Starting phenix.real_space_refine
on Tue Mar  3 10:48:24 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ggo_40015/03_2026/8ggo_40015.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ggo_40015/03_2026/8ggo_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_40015/03_2026/8ggo_40015.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ggo_40015/03_2026/8ggo_40015.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ggo_40015/03_2026/8ggo_40015.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ggo_40015/03_2026/8ggo_40015.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'GLU:plan': 8, 'ARG:plan': 5, 'ASP:plan': 5, 'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 1}
          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: 0.71, per 1000 atoms: 0.34
  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: 0.21
  Conformation dependent library (CDL) restraints added in 58.7 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: 0.06
  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: 0.29

  Time building geometry restraints manager: 0.27 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:             2.040
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     3.730
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.700
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.001   0.000   ARG R 151 
 TYR   0.010   0.001   TYR R 132 
 PHE   0.010   0.001   PHE R  89 
 TRP   0.007   0.001   TRP R 109 
 HIS   0.005   0.001   HIS R 296 

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

*********************** 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  : 0.042 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 14
  average time/residue: 0.0385
  time to fit residues: 0.6771
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  : 0.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 9 optimal weight:    0.5980
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3479 r_free = 0.3479 target = 0.133307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.119083 restraints weight = 2877.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 1.64
r_work: 0.3264 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3157 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.0864

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= 0.161
  Angle     :  0.514   5.299   2959  Z= 0.291
  Chirality :  0.041   0.118    368
  Planarity :  0.004   0.028    354
  Dihedral  :  4.697  19.851    308
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 1.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  :  3.45 %
    Favored  : 94.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.29 (0.51), residues: 275
  helix:  2.12 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.16 (0.79), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 175 
 TYR   0.011   0.002   TYR R 199 
 PHE   0.010   0.001   PHE R 101 
 TRP   0.006   0.001   TRP R 109 
 HIS   0.005   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 2151)
  covalent geometry    : angle       0.51323 ( 2957)
  SS BOND              : bond        0.00142 (    1)
  SS BOND              : angle       1.28475 (    2)
  hydrogen bonds       : bond        0.06769 (  161)
  hydrogen bonds       : angle       4.07339 (  483)

*********************** 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
  16 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 12
  time to evaluate  : 0.067 
Fit side-chains
REVERT: R   82 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7520 (mtm)
  outliers start: 4
  outliers final: 1
  residues processed: 15
  average time/residue: 0.0247
  time to fit residues: 0.5920
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  : 0.067 
-------------------------------------------------------------------------------
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 22 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0980
   chunk 21 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0050
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.4194

-------------------------------------------------------------------------------
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 = 0.3515 r_free = 0.3515 target = 0.136386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.122109 restraints weight = 2848.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 1.65
r_work: 0.3273 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.1005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2152  Z= 0.124
  Angle     :  0.460   5.288   2959  Z= 0.258
  Chirality :  0.038   0.116    368
  Planarity :  0.003   0.025    354
  Dihedral  :  4.326  19.882    308
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  :  4.43 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.58 (0.51), residues: 275
  helix:  2.29 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -0.90 (0.81), residues: 53

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 2151)
  covalent geometry    : angle       0.45956 ( 2957)
  SS BOND              : bond        0.00130 (    1)
  SS BOND              : angle       0.42598 (    2)
  hydrogen bonds       : bond        0.05608 (  161)
  hydrogen bonds       : angle       3.81005 (  483)

*********************** 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
  16 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 12
  time to evaluate  : 0.068 
Fit side-chains
  outliers start: 4
  outliers final: 1
  residues processed: 15
  average time/residue: 0.0287
  time to fit residues: 0.6633
Evaluate side-chains
  11 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 10
  time to evaluate  : 0.068 
-------------------------------------------------------------------------------
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 2 optimal weight:    0.3980
   chunk 22 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 24 optimal weight:    0.1980
   chunk 21 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   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 = 0.3497 r_free = 0.3497 target = 0.134683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.120011 restraints weight = 2892.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 1.71
r_work: 0.3255 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3147 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.1176

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     :  0.466   5.269   2959  Z= 0.261
  Chirality :  0.039   0.113    368
  Planarity :  0.003   0.026    354
  Dihedral  :  4.304  20.368    308
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  :  7.39 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.59 (0.52), residues: 275
  helix:  2.29 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -0.84 (0.84), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 328 
 TYR   0.010   0.001   TYR R 199 
 PHE   0.008   0.001   PHE R  61 
 TRP   0.006   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 2151)
  covalent geometry    : angle       0.46533 ( 2957)
  SS BOND              : bond        0.00212 (    1)
  SS BOND              : angle       0.67552 (    2)
  hydrogen bonds       : bond        0.05939 (  161)
  hydrogen bonds       : angle       3.76122 (  483)

*********************** 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
  15 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 11
  time to evaluate  : 0.075 
Fit side-chains
  outliers start: 4
  outliers final: 2
  residues processed: 14
  average time/residue: 0.0270
  time to fit residues: 0.6113
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  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 MET
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 18 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0870
   chunk 26 optimal weight:    0.0370
   chunk 8 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 4 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 15 optimal weight:    0.4980
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.3836

-------------------------------------------------------------------------------
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 = 0.3514 r_free = 0.3514 target = 0.136330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.121369 restraints weight = 2808.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3363 rms_B_bonded: 1.80
r_work: 0.3282 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.1301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   2152  Z= 0.116
  Angle     :  0.434   5.244   2959  Z= 0.243
  Chirality :  0.038   0.112    368
  Planarity :  0.003   0.027    354
  Dihedral  :  4.170  20.446    308
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 10.34 %
    Favored  : 88.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.71 (0.52), residues: 275
  helix:  2.41 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -0.98 (0.83), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 328 
 TYR   0.007   0.001   TYR R 199 
 PHE   0.007   0.001   PHE R  61 
 TRP   0.006   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 2151)
  covalent geometry    : angle       0.43404 ( 2957)
  SS BOND              : bond        0.00196 (    1)
  SS BOND              : angle       0.37992 (    2)
  hydrogen bonds       : bond        0.05224 (  161)
  hydrogen bonds       : angle       3.62763 (  483)

*********************** 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
  15 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 12
  time to evaluate  : 0.069 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 14
  average time/residue: 0.0265
  time to fit residues: 0.5968
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  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 MET
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 13 optimal weight:    0.5980
   chunk 12 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3452 r_free = 0.3452 target = 0.130788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.115730 restraints weight = 2855.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 1.80
r_work: 0.3204 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3094 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.1343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2152  Z= 0.155
  Angle     :  0.476   5.286   2959  Z= 0.269
  Chirality :  0.040   0.115    368
  Planarity :  0.003   0.027    354
  Dihedral  :  4.333  20.332    308
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 2.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 12.32 %
    Favored  : 86.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.49 (0.52), residues: 275
  helix:  2.26 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.08 (0.85), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 175 
 TYR   0.011   0.001   TYR R 199 
 PHE   0.009   0.001   PHE R  61 
 TRP   0.005   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 2151)
  covalent geometry    : angle       0.47615 ( 2957)
  SS BOND              : bond        0.00234 (    1)
  SS BOND              : angle       0.85062 (    2)
  hydrogen bonds       : bond        0.06546 (  161)
  hydrogen bonds       : angle       3.79577 (  483)

*********************** 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
  13 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 10
  time to evaluate  : 0.080 
Fit side-chains
  outliers start: 3
  outliers final: 3
  residues processed: 12
  average time/residue: 0.0282
  time to fit residues: 0.5595
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  : 0.070 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 11 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 15 optimal weight:    0.2980
   chunk 9 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   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 = 0.3463 r_free = 0.3463 target = 0.131874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.117477 restraints weight = 2857.510|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 1.65
r_work: 0.3232 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3128 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.1381

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= 0.139
  Angle     :  0.460   5.249   2959  Z= 0.260
  Chirality :  0.039   0.116    368
  Planarity :  0.003   0.027    354
  Dihedral  :  4.303  20.684    308
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 1.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.46 (0.52), residues: 275
  helix:  2.26 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.18 (0.82), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 328 
 TYR   0.009   0.001   TYR R 199 
 PHE   0.008   0.001   PHE R  61 
 TRP   0.005   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 2151)
  covalent geometry    : angle       0.46017 ( 2957)
  SS BOND              : bond        0.00254 (    1)
  SS BOND              : angle       0.75488 (    2)
  hydrogen bonds       : bond        0.06221 (  161)
  hydrogen bonds       : angle       3.75158 (  483)

*********************** 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
  13 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 10
  time to evaluate  : 0.077 
Fit side-chains
  outliers start: 3
  outliers final: 3
  residues processed: 12
  average time/residue: 0.0242
  time to fit residues: 0.4875
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  : 0.074 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3444 r_free = 0.3444 target = 0.130142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.115216 restraints weight = 2856.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 1.79
r_work: 0.3202 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3095 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
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      :  0.004   0.031   2152  Z= 0.158
  Angle     :  0.481   5.276   2959  Z= 0.272
  Chirality :  0.040   0.117    368
  Planarity :  0.003   0.028    354
  Dihedral  :  4.387  20.579    308
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 2.20
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.33 (0.52), residues: 275
  helix:  2.16 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.20 (0.82), residues: 53

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 2151)
  covalent geometry    : angle       0.48028 ( 2957)
  SS BOND              : bond        0.00262 (    1)
  SS BOND              : angle       0.94154 (    2)
  hydrogen bonds       : bond        0.06753 (  161)
  hydrogen bonds       : angle       3.83128 (  483)

*********************** 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
  13 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 10
  time to evaluate  : 0.078 
Fit side-chains
  outliers start: 3
  outliers final: 3
  residues processed: 12
  average time/residue: 0.0282
  time to fit residues: 0.5642
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  : 0.078 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 15 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   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 = 0.3481 r_free = 0.3481 target = 0.133073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.118419 restraints weight = 2849.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 1.67
r_work: 0.3210 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3106 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.1467

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= 0.152
  Angle     :  0.474   5.242   2959  Z= 0.268
  Chirality :  0.040   0.115    368
  Planarity :  0.003   0.028    354
  Dihedral  :  4.376  20.772    308
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 12.81 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.32 (0.52), residues: 275
  helix:  2.23 (0.35), residues: 220
  sheet:  None (None), residues: 0
  loop : -1.44 (0.80), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 175 
 TYR   0.010   0.001   TYR R 199 
 PHE   0.008   0.001   PHE R  61 
 TRP   0.004   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 2151)
  covalent geometry    : angle       0.47331 ( 2957)
  SS BOND              : bond        0.00270 (    1)
  SS BOND              : angle       0.86191 (    2)
  hydrogen bonds       : bond        0.06596 (  161)
  hydrogen bonds       : angle       3.81453 (  483)

*********************** 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
  14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 10
  time to evaluate  : 0.071 
Fit side-chains
  outliers start: 4
  outliers final: 4
  residues processed: 13
  average time/residue: 0.0287
  time to fit residues: 0.6036
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  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue   96 THR
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 7 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 13 optimal weight:    0.6980
   chunk 14 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.132515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.117723 restraints weight = 2917.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 1.72
r_work: 0.3209 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3103 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.1482

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= 0.150
  Angle     :  0.472   5.237   2959  Z= 0.267
  Chirality :  0.039   0.115    368
  Planarity :  0.003   0.028    354
  Dihedral  :  4.357  20.817    308
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 12.81 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.31 (0.52), residues: 275
  helix:  2.22 (0.35), residues: 220
  sheet:  None (None), residues: 0
  loop : -1.44 (0.79), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 175 
 TYR   0.010   0.001   TYR R 199 
 PHE   0.009   0.001   PHE R  61 
 TRP   0.004   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 2151)
  covalent geometry    : angle       0.47139 ( 2957)
  SS BOND              : bond        0.00273 (    1)
  SS BOND              : angle       0.85332 (    2)
  hydrogen bonds       : bond        0.06542 (  161)
  hydrogen bonds       : angle       3.80932 (  483)

********************** 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
  14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 10
  time to evaluate  : 0.045 
Fit side-chains
  outliers start: 4
  outliers final: 4
  residues processed: 13
  average time/residue: 0.0233
  time to fit residues: 0.5013
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  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue   96 THR
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 5 optimal weight:    0.2980
   chunk 8 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 16 optimal weight:    0.3980
   chunk 6 optimal weight:    0.0970
   chunk 7 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.4178

-------------------------------------------------------------------------------
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 = 0.3515 r_free = 0.3515 target = 0.136534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.121843 restraints weight = 2843.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 1.70
r_work: 0.3273 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3167 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.1486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   2152  Z= 0.120
  Angle     :  0.437   5.187   2959  Z= 0.245
  Chirality :  0.038   0.112    368
  Planarity :  0.003   0.028    354
  Dihedral  :  4.182  21.172    308
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.51 (0.52), residues: 275
  helix:  2.30 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.21 (0.81), residues: 53

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 2151)
  covalent geometry    : angle       0.43681 ( 2957)
  SS BOND              : bond        0.00256 (    1)
  SS BOND              : angle       0.46687 (    2)
  hydrogen bonds       : bond        0.05463 (  161)
  hydrogen bonds       : angle       3.64704 (  483)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 783.16 seconds
wall clock time: 14 minutes 2.49 seconds (842.49 seconds total)