 (mm-30)
REVERT: B  309 ARG cc_start: 0.5827 (mtm180) cc_final: 0.4728 (mmt-90)
REVERT: B  348 VAL cc_start: 0.8702 (t) cc_final: 0.8263 (m)
REVERT: B  408 ARG cc_start: 0.4386 (mmm160) cc_final: 0.3770 (tpp-160)
REVERT: B  450 THR cc_start: 0.8251 (m) cc_final: 0.7912 (p)
REVERT: B  483 ASP cc_start: 0.6746 (t70) cc_final: 0.6307 (m-30)
REVERT: B  557 ILE cc_start: 0.8105 (tp) cc_final: 0.7834 (tp)
  outliers start: 21
  outliers final: 19
  residues processed: 171
  average time/residue: 0.0836
  time to fit residues: 19.4770
Evaluate side-chains
  167 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 148
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  557 ILE
Chi-restraints excluded: chain B residue   92 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  215 CYS
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  515 VAL
Chi-restraints excluded: chain B residue  516 SER
Chi-restraints excluded: chain B residue  555 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 90 optimal weight:    0.2980
   chunk 16 optimal weight:    0.5980
   chunk 41 optimal weight:    0.8980
   chunk 81 optimal weight:    0.7980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3804 r_free = 0.3804 target = 0.164772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.134579 restraints weight = 9961.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.137816 restraints weight = 6589.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.139882 restraints weight = 5146.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.141241 restraints weight = 4426.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.141911 restraints weight = 4029.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.6340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7460  Z= 0.138
  Angle     :  0.595  11.810  10160  Z= 0.304
  Chirality :  0.042   0.227   1200
  Planarity :  0.004   0.039   1256
  Dihedral  :  3.353  11.332   1002
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 17.62 %
    Favored  : 79.63 %
  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:  2.53 (0.28), residues: 940
  helix:  2.54 (0.19), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.97 (0.42), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 350 
 TYR   0.026   0.002   TYR B 134 
 PHE   0.026   0.002   PHE A 279 
 TRP   0.010   0.001   TRP A 444 
 HIS   0.004   0.001   HIS A 513 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 7460)
  covalent geometry    : angle       0.59540 (10160)
  hydrogen bonds       : bond        0.04104 (  569)
  hydrogen bonds       : angle       3.80500 ( 1635)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 152
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
REVERT: A  309 ARG cc_start: 0.6470 (ttp-170) cc_final: 0.5175 (mmt-90)
REVERT: A  408 ARG cc_start: 0.5562 (mmp-170) cc_final: 0.4538 (tpp-160)
REVERT: A  425 ASN cc_start: 0.7775 (t0) cc_final: 0.7481 (m-40)
REVERT: A  460 MET cc_start: 0.7890 (tpp) cc_final: 0.7624 (tpp)
REVERT: B  108 MET cc_start: 0.7693 (mtp) cc_final: 0.7419 (mtp)
REVERT: B  222 PHE cc_start: 0.6786 (t80) cc_final: 0.5085 (m-10)
REVERT: B  262 SER cc_start: 0.8748 (t) cc_final: 0.8451 (m)
REVERT: B  264 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7142 (mm-30)
REVERT: B  309 ARG cc_start: 0.5851 (mtm180) cc_final: 0.4774 (mmt-90)
REVERT: B  348 VAL cc_start: 0.8700 (t) cc_final: 0.8275 (m)
REVERT: B  408 ARG cc_start: 0.4401 (mmm160) cc_final: 0.4034 (tpm170)
REVERT: B  450 THR cc_start: 0.8258 (m) cc_final: 0.7922 (p)
REVERT: B  483 ASP cc_start: 0.6685 (t70) cc_final: 0.6303 (m-30)
REVERT: B  557 ILE cc_start: 0.8103 (tp) cc_final: 0.7856 (tp)
  outliers start: 21
  outliers final: 18
  residues processed: 170
  average time/residue: 0.0828
  time to fit residues: 19.0932
Evaluate side-chains
  169 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 151
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain B residue   92 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  215 CYS
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  515 VAL
Chi-restraints excluded: chain B residue  516 SER
Chi-restraints excluded: chain B residue  555 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 23 optimal weight:    0.3980
   chunk 17 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   chunk 84 optimal weight:    0.6980
   chunk 54 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9980
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3799 r_free = 0.3799 target = 0.164260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.134002 restraints weight = 10033.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.137151 restraints weight = 6659.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.139221 restraints weight = 5204.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.140030 restraints weight = 4476.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.141226 restraints weight = 4155.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.6412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7460  Z= 0.136
  Angle     :  0.594   9.761  10160  Z= 0.304
  Chirality :  0.042   0.214   1200
  Planarity :  0.004   0.039   1256
  Dihedral  :  3.355  13.278   1002
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 17.62 %
    Favored  : 79.77 %
  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:  2.53 (0.28), residues: 940
  helix:  2.55 (0.19), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.99 (0.42), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 350 
 TYR   0.015   0.001   TYR A 275 
 PHE   0.025   0.001   PHE A 279 
 TRP   0.010   0.001   TRP A 444 
 HIS   0.009   0.002   HIS B 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 7460)
  covalent geometry    : angle       0.59391 (10160)
  hydrogen bonds       : bond        0.04063 (  569)
  hydrogen bonds       : angle       3.82806 ( 1635)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1298.75 seconds
wall clock time: 23 minutes 3.03 seconds (1383.03 seconds total)