Starting phenix.real_space_refine
on Tue Jan 14 10:03:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uyf_42804/01_2025/8uyf_42804.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uyf_42804/01_2025/8uyf_42804.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uyf_42804/01_2025/8uyf_42804.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uyf_42804/01_2025/8uyf_42804.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uyf_42804/01_2025/8uyf_42804.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uyf_42804/01_2025/8uyf_42804.cif"
  }
  resolution = 2.75
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.007 sd=   0.044
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      44      5.16       5
     C    4124      2.51       5
     N    1090      2.21       5
     O    1200      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 6460
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 400, 3231
          Classifications: {'peptide': 400}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 18, 'TRANS': 381}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'TPO:plan-1': 1, 'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "B"
      Number of atoms: 3229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 401, 3229
          Classifications: {'peptide': 401}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 18, 'TRANS': 382}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'TYR:plan': 1, 'TPO:plan-1': 1, 'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 18
  Time building chain proxies: 4.61, per 1000 atoms: 0.71
  Number of scatterers: 6460
  At special positions: 0
  Unit cell: (115.544, 75.952, 76.76, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      44     16.00
     P       2     15.00
     O    1200      8.00
     N    1090      7.00
     C    4124      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.57
  Conformation dependent library (CDL) restraints added in 911.5 milliseconds
  

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1554

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 7 sheets defined
      43.2% alpha, 11.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 120 through 137
    Processing helix  chain 'A' and resid 203 through 215
    Processing helix  chain 'A' and resid 297 through 304
    Processing helix  chain 'A' and resid 307 through 328
      removed outlier: 3.533A  pdb=" N   HIS A 328 " --> pdb=" O   HIS A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 393
    Processing helix  chain 'A' and resid 406 through 420
      removed outlier: 3.750A  pdb=" N   TYR A 417 " --> pdb=" O   GLY A 413 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   GLU A 418 " --> pdb=" O   ALA A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 462
    Processing helix  chain 'A' and resid 471 through 485
    Processing helix  chain 'A' and resid 486 through 490
    Processing helix  chain 'A' and resid 498 through 515
    Processing helix  chain 'A' and resid 542 through 556
      removed outlier: 3.701A  pdb=" N   ARG A 555 " --> pdb=" O   SER A 551 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 574
      removed outlier: 3.779A  pdb=" N   HIS A 572 " --> pdb=" O   ILE A 568 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 137
      removed outlier: 4.242A  pdb=" N   GLY B 126 " --> pdb=" O   ASP B 122 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   ILE B 127 " --> pdb=" O   GLU B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 215
    Processing helix  chain 'B' and resid 231 through 236
      removed outlier: 4.416A  pdb=" N   ASP B 235 " --> pdb=" O   ASN B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 304
    Processing helix  chain 'B' and resid 307 through 328
      removed outlier: 3.556A  pdb=" N   HIS B 328 " --> pdb=" O   HIS B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 361
      removed outlier: 4.542A  pdb=" N   CYS B 360 " --> pdb=" O   ASP B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 393
    Processing helix  chain 'B' and resid 406 through 420
      removed outlier: 3.979A  pdb=" N   TYR B 417 " --> pdb=" O   GLY B 413 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   GLU B 418 " --> pdb=" O   ALA B 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 439 through 443
    Processing helix  chain 'B' and resid 451 through 462
    Processing helix  chain 'B' and resid 471 through 485
    Processing helix  chain 'B' and resid 486 through 491
      removed outlier: 3.738A  pdb=" N   LEU B 490 " --> pdb=" O   PRO B 486 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 498 through 516
    Processing helix  chain 'B' and resid 542 through 555
      removed outlier: 3.773A  pdb=" N   ARG B 555 " --> pdb=" O   SER B 551 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 557 through 574
      removed outlier: 3.630A  pdb=" N   HIS B 572 " --> pdb=" O   ILE B 568 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 160
    Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 160
      removed outlier: 3.597A  pdb=" N   SER A 251 " --> pdb=" O   VAL A 289 " (cutoff:3.500A)
      removed outlier: 7.220A  pdb=" N   LYS A 291 " --> pdb=" O   MET A 249 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   MET A 249 " --> pdb=" O   LYS A 291 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ALA A 254 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 295 through 296
      removed outlier: 3.604A  pdb=" N   CYS A 295 " --> pdb=" O   VAL A 342 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 370 through 372
    Processing sheet with id=AA5, first strand: chain 'B' and resid 165 through 166
      removed outlier: 3.651A  pdb=" N   SER B 251 " --> pdb=" O   VAL B 289 " (cutoff:3.500A)
      removed outlier: 7.249A  pdb=" N   LYS B 291 " --> pdb=" O   MET B 249 " (cutoff:3.500A)
      removed outlier: 7.134A  pdb=" N   MET B 249 " --> pdb=" O   LYS B 291 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 295 through 296
      removed outlier: 3.573A  pdb=" N   CYS B 295 " --> pdb=" O   VAL B 342 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 370 through 372

    290 hydrogen bonds defined for protein.
    831 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.95

  Time building geometry restraints manager: 1.82 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2089
        1.34 -     1.46: 1405
        1.46 -     1.58: 3019
        1.58 -     1.69: 6
        1.69 -     1.81: 68
  Bond restraints: 6587
  Sorted by residual:
  bond pdb=" OG1 TPO B 305 "
       pdb=" P   TPO B 305 "
    ideal  model  delta    sigma   weight residual
    1.717  1.608  0.109 2.00e-02 2.50e+03 2.95e+01
  bond pdb=" OG1 TPO A 305 "
       pdb=" P   TPO A 305 "
    ideal  model  delta    sigma   weight residual
    1.717  1.609  0.108 2.00e-02 2.50e+03 2.92e+01
  bond pdb=" O1P TPO B 305 "
       pdb=" P   TPO B 305 "
    ideal  model  delta    sigma   weight residual
    1.525  1.610 -0.085 2.00e-02 2.50e+03 1.79e+01
  bond pdb=" O2P TPO A 305 "
       pdb=" P   TPO A 305 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.67e+01
  bond pdb=" O3P TPO A 305 "
       pdb=" P   TPO A 305 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.67e+01
  ... (remaining 6582 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.58: 8862
        2.58 -     5.16: 46
        5.16 -     7.74: 3
        7.74 -    10.32: 2
       10.32 -    12.90: 2
  Bond angle restraints: 8915
  Sorted by residual:
  angle pdb=" CB  TPO B 305 "
        pdb=" OG1 TPO B 305 "
        pdb=" P   TPO B 305 "
      ideal   model   delta    sigma   weight residual
     119.31  106.41   12.90 3.00e+00 1.11e-01 1.85e+01
  angle pdb=" CB  TPO A 305 "
        pdb=" OG1 TPO A 305 "
        pdb=" P   TPO A 305 "
      ideal   model   delta    sigma   weight residual
     119.31  107.04   12.27 3.00e+00 1.11e-01 1.67e+01
  angle pdb=" OG1 TPO A 305 "
        pdb=" P   TPO A 305 "
        pdb=" O1P TPO A 305 "
      ideal   model   delta    sigma   weight residual
     100.43  109.64   -9.21 3.00e+00 1.11e-01 9.42e+00
  angle pdb=" OG1 TPO B 305 "
        pdb=" P   TPO B 305 "
        pdb=" O1P TPO B 305 "
      ideal   model   delta    sigma   weight residual
     100.43  109.40   -8.97 3.00e+00 1.11e-01 8.95e+00
  angle pdb=" C   THR A 215 "
        pdb=" N   VAL A 216 "
        pdb=" CA  VAL A 216 "
      ideal   model   delta    sigma   weight residual
     120.33  122.15   -1.82 8.00e-01 1.56e+00 5.16e+00
  ... (remaining 8910 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.76: 3722
       11.76 -    23.53: 232
       23.53 -    35.29: 53
       35.29 -    47.06: 16
       47.06 -    58.82: 10
  Dihedral angle restraints: 4033
    sinusoidal: 1653
      harmonic: 2380
  Sorted by residual:
  dihedral pdb=" CB  ARG B 554 "
           pdb=" CG  ARG B 554 "
           pdb=" CD  ARG B 554 "
           pdb=" NE  ARG B 554 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -116.26   56.26     3      1.50e+01 4.44e-03 9.39e+00
  dihedral pdb=" N   GLU B 376 "
           pdb=" CA  GLU B 376 "
           pdb=" CB  GLU B 376 "
           pdb=" CG  GLU B 376 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -124.69  -55.31     3      1.50e+01 4.44e-03 9.34e+00
  dihedral pdb=" N   LEU B 560 "
           pdb=" CA  LEU B 560 "
           pdb=" CB  LEU B 560 "
           pdb=" CG  LEU B 560 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -114.70   54.70     3      1.50e+01 4.44e-03 9.30e+00
  ... (remaining 4030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 640
       0.028 -    0.055: 235
       0.055 -    0.083: 77
       0.083 -    0.110: 37
       0.110 -    0.138: 12
  Chirality restraints: 1001
  Sorted by residual:
  chirality pdb=" CA  ILE A 450 "
            pdb=" N   ILE A 450 "
            pdb=" C   ILE A 450 "
            pdb=" CB  ILE A 450 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.74e-01
  chirality pdb=" CA  ILE B 450 "
            pdb=" N   ILE B 450 "
            pdb=" C   ILE B 450 "
            pdb=" CB  ILE B 450 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.68e-01
  chirality pdb=" CA  VAL B 172 "
            pdb=" N   VAL B 172 "
            pdb=" C   VAL B 172 "
            pdb=" CB  VAL B 172 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.88e-01
  ... (remaining 998 not shown)

  Planarity restraints: 1131
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 450 "    0.023 5.00e-02 4.00e+02   3.47e-02 1.93e+00
        pdb=" N   PRO B 451 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO B 451 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 451 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 450 "   -0.020 5.00e-02 4.00e+02   3.08e-02 1.52e+00
        pdb=" N   PRO A 451 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A 451 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 451 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 485 "    0.018 5.00e-02 4.00e+02   2.74e-02 1.20e+00
        pdb=" N   PRO A 486 "   -0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO A 486 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 486 "    0.015 5.00e-02 4.00e+02
  ... (remaining 1128 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.82: 1894
        2.82 -     3.34: 5921
        3.34 -     3.86: 10404
        3.86 -     4.38: 12995
        4.38 -     4.90: 21551
  Nonbonded interactions: 52765
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 491 "
            pdb=" O   ASN A 493 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" N   ASP A 379 "
            pdb=" OD1 ASP A 379 "
     model   vdw
     2.322 3.120
  nonbonded pdb=" O   PHE B 452 "
            pdb=" ND2 ASN B 456 "
     model   vdw
     2.328 3.120
  nonbonded pdb=" N   ASP A 423 "
            pdb=" OD1 ASP A 423 "
     model   vdw
     2.336 3.120
  nonbonded pdb=" O   PRO A 389 "
            pdb=" ND2 ASN A 393 "
     model   vdw
     2.346 3.120
  ... (remaining 52760 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and ((resid 120 and (name N or name CA or name C or name O or name CB \ 
 )) or resid 121 through 573 or (resid 574 and (name N or name CA or name C or n \ 
ame O or name CB ))))
  selection = (chain 'B' and (resid 120 through 515 or resid 540 through 574))
}

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 individual isotropic
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:             1.130
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     18.550
  Find NCS groups from input model:        0.250
  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:12.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
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   0.109   6587  Z= 0.181
  Angle     :  0.515  12.902   8915  Z= 0.264
  Chirality :  0.037   0.138   1001
  Planarity :  0.003   0.035   1131
  Dihedral  :  9.080  58.823   2479
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  4.18 %
    Favored  : 94.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.30), residues: 775
  helix:  2.01 (0.29), residues: 317
  sheet: -0.42 (0.48), residues: 123
  loop :  0.10 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 484 
 HIS   0.002   0.001   HIS A 328 
 PHE   0.007   0.001   PHE A 253 
 TYR   0.008   0.001   TYR A 174 
 ARG   0.002   0.000   ARG B 374 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 174
  time to evaluate  : 0.707 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 ASP cc_start: 0.7121 (m-30) cc_final: 0.6886 (m-30)
REVERT: A  178 LEU cc_start: 0.8312 (mt) cc_final: 0.7799 (pp)
REVERT: A  201 GLU cc_start: 0.8231 (mm-30) cc_final: 0.8031 (mm-30)
REVERT: A  215 THR cc_start: 0.9419 (p) cc_final: 0.9182 (p)
REVERT: A  232 ASN cc_start: 0.8509 (m-40) cc_final: 0.8184 (m110)
REVERT: A  282 ARG cc_start: 0.7907 (mtp180) cc_final: 0.7395 (mpp-170)
REVERT: A  384 ARG cc_start: 0.8488 (mtp-110) cc_final: 0.7923 (mtm110)
REVERT: A  395 LYS cc_start: 0.8681 (mttt) cc_final: 0.8441 (mtpm)
REVERT: A  500 ASN cc_start: 0.7923 (t0) cc_final: 0.7403 (t0)
REVERT: A  563 LYS cc_start: 0.8363 (mttt) cc_final: 0.8035 (mptt)
REVERT: A  570 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6865 (mp0)
REVERT: B  133 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7638 (pp20)
REVERT: B  178 LEU cc_start: 0.7388 (mt) cc_final: 0.7133 (pt)
REVERT: B  179 LYS cc_start: 0.7529 (tttt) cc_final: 0.7248 (tppt)
REVERT: B  209 LYS cc_start: 0.8523 (mmtp) cc_final: 0.8293 (mttp)
REVERT: B  264 LYS cc_start: 0.6976 (mttt) cc_final: 0.6739 (mmmt)
REVERT: B  338 ASP cc_start: 0.8435 (t0) cc_final: 0.8168 (t0)
REVERT: B  366 GLN cc_start: 0.8720 (mt0) cc_final: 0.8508 (pt0)
REVERT: B  379 ASP cc_start: 0.8282 (p0) cc_final: 0.8052 (OUTLIER)
REVERT: B  558 LEU cc_start: 0.8735 (tp) cc_final: 0.8521 (tm)
REVERT: B  559 HIS cc_start: 0.6704 (t70) cc_final: 0.6496 (t70)
REVERT: B  563 LYS cc_start: 0.8743 (mtpt) cc_final: 0.8408 (mtpp)
  outliers start: 8
  outliers final: 2
  residues processed: 179
  average time/residue: 1.2487
  time to fit residues: 233.7703
Evaluate side-chains
  134 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 133
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  496 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 60 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   chunk 40 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 62 optimal weight:    5.9990
   chunk 24 optimal weight:    0.0980
   chunk 38 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9990
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
B 197 ASN
B 339 ASN
B 378 GLN
B 467 ASN
B 504 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.118987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.105550 restraints weight = 9769.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 2.28
r_work: 0.3288 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.1870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6587  Z= 0.181
  Angle     :  0.521   4.829   8915  Z= 0.275
  Chirality :  0.040   0.141   1001
  Planarity :  0.004   0.034   1131
  Dihedral  :  3.990  38.448    870
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 11.44 %
    Favored  : 85.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.30), residues: 775
  helix:  2.23 (0.28), residues: 328
  sheet: -0.31 (0.46), residues: 124
  loop :  0.22 (0.33), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 505 
 HIS   0.003   0.001   HIS B 559 
 PHE   0.012   0.001   PHE A 452 
 TYR   0.016   0.001   TYR A 494 
 ARG   0.005   0.001   ARG A 248 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 138
  time to evaluate  : 0.726 
Fit side-chains
REVERT: A  178 LEU cc_start: 0.8071 (mt) cc_final: 0.7570 (pp)
REVERT: A  237 LYS cc_start: 0.8574 (ptpt) cc_final: 0.8293 (ptpp)
REVERT: A  282 ARG cc_start: 0.8122 (mtp180) cc_final: 0.7438 (mtt90)
REVERT: A  384 ARG cc_start: 0.8813 (mtp-110) cc_final: 0.8275 (mtm110)
REVERT: A  395 LYS cc_start: 0.8865 (mttt) cc_final: 0.8599 (mtpp)
REVERT: A  563 LYS cc_start: 0.8454 (mttt) cc_final: 0.8078 (mmtm)
REVERT: B  133 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7722 (pp20)
REVERT: B  174 TYR cc_start: 0.8941 (OUTLIER) cc_final: 0.8167 (m-80)
REVERT: B  178 LEU cc_start: 0.7370 (mt) cc_final: 0.7143 (pt)
REVERT: B  179 LYS cc_start: 0.7765 (tttt) cc_final: 0.7486 (tppt)
REVERT: B  209 LYS cc_start: 0.8693 (mmtp) cc_final: 0.8469 (mtmm)
REVERT: B  264 LYS cc_start: 0.7200 (mttt) cc_final: 0.6929 (mmmt)
REVERT: B  284 MET cc_start: 0.8484 (tpp) cc_final: 0.7855 (tpp)
REVERT: B  338 ASP cc_start: 0.8689 (t0) cc_final: 0.8376 (t0)
REVERT: B  366 GLN cc_start: 0.8767 (mt0) cc_final: 0.8231 (pt0)
REVERT: B  563 LYS cc_start: 0.8832 (mtpt) cc_final: 0.8619 (mtpp)
  outliers start: 19
  outliers final: 10
  residues processed: 150
  average time/residue: 1.2036
  time to fit residues: 189.5201
Evaluate side-chains
  129 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  504 GLN
Chi-restraints excluded: chain A residue  510 SER
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  379 ASP
Chi-restraints excluded: chain B residue  471 ASP
Chi-restraints excluded: chain B residue  488 SER
Chi-restraints excluded: chain B residue  515 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 71 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 54 optimal weight:    7.9990
   chunk 74 optimal weight:    0.0570
   chunk 38 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.9904

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

Flipped N/Q/H residues before XYZ refinement:
A 229 ASN
B 197 ASN
B 339 ASN
B 378 GLN
B 504 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.119436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.105702 restraints weight = 9689.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 2.33
r_work: 0.3282 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3141 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6587  Z= 0.177
  Angle     :  0.486   5.898   8915  Z= 0.253
  Chirality :  0.039   0.141   1001
  Planarity :  0.003   0.033   1131
  Dihedral  :  4.006  37.996    870
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 13.53 %
    Favored  : 84.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.30), residues: 775
  helix:  2.33 (0.28), residues: 323
  sheet: -0.15 (0.47), residues: 117
  loop :  0.10 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 505 
 HIS   0.002   0.001   HIS A 572 
 PHE   0.010   0.001   PHE A 253 
 TYR   0.020   0.001   TYR A 494 
 ARG   0.005   0.000   ARG A 248 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 0.910 
Fit side-chains
REVERT: A  178 LEU cc_start: 0.7980 (mt) cc_final: 0.7486 (pp)
REVERT: A  237 LYS cc_start: 0.8608 (ptpt) cc_final: 0.8334 (ptpp)
REVERT: A  282 ARG cc_start: 0.8162 (mtp180) cc_final: 0.7558 (mpt90)
REVERT: A  384 ARG cc_start: 0.8853 (mtp-110) cc_final: 0.8270 (mtm110)
REVERT: A  395 LYS cc_start: 0.8808 (mttt) cc_final: 0.8573 (mtpm)
REVERT: A  431 MET cc_start: 0.5044 (OUTLIER) cc_final: 0.4822 (ttt)
REVERT: A  440 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7087 (mp0)
REVERT: A  563 LYS cc_start: 0.8510 (mttt) cc_final: 0.8101 (mmtm)
REVERT: B  178 LEU cc_start: 0.7352 (mt) cc_final: 0.7149 (pt)
REVERT: B  179 LYS cc_start: 0.7682 (tttt) cc_final: 0.7275 (tppt)
REVERT: B  209 LYS cc_start: 0.8702 (mmtp) cc_final: 0.8395 (mtmm)
REVERT: B  264 LYS cc_start: 0.7179 (mttt) cc_final: 0.6946 (mmmt)
REVERT: B  284 MET cc_start: 0.8505 (tpp) cc_final: 0.7866 (tpp)
REVERT: B  338 ASP cc_start: 0.8709 (t0) cc_final: 0.8352 (t0)
REVERT: B  366 GLN cc_start: 0.8814 (mt0) cc_final: 0.8493 (pt0)
REVERT: B  563 LYS cc_start: 0.8868 (mtpt) cc_final: 0.8653 (mtpp)
  outliers start: 15
  outliers final: 7
  residues processed: 136
  average time/residue: 1.3782
  time to fit residues: 196.0658
Evaluate side-chains
  125 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 117
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  229 ASN
Chi-restraints excluded: chain A residue  267 TYR
Chi-restraints excluded: chain A residue  379 ASP
Chi-restraints excluded: chain A residue  431 MET
Chi-restraints excluded: chain A residue  504 GLN
Chi-restraints excluded: chain B residue  488 SER
Chi-restraints excluded: chain B residue  515 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 24 optimal weight:    0.2980
   chunk 73 optimal weight:    2.9990
   chunk 68 optimal weight:    6.9990
   chunk 37 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 42 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 78 optimal weight:    0.8980
   chunk 9 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
B 197 ASN
B 339 ASN
B 378 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.118826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.105209 restraints weight = 9838.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 2.31
r_work: 0.3277 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          0.2284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6587  Z= 0.219
  Angle     :  0.512  10.574   8915  Z= 0.262
  Chirality :  0.039   0.139   1001
  Planarity :  0.004   0.035   1131
  Dihedral  :  3.809  14.814    868
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 12.97 %
    Favored  : 83.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.30), residues: 775
  helix:  2.35 (0.28), residues: 323
  sheet: -0.12 (0.48), residues: 117
  loop : -0.01 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 505 
 HIS   0.002   0.001   HIS A 328 
 PHE   0.011   0.001   PHE A 253 
 TYR   0.018   0.001   TYR A 494 
 ARG   0.006   0.000   ARG A 248 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 118
  time to evaluate  : 0.755 
Fit side-chains
REVERT: A  178 LEU cc_start: 0.7934 (mt) cc_final: 0.7501 (pp)
REVERT: A  282 ARG cc_start: 0.8170 (mtp180) cc_final: 0.7567 (mpt90)
REVERT: A  379 ASP cc_start: 0.8261 (p0) cc_final: 0.7916 (p0)
REVERT: A  384 ARG cc_start: 0.8871 (mtp-110) cc_final: 0.8434 (mtm110)
REVERT: A  395 LYS cc_start: 0.8844 (mttt) cc_final: 0.8604 (mtpm)
REVERT: A  440 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7025 (mp0)
REVERT: A  543 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8192 (tm)
REVERT: A  563 LYS cc_start: 0.8523 (mttt) cc_final: 0.8123 (mmtm)
REVERT: B  174 TYR cc_start: 0.8942 (OUTLIER) cc_final: 0.8351 (m-80)
REVERT: B  178 LEU cc_start: 0.7337 (mt) cc_final: 0.7134 (pt)
REVERT: B  179 LYS cc_start: 0.7678 (tttt) cc_final: 0.7334 (tppt)
REVERT: B  213 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7200 (mtp85)
REVERT: B  264 LYS cc_start: 0.7148 (mttt) cc_final: 0.6922 (mmmt)
REVERT: B  338 ASP cc_start: 0.8682 (t0) cc_final: 0.8320 (t0)
REVERT: B  366 GLN cc_start: 0.8902 (mt0) cc_final: 0.8343 (pt0)
REVERT: B  377 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7484 (t0)
REVERT: B  563 LYS cc_start: 0.8865 (mtpt) cc_final: 0.8591 (mtpp)
  outliers start: 24
  outliers final: 11
  residues processed: 132
  average time/residue: 1.3271
  time to fit residues: 183.4473
Evaluate side-chains
  127 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain A residue  195 MET
Chi-restraints excluded: chain A residue  267 TYR
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  495 THR
Chi-restraints excluded: chain A residue  504 GLN
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  213 ARG
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  377 ASP
Chi-restraints excluded: chain B residue  488 SER
Chi-restraints excluded: chain B residue  515 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 57 optimal weight:    5.9990
   chunk 33 optimal weight:    0.6980
   chunk 15 optimal weight:    5.9990
   chunk 59 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
B 197 ASN
B 339 ASN
B 378 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.118144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.104814 restraints weight = 9892.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 2.27
r_work: 0.3270 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.2362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6587  Z= 0.228
  Angle     :  0.503   8.538   8915  Z= 0.259
  Chirality :  0.039   0.139   1001
  Planarity :  0.003   0.034   1131
  Dihedral  :  3.849  15.004    868
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 13.39 %
    Favored  : 83.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.30), residues: 775
  helix:  2.37 (0.28), residues: 323
  sheet: -0.02 (0.48), residues: 117
  loop : -0.09 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 505 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.012   0.001   PHE A 452 
 TYR   0.018   0.001   TYR A 494 
 ARG   0.006   0.000   ARG A 248 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 117
  time to evaluate  : 0.769 
Fit side-chains
REVERT: A  178 LEU cc_start: 0.7965 (mt) cc_final: 0.7549 (pp)
REVERT: A  261 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.6820 (mm-40)
REVERT: A  282 ARG cc_start: 0.8177 (mtp180) cc_final: 0.7560 (mpt90)
REVERT: A  384 ARG cc_start: 0.8881 (mtp-110) cc_final: 0.8333 (mtm110)
REVERT: A  395 LYS cc_start: 0.8836 (mttt) cc_final: 0.8594 (mtpm)
REVERT: A  439 LYS cc_start: 0.7931 (mttt) cc_final: 0.7684 (mtpt)
REVERT: A  440 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7042 (mp0)
REVERT: A  543 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8222 (tm)
REVERT: A  563 LYS cc_start: 0.8523 (mttt) cc_final: 0.8124 (mmtm)
REVERT: B  174 TYR cc_start: 0.8943 (OUTLIER) cc_final: 0.8310 (m-80)
REVERT: B  178 LEU cc_start: 0.7314 (mt) cc_final: 0.7113 (pt)
REVERT: B  179 LYS cc_start: 0.7656 (tttt) cc_final: 0.7303 (tppt)
REVERT: B  213 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7164 (mtp85)
REVERT: B  264 LYS cc_start: 0.7180 (mttt) cc_final: 0.6969 (mmmt)
REVERT: B  284 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.7820 (tpp)
REVERT: B  338 ASP cc_start: 0.8684 (t0) cc_final: 0.8303 (t0)
REVERT: B  366 GLN cc_start: 0.8931 (mt0) cc_final: 0.8507 (pt0)
REVERT: B  441 GLU cc_start: 0.7954 (pm20) cc_final: 0.7730 (pm20)
REVERT: B  563 LYS cc_start: 0.8885 (mtpt) cc_final: 0.8614 (mtpp)
  outliers start: 24
  outliers final: 12
  residues processed: 132
  average time/residue: 1.2984
  time to fit residues: 179.5320
Evaluate side-chains
  131 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain A residue  195 MET
Chi-restraints excluded: chain A residue  261 GLN
Chi-restraints excluded: chain A residue  267 TYR
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  495 THR
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  504 GLN
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  213 ARG
Chi-restraints excluded: chain B residue  284 MET
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  488 SER
Chi-restraints excluded: chain B residue  515 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    1.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 229 ASN
B 197 ASN
B 339 ASN
B 569 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.118621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.105322 restraints weight = 9839.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 2.27
r_work: 0.3278 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3141 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.2459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6587  Z= 0.192
  Angle     :  0.520  15.778   8915  Z= 0.260
  Chirality :  0.039   0.161   1001
  Planarity :  0.003   0.033   1131
  Dihedral  :  3.789  15.395    868
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 14.92 %
    Favored  : 82.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.30), residues: 775
  helix:  2.42 (0.28), residues: 323
  sheet:  0.01 (0.48), residues: 117
  loop : -0.10 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 129 
 HIS   0.002   0.001   HIS A 572 
 PHE   0.011   0.001   PHE A 253 
 TYR   0.020   0.001   TYR A 494 
 ARG   0.006   0.000   ARG A 248 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 0.738 
Fit side-chains
   revert: symmetry clash
REVERT: A  178 LEU cc_start: 0.7953 (mt) cc_final: 0.7513 (pp)
REVERT: A  235 ASP cc_start: 0.8171 (m-30) cc_final: 0.7922 (m-30)
REVERT: A  237 LYS cc_start: 0.8615 (ptpt) cc_final: 0.8316 (ptpp)
REVERT: A  261 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.6774 (mm-40)
REVERT: A  282 ARG cc_start: 0.8171 (mtp180) cc_final: 0.7460 (mtt90)
REVERT: A  395 LYS cc_start: 0.8830 (mttt) cc_final: 0.8597 (mtpm)
REVERT: A  439 LYS cc_start: 0.7908 (mttt) cc_final: 0.7666 (mtpt)
REVERT: A  440 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7013 (mp0)
REVERT: A  504 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7900 (mp10)
REVERT: A  543 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8217 (tm)
REVERT: A  563 LYS cc_start: 0.8526 (mttt) cc_final: 0.8126 (mmtm)
REVERT: B  174 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.8274 (m-80)
REVERT: B  178 LEU cc_start: 0.7407 (mt) cc_final: 0.7169 (pt)
REVERT: B  179 LYS cc_start: 0.7583 (tttt) cc_final: 0.7226 (tppt)
REVERT: B  264 LYS cc_start: 0.7175 (mttt) cc_final: 0.6949 (mmmt)
REVERT: B  284 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7813 (tpp)
REVERT: B  338 ASP cc_start: 0.8683 (t0) cc_final: 0.8305 (t0)
REVERT: B  366 GLN cc_start: 0.8939 (mt0) cc_final: 0.8360 (pt0)
REVERT: B  563 LYS cc_start: 0.8875 (mtpt) cc_final: 0.8603 (mtpp)
  outliers start: 20
  outliers final: 12
  residues processed: 131
  average time/residue: 1.3023
  time to fit residues: 178.4939
Evaluate side-chains
  130 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain A residue  195 MET
Chi-restraints excluded: chain A residue  229 ASN
Chi-restraints excluded: chain A residue  261 GLN
Chi-restraints excluded: chain A residue  267 TYR
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  504 GLN
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  235 ASP
Chi-restraints excluded: chain B residue  284 MET
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  488 SER
Chi-restraints excluded: chain B residue  569 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 12 optimal weight:    0.0980
   chunk 72 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 229 ASN
B 197 ASN
B 378 GLN
B 569 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.119416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.106018 restraints weight = 9866.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 2.28
r_work: 0.3289 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3153 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.2556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6587  Z= 0.158
  Angle     :  0.523  16.825   8915  Z= 0.259
  Chirality :  0.039   0.140   1001
  Planarity :  0.003   0.032   1131
  Dihedral  :  3.729  15.216    868
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 16.18 %
    Favored  : 81.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.30), residues: 775
  helix:  2.47 (0.29), residues: 323
  sheet: -0.01 (0.47), residues: 117
  loop : -0.04 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 129 
 HIS   0.002   0.001   HIS A 572 
 PHE   0.010   0.001   PHE A 253 
 TYR   0.021   0.001   TYR A 494 
 ARG   0.006   0.000   ARG A 248 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.744 
Fit side-chains
REVERT: A  178 LEU cc_start: 0.7927 (mt) cc_final: 0.7466 (pp)
REVERT: A  235 ASP cc_start: 0.8146 (m-30) cc_final: 0.7893 (m-30)
REVERT: A  237 LYS cc_start: 0.8594 (ptpt) cc_final: 0.8292 (ptpp)
REVERT: A  282 ARG cc_start: 0.8155 (mtp180) cc_final: 0.7456 (mtt90)
REVERT: A  395 LYS cc_start: 0.8825 (mttt) cc_final: 0.8586 (mtpm)
REVERT: A  440 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7043 (mp0)
REVERT: A  543 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8222 (tm)
REVERT: A  563 LYS cc_start: 0.8506 (mttt) cc_final: 0.8101 (mmtm)
REVERT: B  174 TYR cc_start: 0.8888 (OUTLIER) cc_final: 0.8242 (m-80)
REVERT: B  178 LEU cc_start: 0.7410 (mt) cc_final: 0.7171 (pt)
REVERT: B  179 LYS cc_start: 0.7493 (tttt) cc_final: 0.7144 (tppt)
REVERT: B  264 LYS cc_start: 0.7172 (mttt) cc_final: 0.6956 (mmmt)
REVERT: B  284 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.7855 (tpp)
REVERT: B  338 ASP cc_start: 0.8666 (t0) cc_final: 0.8270 (t0)
REVERT: B  366 GLN cc_start: 0.8935 (mt0) cc_final: 0.8367 (pt0)
REVERT: B  441 GLU cc_start: 0.7946 (pm20) cc_final: 0.7704 (pm20)
REVERT: B  563 LYS cc_start: 0.8876 (mtpt) cc_final: 0.8603 (mtpp)
  outliers start: 17
  outliers final: 6
  residues processed: 126
  average time/residue: 1.3389
  time to fit residues: 176.5834
Evaluate side-chains
  123 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 114
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASN
Chi-restraints excluded: chain A residue  267 TYR
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  504 GLN
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  284 MET
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  488 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 73 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 79 optimal weight:    4.9990
   chunk 44 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 229 ASN
B 197 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.119235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.105858 restraints weight = 9809.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 2.28
r_work: 0.3284 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3150 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.2588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6587  Z= 0.175
  Angle     :  0.527  17.309   8915  Z= 0.261
  Chirality :  0.039   0.139   1001
  Planarity :  0.003   0.033   1131
  Dihedral  :  3.722  15.203    868
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 16.60 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.30), residues: 775
  helix:  2.52 (0.28), residues: 323
  sheet:  0.00 (0.47), residues: 117
  loop : -0.05 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 129 
 HIS   0.002   0.001   HIS A 328 
 PHE   0.011   0.001   PHE A 253 
 TYR   0.020   0.001   TYR A 494 
 ARG   0.007   0.000   ARG A 248 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 0.803 
Fit side-chains
REVERT: A  178 LEU cc_start: 0.7875 (mt) cc_final: 0.7427 (pp)
REVERT: A  235 ASP cc_start: 0.8135 (m-30) cc_final: 0.7912 (m-30)
REVERT: A  282 ARG cc_start: 0.8160 (mtp180) cc_final: 0.7426 (mtt90)
REVERT: A  395 LYS cc_start: 0.8826 (mttt) cc_final: 0.8586 (mtpm)
REVERT: A  440 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7048 (mp0)
REVERT: A  543 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8245 (tm)
REVERT: A  563 LYS cc_start: 0.8495 (mttt) cc_final: 0.8086 (mmtm)
REVERT: B  174 TYR cc_start: 0.8901 (OUTLIER) cc_final: 0.8252 (m-80)
REVERT: B  178 LEU cc_start: 0.7437 (mt) cc_final: 0.7189 (pt)
REVERT: B  179 LYS cc_start: 0.7499 (tttt) cc_final: 0.7157 (tppt)
REVERT: B  264 LYS cc_start: 0.7158 (mttt) cc_final: 0.6947 (mmmt)
REVERT: B  284 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7839 (tpp)
REVERT: B  338 ASP cc_start: 0.8682 (t0) cc_final: 0.8280 (t0)
REVERT: B  366 GLN cc_start: 0.8924 (mt0) cc_final: 0.8525 (pt0)
REVERT: B  377 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7350 (t70)
REVERT: B  441 GLU cc_start: 0.7914 (pm20) cc_final: 0.7657 (pm20)
REVERT: B  563 LYS cc_start: 0.8863 (mtpt) cc_final: 0.8583 (mtpp)
  outliers start: 16
  outliers final: 8
  residues processed: 125
  average time/residue: 1.3046
  time to fit residues: 171.2448
Evaluate side-chains
  123 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 MET
Chi-restraints excluded: chain A residue  229 ASN
Chi-restraints excluded: chain A residue  267 TYR
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  504 GLN
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  284 MET
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  377 ASP
Chi-restraints excluded: chain B residue  488 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 46 optimal weight:    7.9990
   chunk 4 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 74 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
A 226 ASN
A 229 ASN
B 197 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.117635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.104320 restraints weight = 9951.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 2.28
r_work: 0.3260 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3123 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6587  Z= 0.253
  Angle     :  0.566  17.535   8915  Z= 0.280
  Chirality :  0.040   0.138   1001
  Planarity :  0.004   0.035   1131
  Dihedral  :  3.833  15.178    868
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 17.02 %
    Favored  : 80.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.30), residues: 775
  helix:  2.40 (0.29), residues: 323
  sheet:  0.04 (0.48), residues: 117
  loop : -0.14 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 129 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.012   0.001   PHE A 253 
 TYR   0.018   0.001   TYR A 494 
 ARG   0.007   0.001   ARG A 248 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.790 
Fit side-chains
REVERT: A  178 LEU cc_start: 0.7913 (mt) cc_final: 0.7527 (pp)
REVERT: A  235 ASP cc_start: 0.8171 (m-30) cc_final: 0.7944 (m-30)
REVERT: A  282 ARG cc_start: 0.8191 (mtp180) cc_final: 0.7468 (mtt90)
REVERT: A  395 LYS cc_start: 0.8845 (mttt) cc_final: 0.8610 (mtpm)
REVERT: A  439 LYS cc_start: 0.7956 (mttt) cc_final: 0.7704 (mtpt)
REVERT: A  440 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7050 (mp0)
REVERT: A  543 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8255 (tm)
REVERT: A  563 LYS cc_start: 0.8514 (mttt) cc_final: 0.8112 (mmtm)
REVERT: B  174 TYR cc_start: 0.8946 (OUTLIER) cc_final: 0.8308 (m-80)
REVERT: B  178 LEU cc_start: 0.7424 (mt) cc_final: 0.7187 (pt)
REVERT: B  179 LYS cc_start: 0.7622 (tttt) cc_final: 0.7259 (tppt)
REVERT: B  264 LYS cc_start: 0.7194 (mttt) cc_final: 0.6977 (mmmt)
REVERT: B  338 ASP cc_start: 0.8680 (t0) cc_final: 0.8269 (t0)
REVERT: B  366 GLN cc_start: 0.8966 (mt0) cc_final: 0.8381 (pt0)
REVERT: B  377 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7403 (t70)
REVERT: B  563 LYS cc_start: 0.8885 (mtpt) cc_final: 0.8609 (mtpp)
  outliers start: 16
  outliers final: 11
  residues processed: 121
  average time/residue: 1.3401
  time to fit residues: 170.0827
Evaluate side-chains
  124 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 MET
Chi-restraints excluded: chain A residue  229 ASN
Chi-restraints excluded: chain A residue  267 TYR
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  495 THR
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  504 GLN
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  377 ASP
Chi-restraints excluded: chain B residue  488 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 73 optimal weight:    0.0370
   chunk 17 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0670
   chunk 78 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 32 optimal weight:    3.9990
   chunk 68 optimal weight:    4.9990
   chunk 65 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
A 226 ASN
A 229 ASN
B 197 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.119935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.106630 restraints weight = 10000.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 2.30
r_work: 0.3295 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3159 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.2692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   6587  Z= 0.148
  Angle     :  0.548  17.068   8915  Z= 0.271
  Chirality :  0.039   0.141   1001
  Planarity :  0.003   0.032   1131
  Dihedral  :  3.671  15.094    868
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 17.57 %
    Favored  : 80.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.30), residues: 775
  helix:  2.48 (0.29), residues: 330
  sheet:  0.04 (0.47), residues: 117
  loop : -0.00 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 129 
 HIS   0.001   0.000   HIS B 328 
 PHE   0.010   0.001   PHE A 253 
 TYR   0.020   0.001   TYR A 494 
 ARG   0.007   0.000   ARG A 248 

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 114
  time to evaluate  : 0.746 
Fit side-chains
REVERT: A  178 LEU cc_start: 0.7835 (mt) cc_final: 0.7385 (pp)
REVERT: A  235 ASP cc_start: 0.8135 (m-30) cc_final: 0.7922 (m-30)
REVERT: A  282 ARG cc_start: 0.8154 (mtp180) cc_final: 0.7360 (mtt90)
REVERT: A  384 ARG cc_start: 0.8666 (mtm-85) cc_final: 0.8290 (mtm110)
REVERT: A  395 LYS cc_start: 0.8819 (mttt) cc_final: 0.8585 (mtpm)
REVERT: A  440 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7043 (mp0)
REVERT: A  504 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7918 (mp10)
REVERT: A  543 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8229 (tm)
REVERT: A  563 LYS cc_start: 0.8477 (mttt) cc_final: 0.8062 (mmtm)
REVERT: B  174 TYR cc_start: 0.8865 (OUTLIER) cc_final: 0.8193 (m-80)
REVERT: B  178 LEU cc_start: 0.7422 (mt) cc_final: 0.7180 (pt)
REVERT: B  179 LYS cc_start: 0.7447 (tttt) cc_final: 0.7183 (tppt)
REVERT: B  264 LYS cc_start: 0.7163 (mttt) cc_final: 0.6948 (mmmt)
REVERT: B  338 ASP cc_start: 0.8654 (t0) cc_final: 0.8239 (t0)
REVERT: B  366 GLN cc_start: 0.8942 (mt0) cc_final: 0.8364 (pt0)
REVERT: B  377 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7136 (t0)
REVERT: B  441 GLU cc_start: 0.7863 (pm20) cc_final: 0.7597 (pm20)
REVERT: B  563 LYS cc_start: 0.8865 (mtpt) cc_final: 0.8607 (mtpp)
REVERT: B  573 ILE cc_start: 0.7378 (mm) cc_final: 0.7077 (mp)
  outliers start: 12
  outliers final: 6
  residues processed: 119
  average time/residue: 1.3391
  time to fit residues: 166.9570
Evaluate side-chains
  121 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 MET
Chi-restraints excluded: chain A residue  267 TYR
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  504 GLN
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  377 ASP
Chi-restraints excluded: chain B residue  488 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 73 optimal weight:    0.7980
   chunk 13 optimal weight:    5.9990
   chunk 78 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0060
   chunk 3 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9990
   overall best weight:    0.6998

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

Flipped N/Q/H residues before XYZ refinement:
A 226 ASN
A 229 ASN
B 197 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.119865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.106487 restraints weight = 10079.703|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 2.32
r_work: 0.3299 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3163 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.2789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   6587  Z= 0.155
  Angle     :  0.542  17.095   8915  Z= 0.267
  Chirality :  0.039   0.139   1001
  Planarity :  0.003   0.032   1131
  Dihedral  :  3.609  15.228    868
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 17.29 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.30), residues: 775
  helix:  2.64 (0.28), residues: 323
  sheet:  0.06 (0.46), residues: 124
  loop :  0.01 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 129 
 HIS   0.002   0.001   HIS A 328 
 PHE   0.010   0.001   PHE A 253 
 TYR   0.019   0.001   TYR A 494 
 ARG   0.007   0.000   ARG A 248 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4943.18 seconds
wall clock time: 89 minutes 24.45 seconds (5364.45 seconds total)