Starting phenix.real_space_refine
on Fri May  9 13:18:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ggw_40023/05_2025/8ggw_40023.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ggw_40023/05_2025/8ggw_40023.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ggw_40023/05_2025/8ggw_40023.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ggw_40023/05_2025/8ggw_40023.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ggw_40023/05_2025/8ggw_40023.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ggw_40023/05_2025/8ggw_40023.cif"
  }
  resolution = 3.6
  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=   0.020
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      12      5.16       5
     C    1379      2.51       5
     N     335      2.21       5
     O     353      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 2079
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 2064
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2064
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 60}
          Link IDs: {'PTRANS': 7, 'TRANS': 273}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 198
          Unresolved non-hydrogen angles: 245
          Unresolved non-hydrogen dihedrals: 160
          Unresolved non-hydrogen chiralities: 23
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 6, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 80
    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: 2.63, per 1000 atoms: 1.27
  Number of scatterers: 2079
  At special positions: 0
  Unit cell: (54.6651, 83.2992, 62.4744, 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      12     16.00
     O     353      8.00
     N     335      7.00
     C    1379      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=2.04

  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 288.1 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:
      12 helices and 0 sheets defined
      85.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'R' and resid 32 through 61
      removed outlier: 3.627A  pdb=" N   MET R  36 " --> pdb=" O   TRP R  32 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLY R  37 " --> pdb=" O   VAL R  33 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ILE R  58 " --> pdb=" O   VAL R  54 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 68 through 97
      removed outlier: 3.940A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.888A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
      removed outlier: 3.643A  pdb=" N   ALA R  92 " --> pdb=" O   PRO R  88 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   HIS R  93 " --> pdb=" O   PHE R  89 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ILE R  94 " --> pdb=" O   GLY R  90 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 104 through 137
      removed outlier: 3.847A  pdb=" N   PHE R 108 " --> pdb=" O   PHE R 104 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   SER R 120 " --> pdb=" O   CYS R 116 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 3.790A  pdb=" N   ALA R 150 " --> pdb=" O   THR R 146 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   SER R 165 " --> pdb=" O   SER R 161 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
      removed outlier: 3.619A  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 198 through 208
    Processing helix  chain 'R' and resid 208 through 237
      removed outlier: 3.883A  pdb=" N   ASP R 234 " --> pdb=" O   LEU R 230 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   LYS R 235 " --> pdb=" O   GLN R 231 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   SER R 236 " --> pdb=" O   LYS R 232 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 270 through 299
      Proline residue:  R 288  - end of helix
      removed outlier: 3.918A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
      removed outlier: 3.874A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 317 through 327
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 329 through 340

    161 hydrogen bonds defined for protein.
    483 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: 0.71 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: 638
        1.34 -     1.46: 583
        1.46 -     1.58: 897
        1.58 -     1.70: 0
        1.70 -     1.82: 17
  Bond restraints: 2135
  Sorted by residual:
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.451 -0.054 2.00e-02 2.50e+03 7.18e+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 5.61e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.440 -0.046 2.00e-02 2.50e+03 5.25e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.564 -0.044 2.00e-02 2.50e+03 4.85e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" OAK G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.353  1.323  0.030 2.00e-02 2.50e+03 2.29e+00
  ... (remaining 2130 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.18: 2771
        1.18 -     2.35: 128
        2.35 -     3.53: 22
        3.53 -     4.71: 7
        4.71 -     5.88: 6
  Bond angle restraints: 2934
  Sorted by residual:
  angle pdb=" C   GLU R 180 "
        pdb=" N   ALA R 181 "
        pdb=" CA  ALA R 181 "
      ideal   model   delta    sigma   weight residual
     121.54  127.42   -5.88 1.91e+00 2.74e-01 9.48e+00
  angle pdb=" C   VAL R 295 "
        pdb=" N   HIS R 296 "
        pdb=" CA  HIS R 296 "
      ideal   model   delta    sigma   weight residual
     121.58  116.00    5.58 1.95e+00 2.63e-01 8.20e+00
  angle pdb=" N   ILE R 135 "
        pdb=" CA  ILE R 135 "
        pdb=" C   ILE R 135 "
      ideal   model   delta    sigma   weight residual
     111.00  113.67   -2.67 1.09e+00 8.42e-01 6.01e+00
  angle pdb=" C   ILE R 135 "
        pdb=" CA  ILE R 135 "
        pdb=" CB  ILE R 135 "
      ideal   model   delta    sigma   weight residual
     112.24  109.57    2.67 1.34e+00 5.57e-01 3.98e+00
  angle pdb=" N   HIS R 296 "
        pdb=" CA  HIS R 296 "
        pdb=" CB  HIS R 296 "
      ideal   model   delta    sigma   weight residual
     110.41  113.75   -3.34 1.68e+00 3.54e-01 3.96e+00
  ... (remaining 2929 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.95: 1094
       16.95 -    33.91: 103
       33.91 -    50.86: 15
       50.86 -    67.82: 0
       67.82 -    84.77: 1
  Dihedral angle restraints: 1213
    sinusoidal: 385
      harmonic: 828
  Sorted by residual:
  dihedral pdb=" CB  CYS R 106 "
           pdb=" SG  CYS R 106 "
           pdb=" SG  CYS R 191 "
           pdb=" CB  CYS R 191 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  177.77  -84.77     1      1.00e+01 1.00e-02 8.73e+01
  dihedral pdb=" CA  CYS R 190 "
           pdb=" C   CYS R 190 "
           pdb=" N   CYS R 191 "
           pdb=" CA  CYS R 191 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.79   19.21     0      5.00e+00 4.00e-02 1.48e+01
  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 -162.14  -17.86     0      5.00e+00 4.00e-02 1.28e+01
  ... (remaining 1210 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 227
       0.033 -    0.066: 90
       0.066 -    0.098: 31
       0.098 -    0.131: 5
       0.131 -    0.164: 1
  Chirality restraints: 354
  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 6.73e-01
  chirality pdb=" CA  ILE R 303 "
            pdb=" N   ILE R 303 "
            pdb=" C   ILE R 303 "
            pdb=" CB  ILE R 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.08e-01
  chirality pdb=" CA  TYR R 219 "
            pdb=" N   TYR R 219 "
            pdb=" C   TYR R 219 "
            pdb=" CB  TYR R 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.40    0.11 2.00e-01 2.50e+01 3.04e-01
  ... (remaining 351 not shown)

  Planarity restraints: 361
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER R 329 "   -0.024 5.00e-02 4.00e+02   3.72e-02 2.21e+00
        pdb=" N   PRO R 330 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO R 330 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO R 330 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R 173 "   -0.011 2.00e-02 2.50e+03   8.68e-03 1.88e+00
        pdb=" CG  TRP R 173 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 TRP R 173 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TRP R 173 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP R 173 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP R 173 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE3 TRP R 173 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R 173 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R 173 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP R 173 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 167 "   -0.018 5.00e-02 4.00e+02   2.66e-02 1.13e+00
        pdb=" N   PRO R 168 "    0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO R 168 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO R 168 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 358 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 424
        2.77 -     3.30: 2103
        3.30 -     3.84: 3391
        3.84 -     4.37: 3303
        4.37 -     4.90: 6123
  Nonbonded interactions: 15344
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP R 113 "
            pdb=" OAM G1I R 501 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" OG  SER R 203 "
            pdb=" OAL G1I R 501 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" OG1 THR R 118 "
            pdb=" OG  SER R 161 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" O   LEU R  64 "
            pdb=" ND2 ASN R  69 "
     model   vdw
     2.449 3.120
  nonbonded pdb=" O   VAL R 292 "
            pdb=" ND1 HIS R 296 "
     model   vdw
     2.581 3.120
  ... (remaining 15339 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:             1.420
  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:          0.070
  Check model and map are aligned:         0.020
  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:2.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
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   0.054   2137  Z= 0.188
  Angle     :  0.623   5.882   2938  Z= 0.354
  Chirality :  0.040   0.164    354
  Planarity :  0.004   0.037    361
  Dihedral  : 12.729  44.728    669
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  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:  2.12 (0.50), residues: 277
  helix:  2.43 (0.35), residues: 206
  sheet:  None (None), residues: 0
  loop : -1.87 (0.60), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP R 173 
 HIS   0.002   0.001   HIS R 178 
 PHE   0.009   0.001   PHE R 290 
 TYR   0.014   0.001   TYR R 185 
 ARG   0.002   0.000   ARG R 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17170 (  161)
  hydrogen bonds       : angle       5.31519 (  483)
  SS BOND              : bond        0.00325 (    2)
  SS BOND              : angle       1.40087 (    4)
  covalent geometry    : bond        0.00374 ( 2135)
  covalent geometry    : angle       0.62146 ( 2934)

*********************** 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
  40 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.1399
  time to fit residues: 6.6404
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  : 0.218 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 21 optimal weight:    0.0670
   chunk 11 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0470
   chunk 14 optimal weight:    0.0770
   chunk 8 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.2974

-------------------------------------------------------------------------------
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 = 0.3792 r_free = 0.3792 target = 0.157542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.141281 restraints weight = 3244.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.144820 restraints weight = 1687.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.146561 restraints weight = 988.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.1229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2137  Z= 0.132
  Angle     :  0.519   4.985   2938  Z= 0.289
  Chirality :  0.040   0.136    354
  Planarity :  0.003   0.032    361
  Dihedral  :  5.043  18.524    311
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 12.77 %
    Favored  : 85.11 %
  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:  2.29 (0.51), residues: 277
  helix:  2.42 (0.35), residues: 214
  sheet:  None (None), residues: 0
  loop : -1.86 (0.71), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R 173 
 HIS   0.001   0.000   HIS R 178 
 PHE   0.007   0.001   PHE R 321 
 TYR   0.014   0.001   TYR R 185 
 ARG   0.001   0.000   ARG R 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05237 (  161)
  hydrogen bonds       : angle       4.06095 (  483)
  SS BOND              : bond        0.00359 (    2)
  SS BOND              : angle       1.20965 (    4)
  covalent geometry    : bond        0.00253 ( 2135)
  covalent geometry    : angle       0.51749 ( 2934)

*********************** 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
  39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.225 
Fit side-chains
REVERT: R  163 LEU cc_start: 0.8120 (mm) cc_final: 0.7844 (tt)
REVERT: R  173 TRP cc_start: 0.6989 (m-10) cc_final: 0.6609 (m-90)
REVERT: R  178 HIS cc_start: 0.8214 (p90) cc_final: 0.8005 (p90)
  outliers start: 4
  outliers final: 3
  residues processed: 36
  average time/residue: 0.1256
  time to fit residues: 5.4394
Evaluate side-chains
  38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  314 ILE
Chi-restraints excluded: chain R residue  340 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 8 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   chunk 11 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0670
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.6518

-------------------------------------------------------------------------------
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 = 0.3715 r_free = 0.3715 target = 0.150419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.133117 restraints weight = 3280.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.137505 restraints weight = 1661.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.139289 restraints weight = 873.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.1442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2137  Z= 0.149
  Angle     :  0.545   5.153   2938  Z= 0.301
  Chirality :  0.041   0.129    354
  Planarity :  0.004   0.031    361
  Dihedral  :  4.800  18.450    311
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 15.96 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.29 (0.51), residues: 277
  helix:  2.27 (0.34), residues: 217
  sheet:  None (None), residues: 0
  loop : -1.45 (0.78), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R 173 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.008   0.001   PHE R  61 
 TYR   0.012   0.001   TYR R 185 
 ARG   0.002   0.000   ARG R 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05939 (  161)
  hydrogen bonds       : angle       4.11819 (  483)
  SS BOND              : bond        0.00467 (    2)
  SS BOND              : angle       1.55326 (    4)
  covalent geometry    : bond        0.00325 ( 2135)
  covalent geometry    : angle       0.54247 ( 2934)

*********************** 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
  39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 34
  time to evaluate  : 0.225 
Fit side-chains
REVERT: R  171 MET cc_start: 0.6887 (ppp) cc_final: 0.6431 (ptm)
REVERT: R  173 TRP cc_start: 0.7404 (m-10) cc_final: 0.7037 (m-90)
  outliers start: 5
  outliers final: 3
  residues processed: 37
  average time/residue: 0.1311
  time to fit residues: 5.8945
Evaluate side-chains
  36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  340 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 24 optimal weight:    0.4980
   chunk 7 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.149732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.132308 restraints weight = 3258.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.136741 restraints weight = 1688.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.138531 restraints weight = 873.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.1729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2137  Z= 0.150
  Angle     :  0.541   5.362   2938  Z= 0.299
  Chirality :  0.041   0.129    354
  Planarity :  0.003   0.029    361
  Dihedral  :  4.758  18.663    311
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 19.68 %
    Favored  : 77.13 %
  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:  2.20 (0.51), residues: 277
  helix:  2.23 (0.35), residues: 218
  sheet:  None (None), residues: 0
  loop : -1.61 (0.76), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 173 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.008   0.001   PHE R  61 
 TYR   0.010   0.001   TYR R 185 
 ARG   0.002   0.000   ARG R 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05910 (  161)
  hydrogen bonds       : angle       4.07921 (  483)
  SS BOND              : bond        0.00485 (    2)
  SS BOND              : angle       1.65637 (    4)
  covalent geometry    : bond        0.00331 ( 2135)
  covalent geometry    : angle       0.53816 ( 2934)

*********************** 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
  38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.226 
Fit side-chains
REVERT: R  163 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7360 (tt)
REVERT: R  171 MET cc_start: 0.6928 (ppp) cc_final: 0.6679 (ptm)
  outliers start: 6
  outliers final: 5
  residues processed: 35
  average time/residue: 0.1322
  time to fit residues: 5.5635
Evaluate side-chains
  38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  314 ILE
Chi-restraints excluded: chain R residue  328 ARG
Chi-restraints excluded: chain R residue  340 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 0 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.148871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.131381 restraints weight = 3320.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.135981 restraints weight = 1719.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.137613 restraints weight = 863.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.1762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2137  Z= 0.152
  Angle     :  0.548   5.881   2938  Z= 0.302
  Chirality :  0.041   0.128    354
  Planarity :  0.003   0.028    361
  Dihedral  :  4.798  18.861    311
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 17.55 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.22 (0.51), residues: 277
  helix:  2.38 (0.35), residues: 212
  sheet:  None (None), residues: 0
  loop : -1.79 (0.72), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP R 173 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.007   0.001   PHE R  61 
 TYR   0.010   0.001   TYR R 185 
 ARG   0.002   0.000   ARG R 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05908 (  161)
  hydrogen bonds       : angle       4.07369 (  483)
  SS BOND              : bond        0.00468 (    2)
  SS BOND              : angle       1.70917 (    4)
  covalent geometry    : bond        0.00334 ( 2135)
  covalent geometry    : angle       0.54519 ( 2934)

*********************** 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
  37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 28
  time to evaluate  : 0.216 
Fit side-chains
REVERT: R  163 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7396 (tt)
REVERT: R  171 MET cc_start: 0.6983 (OUTLIER) cc_final: 0.5993 (ppp)
REVERT: R  173 TRP cc_start: 0.7923 (m-10) cc_final: 0.6771 (m-90)
  outliers start: 9
  outliers final: 7
  residues processed: 33
  average time/residue: 0.1360
  time to fit residues: 5.4128
Evaluate side-chains
  37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 28
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   62 GLU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  171 MET
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  314 ILE
Chi-restraints excluded: chain R residue  328 ARG
Chi-restraints excluded: chain R residue  340 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 17 optimal weight:    0.1980
   chunk 0 optimal weight:    0.5980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3701 r_free = 0.3701 target = 0.149622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.132196 restraints weight = 3330.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.136937 restraints weight = 1723.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.138288 restraints weight = 844.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.1909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2137  Z= 0.142
  Angle     :  0.537   6.337   2938  Z= 0.295
  Chirality :  0.041   0.126    354
  Planarity :  0.003   0.027    361
  Dihedral  :  4.738  18.404    311
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 19.68 %
    Favored  : 75.53 %
  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:  2.29 (0.51), residues: 277
  helix:  2.45 (0.34), residues: 212
  sheet:  None (None), residues: 0
  loop : -1.81 (0.73), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP R 173 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.006   0.001   PHE R 101 
 TYR   0.008   0.001   TYR R 185 
 ARG   0.002   0.000   ARG R 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05679 (  161)
  hydrogen bonds       : angle       3.98167 (  483)
  SS BOND              : bond        0.00438 (    2)
  SS BOND              : angle       1.68392 (    4)
  covalent geometry    : bond        0.00308 ( 2135)
  covalent geometry    : angle       0.53426 ( 2934)

*********************** 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
  39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 30
  time to evaluate  : 0.227 
Fit side-chains
REVERT: R  163 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7401 (tt)
REVERT: R  171 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6132 (ppp)
REVERT: R  173 TRP cc_start: 0.7964 (m-10) cc_final: 0.6986 (m-90)
  outliers start: 9
  outliers final: 6
  residues processed: 35
  average time/residue: 0.1348
  time to fit residues: 5.6676
Evaluate side-chains
  38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 30
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   62 GLU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  171 MET
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  314 ILE
Chi-restraints excluded: chain R residue  328 ARG
Chi-restraints excluded: chain R residue  340 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0980
   chunk 2 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0970
   chunk 5 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3710 r_free = 0.3710 target = 0.150501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.133049 restraints weight = 3355.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.137831 restraints weight = 1706.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.139488 restraints weight = 837.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.1932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2137  Z= 0.136
  Angle     :  0.521   5.343   2938  Z= 0.287
  Chirality :  0.041   0.126    354
  Planarity :  0.003   0.026    361
  Dihedral  :  4.655  18.330    311
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 22.34 %
    Favored  : 74.47 %
  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:  2.39 (0.51), residues: 277
  helix:  2.53 (0.34), residues: 212
  sheet:  None (None), residues: 0
  loop : -1.81 (0.74), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 173 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.006   0.001   PHE R 217 
 TYR   0.007   0.001   TYR R 185 
 ARG   0.002   0.000   ARG R 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05435 (  161)
  hydrogen bonds       : angle       3.90885 (  483)
  SS BOND              : bond        0.00424 (    2)
  SS BOND              : angle       1.64595 (    4)
  covalent geometry    : bond        0.00289 ( 2135)
  covalent geometry    : angle       0.51780 ( 2934)

*********************** 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
  36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 30
  time to evaluate  : 0.233 
Fit side-chains
REVERT: R  171 MET cc_start: 0.6976 (ppp) cc_final: 0.6401 (ppp)
REVERT: R  173 TRP cc_start: 0.7880 (m-10) cc_final: 0.7013 (m-90)
  outliers start: 6
  outliers final: 6
  residues processed: 34
  average time/residue: 0.1367
  time to fit residues: 5.5975
Evaluate side-chains
  35 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 29
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   62 GLU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  328 ARG
Chi-restraints excluded: chain R residue  340 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 5 optimal weight:    0.0870
   chunk 12 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 7 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.5558

-------------------------------------------------------------------------------
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 = 0.3737 r_free = 0.3737 target = 0.152567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.135353 restraints weight = 3352.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.139610 restraints weight = 1689.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.141558 restraints weight = 895.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.2048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2137  Z= 0.136
  Angle     :  0.533   7.229   2938  Z= 0.291
  Chirality :  0.040   0.123    354
  Planarity :  0.003   0.026    361
  Dihedral  :  4.635  18.327    311
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 21.81 %
    Favored  : 75.00 %
  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:  2.42 (0.51), residues: 277
  helix:  2.54 (0.34), residues: 212
  sheet:  None (None), residues: 0
  loop : -1.76 (0.76), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 173 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.006   0.001   PHE R 217 
 TYR   0.007   0.001   TYR R 185 
 ARG   0.002   0.000   ARG R 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05433 (  161)
  hydrogen bonds       : angle       3.88766 (  483)
  SS BOND              : bond        0.00409 (    2)
  SS BOND              : angle       1.64301 (    4)
  covalent geometry    : bond        0.00292 ( 2135)
  covalent geometry    : angle       0.52942 ( 2934)

*********************** 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
  35 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 29
  time to evaluate  : 0.224 
Fit side-chains
REVERT: R   40 MET cc_start: 0.8146 (mmm) cc_final: 0.7904 (mmm)
REVERT: R  171 MET cc_start: 0.7009 (ppp) cc_final: 0.6493 (ppp)
REVERT: R  173 TRP cc_start: 0.7832 (m-10) cc_final: 0.7010 (m-10)
  outliers start: 6
  outliers final: 6
  residues processed: 33
  average time/residue: 0.1377
  time to fit residues: 5.4844
Evaluate side-chains
  35 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 29
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   62 GLU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  328 ARG
Chi-restraints excluded: chain R residue  340 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3688 r_free = 0.3688 target = 0.148327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.130793 restraints weight = 3463.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.135319 restraints weight = 1778.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.137092 restraints weight = 893.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2137  Z= 0.156
  Angle     :  0.553   6.606   2938  Z= 0.305
  Chirality :  0.041   0.125    354
  Planarity :  0.003   0.026    361
  Dihedral  :  4.731  19.013    311
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 2.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 21.28 %
    Favored  : 75.00 %
  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:  2.26 (0.51), residues: 277
  helix:  2.41 (0.34), residues: 212
  sheet:  None (None), residues: 0
  loop : -1.78 (0.76), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 173 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.006   0.001   PHE R  61 
 TYR   0.008   0.001   TYR R 185 
 ARG   0.002   0.000   ARG R 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05990 (  161)
  hydrogen bonds       : angle       4.01727 (  483)
  SS BOND              : bond        0.00470 (    2)
  SS BOND              : angle       1.72392 (    4)
  covalent geometry    : bond        0.00348 ( 2135)
  covalent geometry    : angle       0.54923 ( 2934)

*********************** 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
  35 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 28
  time to evaluate  : 0.227 
Fit side-chains
REVERT: R  171 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6038 (ppp)
REVERT: R  173 TRP cc_start: 0.7820 (m-10) cc_final: 0.6874 (m-10)
  outliers start: 7
  outliers final: 6
  residues processed: 32
  average time/residue: 0.1413
  time to fit residues: 5.4238
Evaluate side-chains
  34 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 27
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   62 GLU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  171 MET
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  328 ARG
Chi-restraints excluded: chain R residue  340 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 17 optimal weight:    0.4980
   chunk 2 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 4 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.151213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.133988 restraints weight = 3269.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.138478 restraints weight = 1690.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.140086 restraints weight = 860.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2137  Z= 0.146
  Angle     :  0.539   6.561   2938  Z= 0.297
  Chirality :  0.041   0.128    354
  Planarity :  0.003   0.027    361
  Dihedral  :  4.704  18.914    311
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 2.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 21.28 %
    Favored  : 75.00 %
  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:  2.34 (0.51), residues: 277
  helix:  2.46 (0.34), residues: 212
  sheet:  None (None), residues: 0
  loop : -1.71 (0.78), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 173 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.006   0.001   PHE R 217 
 TYR   0.007   0.001   TYR R 185 
 ARG   0.002   0.000   ARG R 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05752 (  161)
  hydrogen bonds       : angle       3.95740 (  483)
  SS BOND              : bond        0.00456 (    2)
  SS BOND              : angle       1.65849 (    4)
  covalent geometry    : bond        0.00318 ( 2135)
  covalent geometry    : angle       0.53543 ( 2934)

********************** 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
  34 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 27
  time to evaluate  : 0.242 
Fit side-chains
REVERT: R  171 MET cc_start: 0.6938 (OUTLIER) cc_final: 0.6492 (ppp)
REVERT: R  173 TRP cc_start: 0.7833 (m-10) cc_final: 0.7079 (m-10)
  outliers start: 7
  outliers final: 6
  residues processed: 31
  average time/residue: 0.1476
  time to fit residues: 5.5238
Evaluate side-chains
  34 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 27
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   62 GLU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  171 MET
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  328 ARG
Chi-restraints excluded: chain R residue  340 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0970
   chunk 4 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0270
   chunk 15 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0980
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.2836

-------------------------------------------------------------------------------
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 = 0.3768 r_free = 0.3768 target = 0.155711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.139184 restraints weight = 3245.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.142965 restraints weight = 1723.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.144885 restraints weight = 971.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   2137  Z= 0.122
  Angle     :  0.511   6.497   2938  Z= 0.279
  Chirality :  0.040   0.125    354
  Planarity :  0.003   0.026    361
  Dihedral  :  4.497  18.470    311
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 20.21 %
    Favored  : 76.06 %
  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:  2.67 (0.51), residues: 277
  helix:  2.67 (0.35), residues: 213
  sheet:  None (None), residues: 0
  loop : -1.54 (0.77), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 313 
 HIS   0.002   0.000   HIS R 296 
 PHE   0.007   0.001   PHE R 193 
 TYR   0.006   0.001   TYR R 185 
 ARG   0.003   0.000   ARG R 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04695 (  161)
  hydrogen bonds       : angle       3.73371 (  483)
  SS BOND              : bond        0.00332 (    2)
  SS BOND              : angle       1.48978 (    4)
  covalent geometry    : bond        0.00244 ( 2135)
  covalent geometry    : angle       0.50829 ( 2934)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1106.31 seconds
wall clock time: 20 minutes 3.15 seconds (1203.15 seconds total)