Starting phenix.real_space_refine
on Sat Apr 26 16:03:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ggi_40009/04_2025/8ggi_40009.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ggi_40009/04_2025/8ggi_40009.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ggi_40009/04_2025/8ggi_40009.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ggi_40009/04_2025/8ggi_40009.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ggi_40009/04_2025/8ggi_40009.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ggi_40009/04_2025/8ggi_40009.cif"
  }
  resolution = 3.5
  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=   0.025
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      15      5.16       5
     C    1470      2.51       5
     N     348      2.21       5
     O     370      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 2203
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 2186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2186
          Classifications: {'peptide': 284}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 7, 'TRANS': 276}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 97
          Unresolved non-hydrogen angles: 121
          Unresolved non-hydrogen dihedrals: 82
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 67
    Chain: "R"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 17
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1, 'water': 2}
          Link IDs: {None: 2}
  Time building chain proxies: 2.46, per 1000 atoms: 1.12
  Number of scatterers: 2203
  At special positions: 0
  Unit cell: (54.6651, 83.2992, 63.3421, 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      15     16.00
     O     370      8.00
     N     348      7.00
     C    1470      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 184 " - pdb=" SG  CYS R 190 " distance=1.41

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 278.1 milliseconds
  

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  544

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 0 sheets defined
      82.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'R' and resid 29 through 61
      removed outlier: 3.553A  pdb=" N   VAL R  33 " --> pdb=" O   ASP R  29 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   VAL R  39 " --> pdb=" O   GLY R  35 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   VAL R  44 " --> pdb=" O   MET R  40 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU R  53 " --> pdb=" O   PHE R  49 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   VAL R  54 " --> pdb=" O   GLY R  50 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   ILE R  55 " --> pdb=" O   ASN R  51 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 69 through 97
      removed outlier: 4.624A  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 103 through 136
      removed outlier: 4.114A  pdb=" N   GLU R 107 " --> pdb=" O   ASN R 103 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   PHE R 108 " --> pdb=" O   PHE R 104 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   TRP R 109 " --> pdb=" O   TRP R 105 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA R 134 " --> pdb=" O   ASP R 130 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ILE R 135 " --> pdb=" O   ARG R 131 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   THR R 136 " --> pdb=" O   TYR R 132 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 163
      removed outlier: 3.657A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 166 through 171
    Processing helix  chain 'R' and resid 178 through 186
    Processing helix  chain 'R' and resid 196 through 208
      removed outlier: 3.686A  pdb=" N   SER R 204 " --> pdb=" O   ALA R 200 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 208 through 238
      removed outlier: 3.953A  pdb=" N   ARG R 221 " --> pdb=" O   PHE R 217 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   VAL R 222 " --> pdb=" O   VAL R 218 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   PHE R 223 " --> pdb=" O   TYR R 219 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   SER R 236 " --> pdb=" O   LYS R 232 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 269 through 280
    Processing helix  chain 'R' and resid 286 through 299
      removed outlier: 3.692A  pdb=" N   VAL R 292 " --> pdb=" O   PRO R 288 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 4.849A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
      removed outlier: 3.569A  pdb=" N   GLY R 315 " --> pdb=" O   LEU R 311 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 318 through 320
      No H-bonds generated for 'chain 'R' and resid 318 through 320'
    Processing helix  chain 'R' and resid 321 through 327
    Processing helix  chain 'R' and resid 329 through 340

    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: 0.56

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 651
        1.34 -     1.46: 581
        1.46 -     1.58: 1004
        1.58 -     1.70: 0
        1.70 -     1.83: 21
  Bond restraints: 2257
  Sorted by residual:
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.450 -0.053 2.00e-02 2.50e+03 6.97e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.439 -0.045 2.00e-02 2.50e+03 5.06e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.567 -0.044 2.00e-02 2.50e+03 4.87e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.563 -0.043 2.00e-02 2.50e+03 4.54e+00
  bond pdb=" C   CYS R 191 "
       pdb=" O   CYS R 191 "
    ideal  model  delta    sigma   weight residual
    1.235  1.220  0.015 7.50e-03 1.78e+04 4.18e+00
  ... (remaining 2252 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 3021
        1.88 -     3.75: 44
        3.75 -     5.63: 16
        5.63 -     7.51: 3
        7.51 -     9.38: 3
  Bond angle restraints: 3087
  Sorted by residual:
  angle pdb=" N   THR R 189 "
        pdb=" CA  THR R 189 "
        pdb=" C   THR R 189 "
      ideal   model   delta    sigma   weight residual
     114.04  104.66    9.38 1.24e+00 6.50e-01 5.73e+01
  angle pdb=" N   PHE R 193 "
        pdb=" CA  PHE R 193 "
        pdb=" C   PHE R 193 "
      ideal   model   delta    sigma   weight residual
     108.67  116.73   -8.06 1.55e+00 4.16e-01 2.70e+01
  angle pdb=" N   CYS R 191 "
        pdb=" CA  CYS R 191 "
        pdb=" C   CYS R 191 "
      ideal   model   delta    sigma   weight residual
     113.21  106.63    6.58 1.40e+00 5.10e-01 2.21e+01
  angle pdb=" N   CYS R 190 "
        pdb=" CA  CYS R 190 "
        pdb=" C   CYS R 190 "
      ideal   model   delta    sigma   weight residual
     109.96  115.88   -5.92 1.50e+00 4.44e-01 1.56e+01
  angle pdb=" N   CYS R 191 "
        pdb=" CA  CYS R 191 "
        pdb=" CB  CYS R 191 "
      ideal   model   delta    sigma   weight residual
     110.65  115.26   -4.61 1.71e+00 3.42e-01 7.28e+00
  ... (remaining 3082 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.08: 1151
       16.08 -    32.17: 122
       32.17 -    48.25: 25
       48.25 -    64.33: 3
       64.33 -    80.42: 3
  Dihedral angle restraints: 1304
    sinusoidal: 467
      harmonic: 837
  Sorted by residual:
  dihedral pdb=" CA  PHE R 208 "
           pdb=" C   PHE R 208 "
           pdb=" N   TYR R 209 "
           pdb=" CA  TYR R 209 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.92  -17.08     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CA  SER R 207 "
           pdb=" C   SER R 207 "
           pdb=" N   PHE R 208 "
           pdb=" CA  PHE R 208 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.16  -15.84     0      5.00e+00 4.00e-02 1.00e+01
  dihedral pdb=" CB  MET R 171 "
           pdb=" CG  MET R 171 "
           pdb=" SD  MET R 171 "
           pdb=" CE  MET R 171 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  117.75  -57.75     3      1.50e+01 4.44e-03 9.45e+00
  ... (remaining 1301 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 232
       0.033 -    0.066: 102
       0.066 -    0.098: 33
       0.098 -    0.131: 10
       0.131 -    0.164: 1
  Chirality restraints: 378
  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    2.56   -0.16 2.00e-01 2.50e+01 6.70e-01
  chirality pdb=" CA  LEU R 287 "
            pdb=" N   LEU R 287 "
            pdb=" C   LEU R 287 "
            pdb=" CB  LEU R 287 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.40    0.11 2.00e-01 2.50e+01 3.02e-01
  chirality pdb=" CA  PRO R  88 "
            pdb=" N   PRO R  88 "
            pdb=" C   PRO R  88 "
            pdb=" CB  PRO R  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.11 2.00e-01 2.50e+01 2.96e-01
  ... (remaining 375 not shown)

  Planarity restraints: 368
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS R 190 "    0.012 2.00e-02 2.50e+03   2.47e-02 6.12e+00
        pdb=" C   CYS R 190 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   CYS R 190 "    0.016 2.00e-02 2.50e+03
        pdb=" N   CYS R 191 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU R 237 "    0.006 2.00e-02 2.50e+03   1.24e-02 1.54e+00
        pdb=" CD  GLU R 237 "   -0.021 2.00e-02 2.50e+03
        pdb=" OE1 GLU R 237 "    0.008 2.00e-02 2.50e+03
        pdb=" OE2 GLU R 237 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R 313 "   -0.006 2.00e-02 2.50e+03   7.40e-03 1.37e+00
        pdb=" CG  TRP R 313 "    0.019 2.00e-02 2.50e+03
        pdb=" CD1 TRP R 313 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TRP R 313 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP R 313 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP R 313 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP R 313 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R 313 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R 313 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP R 313 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 365 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 445
        2.77 -     3.31: 2101
        3.31 -     3.84: 3493
        3.84 -     4.37: 3684
        4.37 -     4.90: 6782
  Nonbonded interactions: 16505
  Sorted by model distance:
  nonbonded pdb=" OG  SER R 203 "
            pdb=" OAL G1I R 501 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" N   GLU R 306 "
            pdb=" OE1 GLU R 306 "
     model   vdw
     2.333 3.120
  nonbonded pdb=" OH  TYR R 326 "
            pdb=" O   HOH R 601 "
     model   vdw
     2.407 3.040
  nonbonded pdb=" OH  TYR R 209 "
            pdb=" O   PHE R 290 "
     model   vdw
     2.450 3.040
  nonbonded pdb=" O   LEU R  64 "
            pdb=" ND2 ASN R  69 "
     model   vdw
     2.495 3.120
  ... (remaining 16500 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     11.060
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
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      :  0.014   0.622   2259  Z= 0.684
  Angle     :  0.805  18.619   3091  Z= 0.435
  Chirality :  0.042   0.164    378
  Planarity :  0.004   0.030    368
  Dihedral  : 13.755  80.416    754
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.51), residues: 280
  helix:  1.60 (0.37), residues: 204
  sheet:  None (None), residues: 0
  loop : -0.70 (0.71), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R 313 
 HIS   0.005   0.002   HIS R 296 
 PHE   0.007   0.001   PHE R 193 
 TYR   0.007   0.001   TYR R 132 
 ARG   0.007   0.001   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16886 (  153)
  hydrogen bonds       : angle       5.56873 (  459)
  SS BOND              : bond        0.43999 (    2)
  SS BOND              : angle      11.40898 (    4)
  covalent geometry    : bond        0.00397 ( 2257)
  covalent geometry    : angle       0.69241 ( 3087)

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

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

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.196 
Fit side-chains
REVERT: R   82 MET cc_start: 0.8318 (ttm) cc_final: 0.8052 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.1620
  time to fit residues: 8.2329
Evaluate side-chains
  34 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 11 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.6780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.112464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.095700 restraints weight = 3044.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.098110 restraints weight = 1737.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.099675 restraints weight = 1228.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.1179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2259  Z= 0.147
  Angle     :  0.532   7.099   3091  Z= 0.282
  Chirality :  0.040   0.105    378
  Planarity :  0.003   0.027    368
  Dihedral  :  4.595  20.606    316
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 2.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  8.00 %
    Favored  : 90.67 %
  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 (0.51), residues: 280
  helix:  1.40 (0.36), residues: 221
  sheet:  None (None), residues: 0
  loop : -0.56 (0.77), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 109 
 HIS   0.006   0.002   HIS R 178 
 PHE   0.009   0.001   PHE R  61 
 TYR   0.008   0.001   TYR R 132 
 ARG   0.001   0.000   ARG R 228 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05446 (  153)
  hydrogen bonds       : angle       4.24114 (  459)
  SS BOND              : bond        0.00264 (    2)
  SS BOND              : angle       2.23494 (    4)
  covalent geometry    : bond        0.00346 ( 2257)
  covalent geometry    : angle       0.52580 ( 3087)

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

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

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.252 
Fit side-chains
REVERT: R  279 MET cc_start: 0.8559 (mmm) cc_final: 0.8239 (mmm)
  outliers start: 3
  outliers final: 2
  residues processed: 38
  average time/residue: 0.2005
  time to fit residues: 8.7937
Evaluate side-chains
  36 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 34
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 3 optimal weight:    0.3980
   chunk 25 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0870
   chunk 10 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.5158

-------------------------------------------------------------------------------
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 = 0.3192 r_free = 0.3192 target = 0.114023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.096844 restraints weight = 3062.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.099314 restraints weight = 1753.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.100863 restraints weight = 1236.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.1287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2259  Z= 0.126
  Angle     :  0.505   9.317   3091  Z= 0.261
  Chirality :  0.039   0.103    378
  Planarity :  0.003   0.026    368
  Dihedral  :  4.470  17.436    316
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 2.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  :  9.78 %
    Favored  : 88.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.51), residues: 280
  helix:  1.47 (0.36), residues: 221
  sheet:  None (None), residues: 0
  loop : -0.59 (0.79), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 109 
 HIS   0.005   0.002   HIS R 296 
 PHE   0.006   0.001   PHE R 332 
 TYR   0.006   0.001   TYR R 132 
 ARG   0.003   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04881 (  153)
  hydrogen bonds       : angle       4.07087 (  459)
  SS BOND              : bond        0.00351 (    2)
  SS BOND              : angle       1.28357 (    4)
  covalent geometry    : bond        0.00291 ( 2257)
  covalent geometry    : angle       0.50354 ( 3087)

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

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

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.252 
Fit side-chains
REVERT: R  279 MET cc_start: 0.8617 (mmm) cc_final: 0.8261 (mmm)
  outliers start: 5
  outliers final: 3
  residues processed: 39
  average time/residue: 0.1842
  time to fit residues: 8.3264
Evaluate side-chains
  38 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  195 THR
Chi-restraints excluded: chain R residue  298 ILE
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 3 optimal weight:    0.4980
   chunk 27 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0980
   chunk 22 optimal weight:    0.4980
   chunk 5 optimal weight:    0.0670
   chunk 18 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.3518

-------------------------------------------------------------------------------
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 = 0.3225 r_free = 0.3225 target = 0.116354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.099409 restraints weight = 2947.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.101888 restraints weight = 1687.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.103466 restraints weight = 1186.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.1555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   2259  Z= 0.105
  Angle     :  0.465   7.567   3091  Z= 0.243
  Chirality :  0.038   0.101    378
  Planarity :  0.003   0.025    368
  Dihedral  :  4.157  17.204    316
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 2.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 11.56 %
    Favored  : 87.11 %
  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:  1.65 (0.51), residues: 280
  helix:  1.55 (0.36), residues: 222
  sheet:  None (None), residues: 0
  loop : -0.55 (0.78), residues: 58

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 178 
 PHE   0.005   0.001   PHE R  61 
 TYR   0.005   0.001   TYR R 132 
 ARG   0.003   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04321 (  153)
  hydrogen bonds       : angle       3.87395 (  459)
  SS BOND              : bond        0.00142 (    2)
  SS BOND              : angle       1.19991 (    4)
  covalent geometry    : bond        0.00226 ( 2257)
  covalent geometry    : angle       0.46372 ( 3087)

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

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

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.254 
Fit side-chains
REVERT: R  279 MET cc_start: 0.8591 (mmm) cc_final: 0.8239 (mmm)
  outliers start: 3
  outliers final: 2
  residues processed: 38
  average time/residue: 0.1763
  time to fit residues: 7.7910
Evaluate side-chains
  36 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 34
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  195 THR
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0870
   chunk 26 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 27 optimal weight:    0.1980
   chunk 2 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.5358

-------------------------------------------------------------------------------
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 = 0.3204 r_free = 0.3204 target = 0.114643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.097444 restraints weight = 3024.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.099929 restraints weight = 1742.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.101633 restraints weight = 1234.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.1594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2259  Z= 0.123
  Angle     :  0.481   7.950   3091  Z= 0.249
  Chirality :  0.039   0.103    378
  Planarity :  0.003   0.025    368
  Dihedral  :  4.165  17.272    316
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 1.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 12.89 %
    Favored  : 85.78 %
  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:  1.60 (0.51), residues: 280
  helix:  1.55 (0.36), residues: 223
  sheet:  None (None), residues: 0
  loop : -0.76 (0.76), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.004   0.002   HIS R 296 
 PHE   0.006   0.001   PHE R 332 
 TYR   0.007   0.001   TYR R 132 
 ARG   0.006   0.001   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04652 (  153)
  hydrogen bonds       : angle       3.85404 (  459)
  SS BOND              : bond        0.00153 (    2)
  SS BOND              : angle       1.26388 (    4)
  covalent geometry    : bond        0.00287 ( 2257)
  covalent geometry    : angle       0.47891 ( 3087)

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

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

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 37
  time to evaluate  : 0.225 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 39
  average time/residue: 0.1923
  time to fit residues: 8.6164
Evaluate side-chains
  38 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 36
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  195 THR
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 23 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 3 optimal weight:    0.5980
   chunk 11 optimal weight:    2.9990
   chunk 19 optimal weight:    0.1980
   chunk 12 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0870
   chunk 14 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.4158

-------------------------------------------------------------------------------
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 = 0.3208 r_free = 0.3208 target = 0.114987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.098004 restraints weight = 2980.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.100546 restraints weight = 1712.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.102223 restraints weight = 1205.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   2259  Z= 0.110
  Angle     :  0.483   8.243   3091  Z= 0.248
  Chirality :  0.039   0.102    378
  Planarity :  0.003   0.024    368
  Dihedral  :  4.174  17.243    316
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 2.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  : 14.67 %
    Favored  : 84.89 %
  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:  1.60 (0.51), residues: 280
  helix:  1.58 (0.36), residues: 224
  sheet:  None (None), residues: 0
  loop : -0.95 (0.73), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.007   0.002   HIS R 296 
 PHE   0.006   0.001   PHE R  61 
 TYR   0.006   0.001   TYR R 132 
 ARG   0.004   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04386 (  153)
  hydrogen bonds       : angle       3.81478 (  459)
  SS BOND              : bond        0.00145 (    2)
  SS BOND              : angle       1.67263 (    4)
  covalent geometry    : bond        0.00245 ( 2257)
  covalent geometry    : angle       0.47963 ( 3087)

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

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

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 35
  time to evaluate  : 0.237 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 35
  average time/residue: 0.1984
  time to fit residues: 8.0867
Evaluate side-chains
  36 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 35
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  195 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0020
   chunk 8 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.5588

-------------------------------------------------------------------------------
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 = 0.3195 r_free = 0.3195 target = 0.113877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.097024 restraints weight = 3002.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.099533 restraints weight = 1703.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.101176 restraints weight = 1195.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2259  Z= 0.125
  Angle     :  0.492   8.524   3091  Z= 0.252
  Chirality :  0.039   0.103    378
  Planarity :  0.003   0.024    368
  Dihedral  :  4.201  17.211    316
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 2.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 12.89 %
    Favored  : 85.33 %
  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:  1.56 (0.51), residues: 280
  helix:  1.56 (0.36), residues: 224
  sheet:  None (None), residues: 0
  loop : -1.04 (0.72), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 178 
 PHE   0.006   0.001   PHE R 332 
 TYR   0.007   0.001   TYR R 132 
 ARG   0.006   0.001   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04647 (  153)
  hydrogen bonds       : angle       3.81630 (  459)
  SS BOND              : bond        0.00112 (    2)
  SS BOND              : angle       1.56406 (    4)
  covalent geometry    : bond        0.00293 ( 2257)
  covalent geometry    : angle       0.48942 ( 3087)

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

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

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.258 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 37
  average time/residue: 0.1851
  time to fit residues: 7.9066
Evaluate side-chains
  38 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue  195 THR
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 19 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0470
   chunk 23 optimal weight:    0.0980
   chunk 3 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.5078

-------------------------------------------------------------------------------
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 = 0.3195 r_free = 0.3195 target = 0.114314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.096791 restraints weight = 3106.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.099533 restraints weight = 1678.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.101291 restraints weight = 1139.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.1761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2259  Z= 0.120
  Angle     :  0.491   8.619   3091  Z= 0.252
  Chirality :  0.039   0.103    378
  Planarity :  0.003   0.028    368
  Dihedral  :  4.203  17.204    316
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 2.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 12.89 %
    Favored  : 85.33 %
  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:  1.60 (0.51), residues: 280
  helix:  1.60 (0.36), residues: 224
  sheet:  None (None), residues: 0
  loop : -1.03 (0.72), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 109 
 HIS   0.005   0.002   HIS R 296 
 PHE   0.006   0.001   PHE R  61 
 TYR   0.009   0.001   TYR R 132 
 ARG   0.006   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04578 (  153)
  hydrogen bonds       : angle       3.82169 (  459)
  SS BOND              : bond        0.00230 (    2)
  SS BOND              : angle       1.51044 (    4)
  covalent geometry    : bond        0.00278 ( 2257)
  covalent geometry    : angle       0.48830 ( 3087)

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

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

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.264 
Fit side-chains
  outliers start: 4
  outliers final: 4
  residues processed: 36
  average time/residue: 0.1884
  time to fit residues: 7.8896
Evaluate side-chains
  38 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue   98 THR
Chi-restraints excluded: chain R residue  195 THR
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0870
   chunk 14 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 5 optimal weight:    0.3980
   chunk 24 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.6358

-------------------------------------------------------------------------------
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 = 0.3188 r_free = 0.3188 target = 0.113535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.096430 restraints weight = 3030.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.098940 restraints weight = 1733.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.100486 restraints weight = 1220.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.1798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2259  Z= 0.135
  Angle     :  0.505   8.801   3091  Z= 0.259
  Chirality :  0.040   0.105    378
  Planarity :  0.003   0.031    368
  Dihedral  :  4.250  17.111    316
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 2.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 14.22 %
    Favored  : 83.56 %
  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:  1.60 (0.51), residues: 280
  helix:  1.58 (0.36), residues: 224
  sheet:  None (None), residues: 0
  loop : -0.95 (0.73), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 109 
 HIS   0.005   0.002   HIS R 296 
 PHE   0.009   0.001   PHE R  61 
 TYR   0.009   0.001   TYR R 132 
 ARG   0.007   0.001   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04786 (  153)
  hydrogen bonds       : angle       3.86050 (  459)
  SS BOND              : bond        0.00115 (    2)
  SS BOND              : angle       1.51989 (    4)
  covalent geometry    : bond        0.00324 ( 2257)
  covalent geometry    : angle       0.50253 ( 3087)

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

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

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.222 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 37
  average time/residue: 0.1931
  time to fit residues: 8.2706
Evaluate side-chains
  40 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue   98 THR
Chi-restraints excluded: chain R residue  195 THR
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 6 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.7780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.112463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.095442 restraints weight = 3034.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.097765 restraints weight = 1743.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.099470 restraints weight = 1243.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.1827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   2259  Z= 0.155
  Angle     :  0.528   9.027   3091  Z= 0.272
  Chirality :  0.040   0.108    378
  Planarity :  0.003   0.031    368
  Dihedral  :  4.337  17.123    316
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 2.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 13.78 %
    Favored  : 84.44 %
  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:  1.53 (0.51), residues: 280
  helix:  1.52 (0.36), residues: 224
  sheet:  None (None), residues: 0
  loop : -0.94 (0.75), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 178 
 PHE   0.008   0.001   PHE R  61 
 TYR   0.011   0.001   TYR R 132 
 ARG   0.007   0.001   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05108 (  153)
  hydrogen bonds       : angle       3.94101 (  459)
  SS BOND              : bond        0.00108 (    2)
  SS BOND              : angle       1.59706 (    4)
  covalent geometry    : bond        0.00378 ( 2257)
  covalent geometry    : angle       0.52522 ( 3087)

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

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

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  560 Ramachandran restraints generated.
    280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.235 
Fit side-chains
  outliers start: 4
  outliers final: 4
  residues processed: 36
  average time/residue: 0.1930
  time to fit residues: 7.9961
Evaluate side-chains
  40 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue   98 THR
Chi-restraints excluded: chain R residue  195 THR
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 14 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 18 optimal weight:    0.5980
   chunk 3 optimal weight:    0.0020
   chunk 22 optimal weight:    0.0070
   chunk 16 optimal weight:    0.0370
   chunk 24 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.2484

-------------------------------------------------------------------------------
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 = 0.3228 r_free = 0.3228 target = 0.116485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.099457 restraints weight = 2960.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.101963 restraints weight = 1696.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.103625 restraints weight = 1192.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   2259  Z= 0.102
  Angle     :  0.484   8.632   3091  Z= 0.249
  Chirality :  0.039   0.101    378
  Planarity :  0.003   0.032    368
  Dihedral  :  4.189  17.201    316
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 1.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 14.22 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.51), residues: 280
  helix:  1.68 (0.36), residues: 224
  sheet:  None (None), residues: 0
  loop : -0.99 (0.74), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 178 
 PHE   0.007   0.001   PHE R  61 
 TYR   0.006   0.001   TYR R 132 
 ARG   0.007   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04234 (  153)
  hydrogen bonds       : angle       3.81503 (  459)
  SS BOND              : bond        0.00115 (    2)
  SS BOND              : angle       1.39309 (    4)
  covalent geometry    : bond        0.00208 ( 2257)
  covalent geometry    : angle       0.48180 ( 3087)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1288.26 seconds
wall clock time: 22 minutes 55.49 seconds (1375.49 seconds total)