Starting phenix.real_space_refine
on Wed Mar  5 14:43:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gh1_40028/03_2025/8gh1_40028.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gh1_40028/03_2025/8gh1_40028.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gh1_40028/03_2025/8gh1_40028.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gh1_40028/03_2025/8gh1_40028.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gh1_40028/03_2025/8gh1_40028.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gh1_40028/03_2025/8gh1_40028.cif"
  }
  resolution = 4.1
  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=   0.000 sd=   0.015
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      10      5.16       5
     C    1299      2.51       5
     N     328      2.21       5
     O     339      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 1976
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 1961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 1961
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 95}
          Link IDs: {'PTRANS': 7, 'TRANS': 273}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 303
          Unresolved non-hydrogen angles: 385
          Unresolved non-hydrogen dihedrals: 234
          Unresolved non-hydrogen chiralities: 46
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 122
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.66, per 1000 atoms: 1.35
  Number of scatterers: 1976
  At special positions: 0
  Unit cell: (55.5328, 86.77, 65.0775, 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      10     16.00
     O     339      8.00
     N     328      7.00
     C    1299      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 184 " - pdb=" SG  CYS R 190 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.99
  Conformation dependent library (CDL) restraints added in 330.3 milliseconds
  

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  538

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 0 sheets defined
      85.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'R' and resid 31 through 60
      removed outlier: 3.557A  pdb=" N   GLY R  35 " --> pdb=" O   VAL R  31 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   VAL R  39 " --> pdb=" O   GLY R  35 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   VAL R  48 " --> pdb=" O   VAL R  44 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   PHE R  49 " --> pdb=" O   LEU R  45 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ASN R  51 " --> pdb=" O   ILE R  47 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LEU R  53 " --> pdb=" O   PHE R  49 " (cutoff:3.500A)
      removed outlier: 4.787A  pdb=" N   VAL R  54 " --> pdb=" O   GLY R  50 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 96
      removed outlier: 3.686A  pdb=" N   TYR R  70 " --> pdb=" O   THR R  66 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 105 through 137
      removed outlier: 3.602A  pdb=" N   SER R 137 " --> pdb=" O   PHE R 133 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 137 through 145
      removed outlier: 3.949A  pdb=" N   GLN R 142 " --> pdb=" O   PRO R 138 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   SER R 143 " --> pdb=" O   PHE R 139 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LEU R 145 " --> pdb=" O   TYR R 141 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 3.662A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   ILE R 153 " --> pdb=" O   LYS R 149 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ILE R 154 " --> pdb=" O   ALA R 150 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
      removed outlier: 3.516A  pdb=" N   MET R 171 " --> pdb=" O   LEU R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 181 through 187
    Processing helix  chain 'R' and resid 196 through 208
      removed outlier: 3.575A  pdb=" N   ALA R 200 " --> pdb=" O   ASN R 196 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ILE R 201 " --> pdb=" O   GLN R 197 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 208 through 236
      removed outlier: 4.037A  pdb=" N   SER R 236 " --> pdb=" O   LYS R 232 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 270 through 296
      removed outlier: 3.973A  pdb=" N   THR R 274 " --> pdb=" O   LYS R 270 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ILE R 278 " --> pdb=" O   THR R 274 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   CYS R 285 " --> pdb=" O   THR R 281 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.710A  pdb=" N   VAL R 295 " --> pdb=" O   ILE R 291 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   HIS R 296 " --> pdb=" O   VAL R 292 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 327
      removed outlier: 3.682A  pdb=" N   GLY R 315 " --> pdb=" O   LEU R 311 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   TYR R 316 " --> pdb=" O   ASN R 312 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 329 through 340
      removed outlier: 3.523A  pdb=" N   LEU R 339 " --> pdb=" O   ALA R 335 " (cutoff:3.500A)

    153 hydrogen bonds defined for protein.
    459 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: 0.52

  Time building geometry restraints manager: 0.61 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: 621
        1.34 -     1.46: 529
        1.46 -     1.58: 867
        1.58 -     1.69: 0
        1.69 -     1.81: 13
  Bond restraints: 2030
  Sorted by residual:
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.452 -0.055 2.00e-02 2.50e+03 7.45e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.443 -0.049 2.00e-02 2.50e+03 6.00e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.570 -0.047 2.00e-02 2.50e+03 5.48e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.567 -0.047 2.00e-02 2.50e+03 5.43e+00
  bond pdb=" CAE G1I R 501 "
       pdb=" CAG G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.506  1.539 -0.033 2.00e-02 2.50e+03 2.66e+00
  ... (remaining 2025 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.12: 2664
        1.12 -     2.23: 105
        2.23 -     3.35: 11
        3.35 -     4.47: 5
        4.47 -     5.58: 9
  Bond angle restraints: 2794
  Sorted by residual:
  angle pdb=" C   GLU R 107 "
        pdb=" N   PHE R 108 "
        pdb=" CA  PHE R 108 "
      ideal   model   delta    sigma   weight residual
     121.58  116.26    5.32 1.95e+00 2.63e-01 7.44e+00
  angle pdb=" N   TYR R 326 "
        pdb=" CA  TYR R 326 "
        pdb=" C   TYR R 326 "
      ideal   model   delta    sigma   weight residual
     111.36  114.23   -2.87 1.09e+00 8.42e-01 6.92e+00
  angle pdb=" CAE G1I R 501 "
        pdb=" CAG G1I R 501 "
        pdb=" CAH G1I R 501 "
      ideal   model   delta    sigma   weight residual
     112.63  117.66   -5.03 3.00e+00 1.11e-01 2.81e+00
  angle pdb=" CA  LEU R 230 "
        pdb=" CB  LEU R 230 "
        pdb=" CG  LEU R 230 "
      ideal   model   delta    sigma   weight residual
     116.30  121.88   -5.58 3.50e+00 8.16e-02 2.54e+00
  angle pdb=" CAG G1I R 501 "
        pdb=" CAH G1I R 501 "
        pdb=" CAI G1I R 501 "
      ideal   model   delta    sigma   weight residual
     110.89  115.56   -4.67 3.00e+00 1.11e-01 2.42e+00
  ... (remaining 2789 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.96: 1028
       14.96 -    29.91: 93
       29.91 -    44.87: 19
       44.87 -    59.82: 3
       59.82 -    74.78: 3
  Dihedral angle restraints: 1146
    sinusoidal: 318
      harmonic: 828
  Sorted by residual:
  dihedral pdb=" CB  CYS R 184 "
           pdb=" SG  CYS R 184 "
           pdb=" SG  CYS R 190 "
           pdb=" CB  CYS R 190 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  167.78  -74.78     1      1.00e+01 1.00e-02 7.08e+01
  dihedral pdb=" CA  ILE R 277 "
           pdb=" C   ILE R 277 "
           pdb=" N   ILE R 278 "
           pdb=" CA  ILE R 278 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.43  -17.57     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" CA  ASP R 234 "
           pdb=" CB  ASP R 234 "
           pdb=" CG  ASP R 234 "
           pdb=" OD1 ASP R 234 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.10   55.10     1      2.00e+01 2.50e-03 1.03e+01
  ... (remaining 1143 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 213
       0.035 -    0.070: 99
       0.070 -    0.105: 17
       0.105 -    0.140: 1
       0.140 -    0.174: 1
  Chirality restraints: 331
  Sorted by residual:
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.57   -0.17 2.00e-01 2.50e+01 7.61e-01
  chirality pdb=" CA  PHE R 108 "
            pdb=" N   PHE R 108 "
            pdb=" C   PHE R 108 "
            pdb=" CB  PHE R 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.39e-01
  chirality pdb=" CA  PRO R 288 "
            pdb=" N   PRO R 288 "
            pdb=" C   PRO R 288 "
            pdb=" CB  PRO R 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.10 2.00e-01 2.50e+01 2.74e-01
  ... (remaining 328 not shown)

  Planarity restraints: 351
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R 283 "    0.004 2.00e-02 2.50e+03   8.55e-03 7.32e-01
        pdb=" C   THR R 283 "   -0.015 2.00e-02 2.50e+03
        pdb=" O   THR R 283 "    0.006 2.00e-02 2.50e+03
        pdb=" N   LEU R 284 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER R 137 "    0.014 5.00e-02 4.00e+02   2.13e-02 7.24e-01
        pdb=" N   PRO R 138 "   -0.037 5.00e-02 4.00e+02
        pdb=" CA  PRO R 138 "    0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO R 138 "    0.012 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP R 109 "    0.004 2.00e-02 2.50e+03   8.40e-03 7.05e-01
        pdb=" C   TRP R 109 "   -0.015 2.00e-02 2.50e+03
        pdb=" O   TRP R 109 "    0.005 2.00e-02 2.50e+03
        pdb=" N   THR R 110 "    0.005 2.00e-02 2.50e+03
  ... (remaining 348 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 451
        2.78 -     3.31: 2008
        3.31 -     3.84: 3205
        3.84 -     4.37: 2963
        4.37 -     4.90: 5438
  Nonbonded interactions: 14065
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP R 113 "
            pdb=" OAM G1I R 501 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" O   SER R 236 "
            pdb=" OG  SER R 236 "
     model   vdw
     2.508 3.040
  nonbonded pdb=" OD2 ASP R 113 "
            pdb=" OH  TYR R 316 "
     model   vdw
     2.522 3.040
  nonbonded pdb=" O   GLU R 107 "
            pdb=" OG1 THR R 110 "
     model   vdw
     2.524 3.040
  nonbonded pdb=" O   TYR R  70 "
            pdb=" OG1 THR R  73 "
     model   vdw
     2.541 3.040
  ... (remaining 14060 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             1.430
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     11.470
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
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      :  0.004   0.055   2030  Z= 0.223
  Angle     :  0.570   5.584   2794  Z= 0.294
  Chirality :  0.040   0.174    331
  Planarity :  0.003   0.025    351
  Dihedral  : 12.639  70.305    605
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  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:  1.62 (0.52), residues: 277
  helix:  1.88 (0.38), residues: 204
  sheet:  None (None), residues: 0
  loop : -1.28 (0.71), residues: 73

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 158 
 HIS   0.003   0.001   HIS R  93 
 PHE   0.011   0.001   PHE R 108 
 TYR   0.005   0.001   TYR R 308 
 ARG   0.007   0.001   ARG R 131 

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.215 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.1256
  time to fit residues: 6.3077
Evaluate side-chains
  32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0270
   chunk 11 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 27 optimal weight:    4.9990
   overall best weight:    0.6638

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

Flipped N/Q/H residues before XYZ refinement:
R 296 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.140170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.125196 restraints weight = 4442.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.127892 restraints weight = 2506.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.129754 restraints weight = 1622.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.1188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2030  Z= 0.194
  Angle     :  0.544   5.250   2794  Z= 0.296
  Chirality :  0.039   0.131    331
  Planarity :  0.004   0.026    351
  Dihedral  :  4.927  15.765    310
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  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:  1.89 (0.52), residues: 277
  helix:  1.91 (0.37), residues: 207
  sheet:  None (None), residues: 0
  loop : -0.75 (0.71), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R  93 
 PHE   0.022   0.002   PHE R 332 
 TYR   0.008   0.001   TYR R 326 
 ARG   0.005   0.001   ARG R 131 

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.225 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.1037
  time to fit residues: 6.5102
Evaluate side-chains
  32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 14 optimal weight:    0.0980
   chunk 9 optimal weight:    0.9990
   chunk 5 optimal weight:    0.3980
   chunk 25 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
R 296 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.141547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.126474 restraints weight = 4413.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.129234 restraints weight = 2473.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.131115 restraints weight = 1588.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.1511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   2030  Z= 0.162
  Angle     :  0.491   5.107   2794  Z= 0.269
  Chirality :  0.038   0.119    331
  Planarity :  0.003   0.027    351
  Dihedral  :  4.592  15.456    310
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.06 (0.51), residues: 277
  helix:  2.27 (0.37), residues: 198
  sheet:  None (None), residues: 0
  loop : -1.06 (0.64), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 158 
 HIS   0.003   0.001   HIS R  93 
 PHE   0.017   0.002   PHE R 108 
 TYR   0.006   0.001   TYR R 199 
 ARG   0.004   0.000   ARG R 131 

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.258 
Fit side-chains
REVERT: R   82 MET cc_start: 0.8838 (tmm) cc_final: 0.8635 (tmm)
REVERT: R  174 TYR cc_start: 0.8244 (p90) cc_final: 0.7799 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.1039
  time to fit residues: 6.1173
Evaluate side-chains
  31 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 6 optimal weight:    6.9990
   chunk 0 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 = 0.3645 r_free = 0.3645 target = 0.133811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.119261 restraints weight = 4463.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.121792 restraints weight = 2537.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.123530 restraints weight = 1650.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.2053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   2030  Z= 0.288
  Angle     :  0.599   5.324   2794  Z= 0.331
  Chirality :  0.040   0.109    331
  Planarity :  0.004   0.032    351
  Dihedral  :  5.020  16.981    310
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  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 (0.49), residues: 277
  helix:  1.78 (0.35), residues: 204
  sheet:  None (None), residues: 0
  loop : -1.44 (0.65), residues: 73

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP R 158 
 HIS   0.005   0.002   HIS R 296 
 PHE   0.017   0.003   PHE R 332 
 TYR   0.007   0.001   TYR R 199 
 ARG   0.007   0.001   ARG R 131 

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.200 
Fit side-chains
REVERT: R   82 MET cc_start: 0.8879 (tmm) cc_final: 0.8672 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.0991
  time to fit residues: 6.2124
Evaluate side-chains
  30 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 26 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 10 optimal weight:    0.2980
   chunk 25 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3699 r_free = 0.3699 target = 0.138667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.123628 restraints weight = 4542.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.126382 restraints weight = 2537.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.128291 restraints weight = 1623.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.1990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2030  Z= 0.182
  Angle     :  0.512   5.238   2794  Z= 0.281
  Chirality :  0.039   0.134    331
  Planarity :  0.004   0.032    351
  Dihedral  :  4.559  15.865    310
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  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:  1.78 (0.51), residues: 277
  helix:  2.09 (0.37), residues: 198
  sheet:  None (None), residues: 0
  loop : -1.24 (0.66), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 158 
 HIS   0.004   0.001   HIS R  93 
 PHE   0.020   0.002   PHE R 108 
 TYR   0.015   0.001   TYR R 174 
 ARG   0.006   0.001   ARG R 131 

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.199 
Fit side-chains
REVERT: R   82 MET cc_start: 0.8903 (tmm) cc_final: 0.8650 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.1237
  time to fit residues: 7.5023
Evaluate side-chains
  35 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 23 optimal weight:    0.0170
   chunk 18 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 25 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0170
   chunk 1 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0770
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.2614

-------------------------------------------------------------------------------
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 = 0.3752 r_free = 0.3752 target = 0.143433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.128835 restraints weight = 4429.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.131660 restraints weight = 2429.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.133616 restraints weight = 1540.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.2137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   2030  Z= 0.140
  Angle     :  0.501   5.056   2794  Z= 0.269
  Chirality :  0.038   0.132    331
  Planarity :  0.004   0.028    351
  Dihedral  :  4.291  15.342    310
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  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:  1.94 (0.51), residues: 277
  helix:  2.23 (0.37), residues: 198
  sheet:  None (None), residues: 0
  loop : -1.24 (0.66), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 158 
 HIS   0.004   0.001   HIS R  93 
 PHE   0.030   0.002   PHE R 332 
 TYR   0.005   0.001   TYR R 308 
 ARG   0.007   0.001   ARG R 131 

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.226 
Fit side-chains
REVERT: R   82 MET cc_start: 0.8933 (tmm) cc_final: 0.8705 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.1071
  time to fit residues: 6.6731
Evaluate side-chains
  33 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0470
   chunk 14 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.6280

-------------------------------------------------------------------------------
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 = 0.3729 r_free = 0.3729 target = 0.141077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.126165 restraints weight = 4635.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.128754 restraints weight = 2643.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.130638 restraints weight = 1732.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.2191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2030  Z= 0.173
  Angle     :  0.518   5.744   2794  Z= 0.279
  Chirality :  0.038   0.114    331
  Planarity :  0.003   0.030    351
  Dihedral  :  4.281  15.704    310
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  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:  1.95 (0.51), residues: 277
  helix:  2.26 (0.37), residues: 198
  sheet:  None (None), residues: 0
  loop : -1.33 (0.64), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 158 
 HIS   0.004   0.001   HIS R  93 
 PHE   0.014   0.001   PHE R 108 
 TYR   0.005   0.001   TYR R 199 
 ARG   0.006   0.001   ARG R 131 

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.208 
Fit side-chains
REVERT: R   82 MET cc_start: 0.8943 (tmm) cc_final: 0.8701 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.1065
  time to fit residues: 6.4955
Evaluate side-chains
  33 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 14 optimal weight:    0.2980
   chunk 6 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0060
   overall best weight:    0.5596

-------------------------------------------------------------------------------
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 = 0.3735 r_free = 0.3735 target = 0.140964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.126394 restraints weight = 4593.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.129218 restraints weight = 2542.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.131144 restraints weight = 1626.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.2196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   2030  Z= 0.169
  Angle     :  0.522   5.611   2794  Z= 0.279
  Chirality :  0.038   0.116    331
  Planarity :  0.004   0.029    351
  Dihedral  :  4.256  15.511    310
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 1.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  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:  2.02 (0.51), residues: 277
  helix:  2.29 (0.37), residues: 198
  sheet:  None (None), residues: 0
  loop : -1.23 (0.66), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 158 
 HIS   0.004   0.001   HIS R  93 
 PHE   0.027   0.002   PHE R 332 
 TYR   0.005   0.001   TYR R 199 
 ARG   0.006   0.001   ARG R 131 

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.215 
Fit side-chains
REVERT: R   82 MET cc_start: 0.8965 (tmm) cc_final: 0.8717 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.1093
  time to fit residues: 6.6290
Evaluate side-chains
  34 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 6 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9990
   chunk 7 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0060
   chunk 27 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.6196

-------------------------------------------------------------------------------
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 = 0.3714 r_free = 0.3714 target = 0.139297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.124178 restraints weight = 4781.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.126957 restraints weight = 2652.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.128893 restraints weight = 1709.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.2322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2030  Z= 0.171
  Angle     :  0.524   5.812   2794  Z= 0.284
  Chirality :  0.038   0.107    331
  Planarity :  0.003   0.031    351
  Dihedral  :  4.236  15.627    310
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  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:  1.99 (0.51), residues: 277
  helix:  2.16 (0.37), residues: 201
  sheet:  None (None), residues: 0
  loop : -1.03 (0.68), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R 158 
 HIS   0.004   0.001   HIS R  93 
 PHE   0.016   0.002   PHE R 108 
 TYR   0.005   0.001   TYR R 199 
 ARG   0.006   0.001   ARG R 131 

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.215 
Fit side-chains
REVERT: R   82 MET cc_start: 0.8957 (tmm) cc_final: 0.8716 (tmm)
REVERT: R  174 TYR cc_start: 0.8249 (p90) cc_final: 0.8005 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.1147
  time to fit residues: 6.3789
Evaluate side-chains
  35 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 22 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0870
   chunk 11 optimal weight:    0.3980
   chunk 9 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 26 optimal weight:    0.1980
   chunk 19 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.3958

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

Flipped N/Q/H residues before XYZ refinement:
R 197 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.142082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.128138 restraints weight = 4580.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.130676 restraints weight = 2613.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.132401 restraints weight = 1714.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.2377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   2030  Z= 0.147
  Angle     :  0.518   6.002   2794  Z= 0.273
  Chirality :  0.038   0.113    331
  Planarity :  0.003   0.028    351
  Dihedral  :  4.114  15.118    310
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  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:  2.09 (0.51), residues: 277
  helix:  2.25 (0.37), residues: 201
  sheet:  None (None), residues: 0
  loop : -1.04 (0.67), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP R 158 
 HIS   0.004   0.001   HIS R  93 
 PHE   0.018   0.001   PHE R 336 
 TYR   0.005   0.001   TYR R 308 
 ARG   0.006   0.001   ARG R 131 

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.213 
Fit side-chains
REVERT: R   82 MET cc_start: 0.8934 (tmm) cc_final: 0.8687 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.1075
  time to fit residues: 6.0041
Evaluate side-chains
  36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 6 optimal weight:    5.9990
   chunk 10 optimal weight:    0.5980
   chunk 3 optimal weight:    0.0570
   chunk 5 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 23 optimal weight:    0.3980
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.5900

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

Flipped N/Q/H residues before XYZ refinement:
R 197 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.140470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.125487 restraints weight = 4490.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.128289 restraints weight = 2459.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.130204 restraints weight = 1560.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.2359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2030  Z= 0.170
  Angle     :  0.540   5.955   2794  Z= 0.287
  Chirality :  0.038   0.110    331
  Planarity :  0.004   0.031    351
  Dihedral  :  4.148  15.424    310
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  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:  2.05 (0.51), residues: 277
  helix:  2.21 (0.37), residues: 201
  sheet:  None (None), residues: 0
  loop : -1.04 (0.66), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP R 158 
 HIS   0.004   0.001   HIS R  93 
 PHE   0.031   0.002   PHE R 332 
 TYR   0.005   0.001   TYR R 199 
 ARG   0.007   0.001   ARG R 131 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1130.86 seconds
wall clock time: 20 minutes 27.22 seconds (1227.22 seconds total)