Starting phenix.real_space_refine
on Sat Apr 26 15:37:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ggo_40015/04_2025/8ggo_40015.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ggo_40015/04_2025/8ggo_40015.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ggo_40015/04_2025/8ggo_40015.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ggo_40015/04_2025/8ggo_40015.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ggo_40015/04_2025/8ggo_40015.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ggo_40015/04_2025/8ggo_40015.cif"
  }
  resolution = 3.2
  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=   0.028
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      13      5.16       5
     C    1403      2.51       5
     N     330      2.21       5
     O     349      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 2095
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 2080
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 279, 2080
          Classifications: {'peptide': 279}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PTRANS': 7, 'TRANS': 271}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 159
          Unresolved non-hydrogen angles: 189
          Unresolved non-hydrogen dihedrals: 131
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 5, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 92
    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: 2.35, per 1000 atoms: 1.12
  Number of scatterers: 2095
  At special positions: 0
  Unit cell: (56.4005, 82.4315, 64.2098, 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      13     16.00
     O     349      8.00
     N     330      7.00
     C    1403      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " 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: 0.61
  Conformation dependent library (CDL) restraints added in 283.9 milliseconds
  

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  534

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 0 sheets defined
      89.2% 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 37 through 61
      removed outlier: 3.566A  pdb=" N   ILE R  43 " --> pdb=" O   VAL R  39 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   VAL R  44 " --> pdb=" O   MET R  40 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 62 through 66
      removed outlier: 3.587A  pdb=" N   GLN R  65 " --> pdb=" O   GLU R  62 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   THR R  66 " --> pdb=" O   ARG R  63 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 62 through 66'
    Processing helix  chain 'R' and resid 67 through 86
      removed outlier: 4.311A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 86 through 97
      removed outlier: 3.534A  pdb=" N   ALA R  92 " --> pdb=" O   PRO R  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 102 through 137
      removed outlier: 3.690A  pdb=" N   SER R 137 " --> pdb=" O   PHE R 133 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 3.844A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
    Processing helix  chain 'R' and resid 208 through 237
    Processing helix  chain 'R' and resid 270 through 299
      removed outlier: 3.741A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.524A  pdb=" N   ILE R 291 " --> pdb=" O   LEU R 287 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   VAL R 292 " --> pdb=" O   PRO R 288 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ILE R 298 " --> pdb=" O   ILE R 294 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
      removed outlier: 3.627A  pdb=" N   TYR R 308 " --> pdb=" O   ARG R 304 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 317 through 326
      removed outlier: 3.819A  pdb=" N   PHE R 321 " --> pdb=" O   VAL R 317 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ASN R 322 " --> pdb=" O   ASN R 318 " (cutoff:3.500A)
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 329 through 340
      removed outlier: 3.649A  pdb=" N   GLU R 338 " --> pdb=" O   ILE R 334 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LEU R 339 " --> pdb=" O   ALA R 335 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   LEU R 340 " --> pdb=" O   PHE R 336 " (cutoff:3.500A)

    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: 0.73 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 359
        1.33 -     1.45: 594
        1.45 -     1.57: 1180
        1.57 -     1.69: 1
        1.69 -     1.81: 17
  Bond restraints: 2151
  Sorted by residual:
  bond pdb=" C   ARG R 328 "
       pdb=" N   SER R 329 "
    ideal  model  delta    sigma   weight residual
    1.331  1.250  0.081 2.07e-02 2.33e+03 1.51e+01
  bond pdb=" C   CYS R 327 "
       pdb=" N   ARG R 328 "
    ideal  model  delta    sigma   weight residual
    1.332  1.284  0.048 1.37e-02 5.33e+03 1.23e+01
  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 6.96e+00
  bond pdb=" CA  VAL R  86 "
       pdb=" C   VAL R  86 "
    ideal  model  delta    sigma   weight residual
    1.523  1.487  0.036 1.37e-02 5.33e+03 6.77e+00
  bond pdb=" CA  VAL R  81 "
       pdb=" C   VAL R  81 "
    ideal  model  delta    sigma   weight residual
    1.523  1.493  0.031 1.27e-02 6.20e+03 5.77e+00
  ... (remaining 2146 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 2879
        1.85 -     3.71: 55
        3.71 -     5.56: 16
        5.56 -     7.42: 5
        7.42 -     9.27: 2
  Bond angle restraints: 2957
  Sorted by residual:
  angle pdb=" N   LEU R  84 "
        pdb=" CA  LEU R  84 "
        pdb=" C   LEU R  84 "
      ideal   model   delta    sigma   weight residual
     111.36  118.41   -7.05 1.09e+00 8.42e-01 4.18e+01
  angle pdb=" N   ALA R  85 "
        pdb=" CA  ALA R  85 "
        pdb=" C   ALA R  85 "
      ideal   model   delta    sigma   weight residual
     113.97  122.12   -8.15 1.28e+00 6.10e-01 4.05e+01
  angle pdb=" N   CYS R 327 "
        pdb=" CA  CYS R 327 "
        pdb=" C   CYS R 327 "
      ideal   model   delta    sigma   weight residual
     111.07  116.65   -5.58 1.07e+00 8.73e-01 2.72e+01
  angle pdb=" N   TYR R 326 "
        pdb=" CA  TYR R 326 "
        pdb=" C   TYR R 326 "
      ideal   model   delta    sigma   weight residual
     111.69  118.05   -6.36 1.23e+00 6.61e-01 2.67e+01
  angle pdb=" C   VAL R  87 "
        pdb=" N   PRO R  88 "
        pdb=" CA  PRO R  88 "
      ideal   model   delta    sigma   weight residual
     119.05  113.44    5.61 1.11e+00 8.12e-01 2.55e+01
  ... (remaining 2952 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.89: 1102
       14.89 -    29.77: 89
       29.77 -    44.65: 25
       44.65 -    59.53: 2
       59.53 -    74.41: 1
  Dihedral angle restraints: 1219
    sinusoidal: 397
      harmonic: 822
  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
     -86.00 -160.41   74.41     1      1.00e+01 1.00e-02 7.02e+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 -163.62  -16.38     0      5.00e+00 4.00e-02 1.07e+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 -163.74  -16.26     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 1216 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 280
       0.048 -    0.096: 71
       0.096 -    0.144: 11
       0.144 -    0.191: 4
       0.191 -    0.239: 2
  Chirality restraints: 368
  Sorted by residual:
  chirality pdb=" CA  ALA R  85 "
            pdb=" N   ALA R  85 "
            pdb=" C   ALA R  85 "
            pdb=" CB  ALA R  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.25    0.24 2.00e-01 2.50e+01 1.43e+00
  chirality pdb=" CA  PHE R  89 "
            pdb=" N   PHE R  89 "
            pdb=" C   PHE R  89 "
            pdb=" CB  PHE R  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CA  CYS R 327 "
            pdb=" N   CYS R 327 "
            pdb=" C   CYS R 327 "
            pdb=" CB  CYS R 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.95e-01
  ... (remaining 365 not shown)

  Planarity restraints: 354
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS R 327 "    0.016 2.00e-02 2.50e+03   3.05e-02 9.28e+00
        pdb=" C   CYS R 327 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   CYS R 327 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ARG R 328 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP R  79 "    0.009 2.00e-02 2.50e+03   1.68e-02 2.83e+00
        pdb=" C   ASP R  79 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   ASP R  79 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LEU R  80 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG R 328 "   -0.007 2.00e-02 2.50e+03   1.37e-02 1.89e+00
        pdb=" C   ARG R 328 "    0.024 2.00e-02 2.50e+03
        pdb=" O   ARG R 328 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   SER R 329 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 351 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 610
        2.83 -     3.34: 2140
        3.34 -     3.86: 3322
        3.86 -     4.38: 3474
        4.38 -     4.90: 6381
  Nonbonded interactions: 15927
  Sorted by model distance:
  nonbonded pdb=" OG  SER R 203 "
            pdb=" OAL G1I R 501 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" O   LEU R  64 "
            pdb=" ND2 ASN R  69 "
     model   vdw
     2.353 3.120
  nonbonded pdb=" OD2 ASP R 113 "
            pdb=" OH  TYR R 316 "
     model   vdw
     2.452 3.040
  nonbonded pdb=" OG  SER R 203 "
            pdb=" OAK G1I R 501 "
     model   vdw
     2.489 3.040
  nonbonded pdb=" O   ALA R 119 "
            pdb=" OG1 THR R 123 "
     model   vdw
     2.532 3.040
  ... (remaining 15922 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.520
  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:                    0.030
  Process input model:                     11.510
  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:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
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      :  0.005   0.081   2152  Z= 0.336
  Angle     :  0.741   9.272   2959  Z= 0.483
  Chirality :  0.046   0.239    368
  Planarity :  0.004   0.030    354
  Dihedral  : 11.582  49.341    682
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  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:  2.30 (0.50), residues: 275
  helix:  2.14 (0.34), residues: 218
  sheet:  None (None), residues: 0
  loop : -0.93 (0.81), residues: 57

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 109 
 HIS   0.005   0.001   HIS R 296 
 PHE   0.010   0.001   PHE R  89 
 TYR   0.010   0.001   TYR R 132 
 ARG   0.001   0.000   ARG R 151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14741 (  161)
  hydrogen bonds       : angle       5.51882 (  483)
  SS BOND              : bond        0.00472 (    1)
  SS BOND              : angle       2.95447 (    2)
  covalent geometry    : bond        0.00548 ( 2151)
  covalent geometry    : angle       0.73742 ( 2957)

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.237 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 14
  average time/residue: 0.1608
  time to fit residues: 2.8887
Evaluate side-chains
  11 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 11
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 22 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 11 optimal weight:    0.3980
   chunk 6 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0980
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
R  93 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.136906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.122079 restraints weight = 2856.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 1.79
r_work: 0.3269 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.0827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2152  Z= 0.134
  Angle     :  0.485   5.201   2959  Z= 0.272
  Chirality :  0.039   0.115    368
  Planarity :  0.004   0.026    354
  Dihedral  :  4.610  19.917    308
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 2.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  :  3.45 %
    Favored  : 95.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.47 (0.51), residues: 275
  helix:  2.25 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.09 (0.78), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.005   0.001   HIS R 296 
 PHE   0.011   0.001   PHE R 108 
 TYR   0.009   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05991 (  161)
  hydrogen bonds       : angle       3.97082 (  483)
  SS BOND              : bond        0.00162 (    1)
  SS BOND              : angle       1.28234 (    2)
  covalent geometry    : bond        0.00281 ( 2151)
  covalent geometry    : angle       0.48369 ( 2957)

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 12
  time to evaluate  : 0.237 
Fit side-chains
REVERT: R   82 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7342 (mtm)
  outliers start: 3
  outliers final: 1
  residues processed: 14
  average time/residue: 0.0697
  time to fit residues: 1.5951
Evaluate side-chains
  13 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 11
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  230 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 20 optimal weight:    0.0870
   chunk 22 optimal weight:    0.7980
   chunk 13 optimal weight:    0.2980
   chunk 25 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0060
   overall best weight:    0.3574

-------------------------------------------------------------------------------
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 = 0.3537 r_free = 0.3537 target = 0.138338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.123483 restraints weight = 2799.512|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 1.80
r_work: 0.3301 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3193 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.0984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   2152  Z= 0.119
  Angle     :  0.451   5.311   2959  Z= 0.252
  Chirality :  0.038   0.115    368
  Planarity :  0.003   0.025    354
  Dihedral  :  4.292  19.735    308
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  :  4.93 %
    Favored  : 93.60 %
  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:  2.68 (0.51), residues: 275
  helix:  2.37 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -0.90 (0.80), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.009   0.001   PHE R 108 
 TYR   0.008   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05360 (  161)
  hydrogen bonds       : angle       3.77557 (  483)
  SS BOND              : bond        0.00128 (    1)
  SS BOND              : angle       0.47933 (    2)
  covalent geometry    : bond        0.00237 ( 2151)
  covalent geometry    : angle       0.45120 ( 2957)

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 12
  time to evaluate  : 0.232 
Fit side-chains
  outliers start: 3
  outliers final: 1
  residues processed: 14
  average time/residue: 0.0749
  time to fit residues: 1.7029
Evaluate side-chains
  12 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 11
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  230 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3489 r_free = 0.3489 target = 0.133740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.119239 restraints weight = 2826.117|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 1.62
r_work: 0.3201 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3096 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.1187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   2152  Z= 0.173
  Angle     :  0.510   5.297   2959  Z= 0.288
  Chirality :  0.040   0.117    368
  Planarity :  0.004   0.027    354
  Dihedral  :  4.530  20.286    308
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 2.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  :  6.90 %
    Favored  : 90.64 %
  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 (0.52), residues: 275
  helix:  2.19 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -0.96 (0.83), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.010   0.001   PHE R  61 
 TYR   0.012   0.002   TYR R 199 
 ARG   0.001   0.000   ARG R 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07139 (  161)
  hydrogen bonds       : angle       3.94976 (  483)
  SS BOND              : bond        0.00188 (    1)
  SS BOND              : angle       0.93200 (    2)
  covalent geometry    : bond        0.00405 ( 2151)
  covalent geometry    : angle       0.50919 ( 2957)

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 11
  time to evaluate  : 0.242 
Fit side-chains
  outliers start: 5
  outliers final: 3
  residues processed: 15
  average time/residue: 0.0843
  time to fit residues: 1.9649
Evaluate side-chains
  13 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 10
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 11 optimal weight:    0.3980
   chunk 0 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 10 optimal weight:    0.2980
   chunk 1 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 2 optimal weight:    0.4980
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.3473 r_free = 0.3473 target = 0.132660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.117658 restraints weight = 2875.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 1.81
r_work: 0.3229 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.1242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2152  Z= 0.133
  Angle     :  0.457   5.268   2959  Z= 0.259
  Chirality :  0.039   0.116    368
  Planarity :  0.003   0.027    354
  Dihedral  :  4.369  20.816    308
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  :  9.36 %
    Favored  : 89.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.58 (0.52), residues: 275
  helix:  2.31 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -0.96 (0.83), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.007   0.001   PHE R  61 
 TYR   0.008   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06003 (  161)
  hydrogen bonds       : angle       3.76899 (  483)
  SS BOND              : bond        0.00248 (    1)
  SS BOND              : angle       0.59121 (    2)
  covalent geometry    : bond        0.00283 ( 2151)
  covalent geometry    : angle       0.45730 ( 2957)

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 11
  time to evaluate  : 0.244 
Fit side-chains
  outliers start: 3
  outliers final: 3
  residues processed: 13
  average time/residue: 0.0719
  time to fit residues: 1.5481
Evaluate side-chains
  14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 11
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 15 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   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 = 0.3478 r_free = 0.3478 target = 0.132714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.118144 restraints weight = 2844.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 1.66
r_work: 0.3221 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.1316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2152  Z= 0.148
  Angle     :  0.473   5.269   2959  Z= 0.268
  Chirality :  0.039   0.115    368
  Planarity :  0.003   0.027    354
  Dihedral  :  4.387  20.697    308
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 1.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 10.84 %
    Favored  : 87.19 %
  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:  2.48 (0.52), residues: 275
  helix:  2.26 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.10 (0.84), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.008   0.001   PHE R  61 
 TYR   0.011   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06461 (  161)
  hydrogen bonds       : angle       3.80465 (  483)
  SS BOND              : bond        0.00257 (    1)
  SS BOND              : angle       0.80942 (    2)
  covalent geometry    : bond        0.00332 ( 2151)
  covalent geometry    : angle       0.47261 ( 2957)

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 11
  time to evaluate  : 0.227 
Fit side-chains
  outliers start: 4
  outliers final: 4
  residues processed: 14
  average time/residue: 0.0710
  time to fit residues: 1.6163
Evaluate side-chains
  14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 10
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 15 optimal weight:    4.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3434 r_free = 0.3434 target = 0.129154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.114236 restraints weight = 2879.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 1.79
r_work: 0.3185 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3077 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.1411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   2152  Z= 0.163
  Angle     :  0.488   5.290   2959  Z= 0.277
  Chirality :  0.040   0.115    368
  Planarity :  0.004   0.028    354
  Dihedral  :  4.463  20.759    308
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 2.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 10.84 %
    Favored  : 86.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.33 (0.52), residues: 275
  helix:  2.23 (0.35), residues: 220
  sheet:  None (None), residues: 0
  loop : -1.41 (0.80), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.009   0.001   PHE R  61 
 TYR   0.011   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06887 (  161)
  hydrogen bonds       : angle       3.86442 (  483)
  SS BOND              : bond        0.00273 (    1)
  SS BOND              : angle       0.96485 (    2)
  covalent geometry    : bond        0.00374 ( 2151)
  covalent geometry    : angle       0.48770 ( 2957)

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 11
  time to evaluate  : 0.227 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 15
  average time/residue: 0.0685
  time to fit residues: 1.6650
Evaluate side-chains
  15 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 11
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 20 optimal weight:    0.5980
   chunk 16 optimal weight:    0.2980
   chunk 3 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 24 optimal weight:    0.3980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.3482 r_free = 0.3482 target = 0.133332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.118294 restraints weight = 2901.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 1.82
r_work: 0.3252 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3143 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.1405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2152  Z= 0.129
  Angle     :  0.448   5.215   2959  Z= 0.253
  Chirality :  0.038   0.114    368
  Planarity :  0.003   0.028    354
  Dihedral  :  4.279  21.126    308
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 12.32 %
    Favored  : 85.71 %
  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:  2.48 (0.52), residues: 275
  helix:  2.28 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.23 (0.82), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.007   0.001   PHE R  61 
 TYR   0.008   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05801 (  161)
  hydrogen bonds       : angle       3.69268 (  483)
  SS BOND              : bond        0.00312 (    1)
  SS BOND              : angle       0.53720 (    2)
  covalent geometry    : bond        0.00276 ( 2151)
  covalent geometry    : angle       0.44779 ( 2957)

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 11
  time to evaluate  : 0.219 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 14
  average time/residue: 0.0697
  time to fit residues: 1.5966
Evaluate side-chains
  14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 11
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  325 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 24 optimal weight:    0.5980
   chunk 15 optimal weight:    0.3980
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3458 r_free = 0.3458 target = 0.131788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.116816 restraints weight = 2918.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 1.82
r_work: 0.3210 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3100 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.1447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2152  Z= 0.139
  Angle     :  0.459   5.223   2959  Z= 0.259
  Chirality :  0.039   0.113    368
  Planarity :  0.003   0.028    354
  Dihedral  :  4.298  20.814    308
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 1.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 13.30 %
    Favored  : 85.22 %
  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:  2.44 (0.52), residues: 275
  helix:  2.24 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.18 (0.82), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 313 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.008   0.001   PHE R  61 
 TYR   0.010   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06199 (  161)
  hydrogen bonds       : angle       3.74570 (  483)
  SS BOND              : bond        0.00240 (    1)
  SS BOND              : angle       0.68254 (    2)
  covalent geometry    : bond        0.00308 ( 2151)
  covalent geometry    : angle       0.45832 ( 2957)

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 10
  time to evaluate  : 0.236 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 13
  average time/residue: 0.0660
  time to fit residues: 1.4464
Evaluate side-chains
  12 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 10
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0970
   chunk 19 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 20 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.5378

-------------------------------------------------------------------------------
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 = 0.3487 r_free = 0.3487 target = 0.134149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.119514 restraints weight = 2861.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 1.70
r_work: 0.3241 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3135 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.1481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2152  Z= 0.131
  Angle     :  0.450   5.226   2959  Z= 0.253
  Chirality :  0.039   0.112    368
  Planarity :  0.003   0.028    354
  Dihedral  :  4.246  20.970    308
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 13.30 %
    Favored  : 85.71 %
  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:  2.48 (0.52), residues: 275
  helix:  2.27 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.17 (0.82), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 313 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.008   0.001   PHE R  61 
 TYR   0.009   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05948 (  161)
  hydrogen bonds       : angle       3.71947 (  483)
  SS BOND              : bond        0.00249 (    1)
  SS BOND              : angle       0.61872 (    2)
  covalent geometry    : bond        0.00284 ( 2151)
  covalent geometry    : angle       0.44939 ( 2957)

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

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

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  550 Ramachandran restraints generated.
    275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  12 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 10
  time to evaluate  : 0.253 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 12
  average time/residue: 0.0829
  time to fit residues: 1.7451
Evaluate side-chains
  12 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 10
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  230 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0000
   chunk 14 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.5784

-------------------------------------------------------------------------------
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 = 0.3464 r_free = 0.3464 target = 0.132347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.117409 restraints weight = 2889.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 1.78
r_work: 0.3221 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3113 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.1510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2152  Z= 0.136
  Angle     :  0.453   5.217   2959  Z= 0.256
  Chirality :  0.039   0.114    368
  Planarity :  0.003   0.028    354
  Dihedral  :  4.255  20.879    308
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 1.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 13.30 %
    Favored  : 85.71 %
  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:  2.46 (0.52), residues: 275
  helix:  2.25 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.16 (0.81), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 313 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.008   0.001   PHE R  61 
 TYR   0.010   0.001   TYR R 199 
 ARG   0.001   0.000   ARG R 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06096 (  161)
  hydrogen bonds       : angle       3.73719 (  483)
  SS BOND              : bond        0.00230 (    1)
  SS BOND              : angle       0.68511 (    2)
  covalent geometry    : bond        0.00298 ( 2151)
  covalent geometry    : angle       0.45330 ( 2957)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1534.71 seconds
wall clock time: 27 minutes 10.99 seconds (1630.99 seconds total)