Starting phenix.real_space_refine
on Fri Aug 22 12:38:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iyx_35832/08_2025/8iyx_35832.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iyx_35832/08_2025/8iyx_35832.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.34
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iyx_35832/08_2025/8iyx_35832.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iyx_35832/08_2025/8iyx_35832.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iyx_35832/08_2025/8iyx_35832.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iyx_35832/08_2025/8iyx_35832.map"
  }
  resolution = 3.34
  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=   0.001 sd=   0.027
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: 5
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     Cl      1      4.86       5
     C    1489      2.51       5
     N     344      2.21       5
     O     353      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2207
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "C"
      Number of atoms: 2165
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2165
          Classifications: {'peptide': 266}
          Link IDs: {'PTRANS': 3, 'TRANS': 262}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 42
          Unusual residues: {'S6R': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.80, per 1000 atoms: 0.36
  Number of scatterers: 2207
  At special positions: 0
  Unit cell: (59.5, 72.25, 58.65, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      20     16.00
     O     353      8.00
     N     344      7.00
     C    1489      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 127 " - pdb=" SG  CYS C 204 " 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: 0.14
  Conformation dependent library (CDL) restraints added in 70.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  516 Ramachandran restraints generated.
    258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  508

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 0 sheets defined
      88.3% 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 'C' and resid 51 through 83
      removed outlier: 3.586A  pdb=" N   ILE C  82 " --> pdb=" O   VAL C  78 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   HIS C  83 " --> pdb=" O   PHE C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 88 through 116
      Proline residue:  C 108  - end of helix
    Processing helix  chain 'C' and resid 124 through 157
      removed outlier: 3.683A  pdb=" N   SER C 149 " --> pdb=" O   LEU C 145 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   LYS C 155 " --> pdb=" O   ASP C 151 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ILE C 156 " --> pdb=" O   ARG C 152 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 168 through 195
      removed outlier: 3.883A  pdb=" N   TRP C 179 " --> pdb=" O   CYS C 175 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   MET C 189 " --> pdb=" O   GLY C 185 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ILE C 190 " --> pdb=" O   PHE C 186 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 213 through 242
      removed outlier: 3.637A  pdb=" N   TRP C 228 " --> pdb=" O   VAL C 224 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 262 through 279
      removed outlier: 3.587A  pdb=" N   PHE C 269 " --> pdb=" O   ALA C 265 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ILE C 270 " --> pdb=" O   ARG C 266 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   VAL C 271 " --> pdb=" O   ASN C 267 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   LEU C 272 " --> pdb=" O   SER C 268 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   PHE C 279 " --> pdb=" O   PHE C 275 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 279 through 294
      removed outlier: 3.505A  pdb=" N   ARG C 286 " --> pdb=" O   TYR C 282 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   PHE C 287 " --> pdb=" O   HIS C 283 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   ILE C 288 " --> pdb=" O   ALA C 284 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 298 through 317
      removed outlier: 3.714A  pdb=" N   GLU C 303 " --> pdb=" O   CYS C 299 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLU C 310 " --> pdb=" O   HIS C 306 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ILE C 311 " --> pdb=" O   LYS C 307 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   VAL C 314 " --> pdb=" O   GLU C 310 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LEU C 315 " --> pdb=" O   ILE C 311 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   SER C 316 " --> pdb=" O   MET C 312 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 318 through 331
      Proline residue:  C 324  - end of helix
      removed outlier: 3.641A  pdb=" N   LEU C 329 " --> pdb=" O   VAL C 325 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   SER C 331 " --> pdb=" O   TYR C 327 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 331 through 343
      removed outlier: 3.694A  pdb=" N   ARG C 335 " --> pdb=" O   SER C 331 " (cutoff:3.500A)

    163 hydrogen bonds defined for protein.
    489 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: 0.30

  Time building geometry restraints manager: 0.16 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 304
        1.31 -     1.43: 653
        1.43 -     1.56: 1270
        1.56 -     1.68: 1
        1.68 -     1.81: 32
  Bond restraints: 2260
  Sorted by residual:
  bond pdb=" C26 S6R C 401 "
       pdb=" N25 S6R C 401 "
    ideal  model  delta    sigma   weight residual
    1.347  1.462 -0.115 2.00e-02 2.50e+03 3.29e+01
  bond pdb=" C02 S6R C 401 "
       pdb=" N18 S6R C 401 "
    ideal  model  delta    sigma   weight residual
    1.348  1.453 -0.105 2.00e-02 2.50e+03 2.78e+01
  bond pdb=" CA  SER C 141 "
       pdb=" CB  SER C 141 "
    ideal  model  delta    sigma   weight residual
    1.528  1.476  0.053 1.56e-02 4.11e+03 1.15e+01
  bond pdb=" CA  SER C 149 "
       pdb=" CB  SER C 149 "
    ideal  model  delta    sigma   weight residual
    1.530  1.478  0.052 1.57e-02 4.06e+03 1.09e+01
  bond pdb=" C19 S6R C 401 "
       pdb=" C23 S6R C 401 "
    ideal  model  delta    sigma   weight residual
    1.538  1.475  0.063 2.00e-02 2.50e+03 9.91e+00
  ... (remaining 2255 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 2860
        1.41 -     2.83: 127
        2.83 -     4.24: 44
        4.24 -     5.66: 21
        5.66 -     7.07: 6
  Bond angle restraints: 3058
  Sorted by residual:
  angle pdb=" C   LEU C 150 "
        pdb=" N   ASP C 151 "
        pdb=" CA  ASP C 151 "
      ideal   model   delta    sigma   weight residual
     120.28  113.26    7.02 1.34e+00 5.57e-01 2.74e+01
  angle pdb=" CA  SER C 141 "
        pdb=" C   SER C 141 "
        pdb=" O   SER C 141 "
      ideal   model   delta    sigma   weight residual
     120.55  116.25    4.30 1.06e+00 8.90e-01 1.64e+01
  angle pdb=" N   LEU C 150 "
        pdb=" CA  LEU C 150 "
        pdb=" C   LEU C 150 "
      ideal   model   delta    sigma   weight residual
     111.11  106.36    4.75 1.20e+00 6.94e-01 1.57e+01
  angle pdb=" N   LEU C 145 "
        pdb=" CA  LEU C 145 "
        pdb=" C   LEU C 145 "
      ideal   model   delta    sigma   weight residual
     112.23  107.64    4.59 1.26e+00 6.30e-01 1.33e+01
  angle pdb=" CA  TYR C 139 "
        pdb=" C   TYR C 139 "
        pdb=" O   TYR C 139 "
      ideal   model   delta    sigma   weight residual
     120.42  116.63    3.79 1.06e+00 8.90e-01 1.28e+01
  ... (remaining 3053 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.98: 1153
       15.98 -    31.97: 119
       31.97 -    47.95: 39
       47.95 -    63.93: 16
       63.93 -    79.92: 2
  Dihedral angle restraints: 1329
    sinusoidal: 544
      harmonic: 785
  Sorted by residual:
  dihedral pdb=" CB  CYS C 127 "
           pdb=" SG  CYS C 127 "
           pdb=" SG  CYS C 204 "
           pdb=" CB  CYS C 204 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -138.93   52.93     1      1.00e+01 1.00e-02 3.81e+01
  dihedral pdb=" C   TYR C 139 "
           pdb=" N   TYR C 139 "
           pdb=" CA  TYR C 139 "
           pdb=" CB  TYR C 139 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.66   10.06     0      2.50e+00 1.60e-01 1.62e+01
  dihedral pdb=" CA  ILE C  82 "
           pdb=" C   ILE C  82 "
           pdb=" N   HIS C  83 "
           pdb=" CA  HIS C  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.99  -17.01     0      5.00e+00 4.00e-02 1.16e+01
  ... (remaining 1326 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 324
       0.069 -    0.138: 34
       0.138 -    0.206: 2
       0.206 -    0.275: 2
       0.275 -    0.344: 1
  Chirality restraints: 363
  Sorted by residual:
  chirality pdb=" CA  TYR C 139 "
            pdb=" N   TYR C 139 "
            pdb=" C   TYR C 139 "
            pdb=" CB  TYR C 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.95e+00
  chirality pdb=" CA  ILE C 140 "
            pdb=" N   ILE C 140 "
            pdb=" C   ILE C 140 "
            pdb=" CB  ILE C 140 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" C19 S6R C 401 "
            pdb=" C20 S6R C 401 "
            pdb=" C23 S6R C 401 "
            pdb=" C42 S6R C 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.88    2.67    0.21 2.00e-01 2.50e+01 1.13e+00
  ... (remaining 360 not shown)

  Planarity restraints: 353
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY C 146 "   -0.011 2.00e-02 2.50e+03   2.31e-02 5.33e+00
        pdb=" C   GLY C 146 "    0.040 2.00e-02 2.50e+03
        pdb=" O   GLY C 146 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   PHE C 147 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 205 "   -0.012 2.00e-02 2.50e+03   1.36e-02 3.26e+00
        pdb=" CG  PHE C 205 "    0.032 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 205 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 205 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 205 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 205 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 205 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG C 152 "    0.009 2.00e-02 2.50e+03   1.69e-02 2.85e+00
        pdb=" C   ARG C 152 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   ARG C 152 "    0.011 2.00e-02 2.50e+03
        pdb=" N   TYR C 153 "    0.010 2.00e-02 2.50e+03
  ... (remaining 350 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 501
        2.78 -     3.31: 2279
        3.31 -     3.84: 3484
        3.84 -     4.37: 3862
        4.37 -     4.90: 6550
  Nonbonded interactions: 16676
  Sorted by model distance:
  nonbonded pdb=" O   LEU C 192 "
            pdb=" N   LYS C 196 "
     model   vdw
     2.252 3.120
  nonbonded pdb=" OH  TYR C 282 "
            pdb=" NH2 ARG C 286 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" O   ALA C  99 "
            pdb=" ND2 ASN C 137 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" O   ARG C 208 "
            pdb=" NE2 GLN C 293 "
     model   vdw
     2.348 3.120
  nonbonded pdb=" OD1 ASN C  95 "
            pdb=" NE1 TRP C 179 "
     model   vdw
     2.353 3.120
  ... (remaining 16671 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     3.570
  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:1.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
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      :  0.007   0.115   2261  Z= 0.397
  Angle     :  0.860   7.071   3060  Z= 0.510
  Chirality :  0.050   0.344    363
  Planarity :  0.004   0.031    353
  Dihedral  : 15.492  79.918    818
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  3.49 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  :  1.63 %
    Favored  : 94.29 %
  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 aren not related in a simple way.
  whole:  0.98 (0.50), residues: 258
  helix:  1.32 (0.34), residues: 207
  sheet:  None (None), residues: 0
  loop : -2.10 (0.83), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 110 
 TYR   0.021   0.002   TYR C 139 
 PHE   0.032   0.002   PHE C 205 
 TRP   0.005   0.001   TRP C 228 
 HIS   0.002   0.001   HIS C 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00685 ( 2260)
  covalent geometry    : angle       0.85745 ( 3058)
  SS BOND              : bond        0.00641 (    1)
  SS BOND              : angle       2.81128 (    2)
  hydrogen bonds       : bond        0.24738 (  163)
  hydrogen bonds       : angle       6.17042 (  489)

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

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

  516 Ramachandran restraints generated.
    258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  516 Ramachandran restraints generated.
    258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.050 
Fit side-chains
   revert: symmetry clash
  outliers start: 10
  outliers final: 5
  residues processed: 83
  average time/residue: 0.0460
  time to fit residues: 4.3588
Evaluate side-chains
  67 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  141 SER
Chi-restraints excluded: chain C residue  145 LEU
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  219 PHE
Chi-restraints excluded: chain C residue  264 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 15 optimal weight:    8.9990
   chunk 25 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 18 optimal weight:   20.0000
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.4196 r_free = 0.4196 target = 0.161748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.130546 restraints weight = 3546.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.3813 rms_B_bonded: 2.64
r_work: 0.3586 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.2550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   2261  Z= 0.177
  Angle     :  0.679   7.255   3060  Z= 0.351
  Chirality :  0.041   0.113    363
  Planarity :  0.004   0.040    353
  Dihedral  :  9.216  57.031    331
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 15.10 %
    Favored  : 80.82 %
  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 aren not related in a simple way.
  whole:  2.20 (0.50), residues: 258
  helix:  1.98 (0.33), residues: 222
  sheet:  None (None), residues: 0
  loop : -1.94 (0.86), residues: 36

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 110 
 TYR   0.014   0.002   TYR C 327 
 PHE   0.014   0.001   PHE C 221 
 TRP   0.004   0.001   TRP C 120 
 HIS   0.002   0.000   HIS C 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 2260)
  covalent geometry    : angle       0.67744 ( 3058)
  SS BOND              : bond        0.00033 (    1)
  SS BOND              : angle       1.79380 (    2)
  hydrogen bonds       : bond        0.07612 (  163)
  hydrogen bonds       : angle       4.28340 (  489)

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

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

  516 Ramachandran restraints generated.
    258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  516 Ramachandran restraints generated.
    258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.092 
Fit side-chains
  outliers start: 10
  outliers final: 4
  residues processed: 75
  average time/residue: 0.0938
  time to fit residues: 7.9075
Evaluate side-chains
  65 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue  115 ILE
Chi-restraints excluded: chain C residue  137 ASN
Chi-restraints excluded: chain C residue  339 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 2 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0570
   chunk 13 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.6098

-------------------------------------------------------------------------------
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 = 0.3997 r_free = 0.3997 target = 0.154749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.120952 restraints weight = 3537.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.3538 rms_B_bonded: 2.75
r_work: 0.3339 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.3185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2261  Z= 0.151
  Angle     :  0.617   5.726   3060  Z= 0.317
  Chirality :  0.040   0.118    363
  Planarity :  0.004   0.038    353
  Dihedral  :  7.012  47.782    323
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 19.18 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.65 (0.50), residues: 258
  helix:  2.32 (0.32), residues: 222
  sheet:  None (None), residues: 0
  loop : -2.01 (0.88), residues: 36

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 110 
 TYR   0.011   0.001   TYR C 238 
 PHE   0.014   0.001   PHE C 221 
 TRP   0.004   0.001   TRP C 120 
 HIS   0.002   0.001   HIS C 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 2260)
  covalent geometry    : angle       0.61581 ( 3058)
  SS BOND              : bond        0.00484 (    1)
  SS BOND              : angle       1.63886 (    2)
  hydrogen bonds       : bond        0.06433 (  163)
  hydrogen bonds       : angle       3.88973 (  489)

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

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

  516 Ramachandran restraints generated.
    258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  516 Ramachandran restraints generated.
    258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.087 
Fit side-chains
REVERT: C  195 LYS cc_start: 0.4376 (mmtt) cc_final: 0.3777 (mptt)
  outliers start: 5
  outliers final: 4
  residues processed: 69
  average time/residue: 0.0717
  time to fit residues: 5.7101
Evaluate side-chains
  62 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue  137 ASN
Chi-restraints excluded: chain C residue  339 CYS
Chi-restraints excluded: chain C residue  343 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 15 optimal weight:   10.0000
   chunk 14 optimal weight:    4.9990
   chunk 3 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
C  83 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.153259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.119139 restraints weight = 3503.339|
|-----------------------------------------------------------------------------|
r_work (start): 0.3530 rms_B_bonded: 2.62
r_work: 0.3330 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.3628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2261  Z= 0.157
  Angle     :  0.614   6.109   3060  Z= 0.314
  Chirality :  0.039   0.112    363
  Planarity :  0.004   0.040    353
  Dihedral  :  6.635  43.748    323
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 20.00 %
    Favored  : 76.73 %
  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 aren not related in a simple way.
  whole:  2.70 (0.50), residues: 258
  helix:  2.40 (0.32), residues: 222
  sheet:  None (None), residues: 0
  loop : -2.42 (0.84), residues: 36

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 110 
 TYR   0.008   0.001   TYR C 238 
 PHE   0.012   0.001   PHE C 205 
 TRP   0.005   0.001   TRP C 120 
 HIS   0.003   0.001   HIS C 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 2260)
  covalent geometry    : angle       0.61341 ( 3058)
  SS BOND              : bond        0.00705 (    1)
  SS BOND              : angle       1.39662 (    2)
  hydrogen bonds       : bond        0.06368 (  163)
  hydrogen bonds       : angle       3.76747 (  489)

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

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

  516 Ramachandran restraints generated.
    258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  516 Ramachandran restraints generated.
    258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.092 
Fit side-chains
REVERT: C  312 MET cc_start: 0.8838 (tpp) cc_final: 0.8442 (mmm)
  outliers start: 8
  outliers final: 3
  residues processed: 63
  average time/residue: 0.0637
  time to fit residues: 4.6975
Evaluate side-chains
  60 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 57
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue  115 ILE
Chi-restraints excluded: chain C residue  137 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.3981 r_free = 0.3981 target = 0.153178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.118702 restraints weight = 3520.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 2.62
r_work: 0.3332 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.3777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2261  Z= 0.153
  Angle     :  0.642  10.761   3060  Z= 0.321
  Chirality :  0.039   0.113    363
  Planarity :  0.004   0.041    353
  Dihedral  :  6.374  40.524    323
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 20.82 %
    Favored  : 76.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.67 (0.50), residues: 258
  helix:  2.38 (0.32), residues: 223
  sheet:  None (None), residues: 0
  loop : -2.54 (0.86), residues: 35

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 110 
 TYR   0.008   0.001   TYR C 139 
 PHE   0.010   0.001   PHE C 205 
 TRP   0.005   0.001   TRP C 120 
 HIS   0.003   0.001   HIS C 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 2260)
  covalent geometry    : angle       0.64169 ( 3058)
  SS BOND              : bond        0.00301 (    1)
  SS BOND              : angle       0.48742 (    2)
  hydrogen bonds       : bond        0.06125 (  163)
  hydrogen bonds       : angle       3.82477 (  489)

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

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

  516 Ramachandran restraints generated.
    258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  516 Ramachandran restraints generated.
    258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.086 
Fit side-chains
REVERT: C  173 TYR cc_start: 0.7736 (m-10) cc_final: 0.7367 (m-80)
  outliers start: 7
  outliers final: 3
  residues processed: 65
  average time/residue: 0.0620
  time to fit residues: 4.7619
Evaluate side-chains
  58 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 55
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  115 ILE
Chi-restraints excluded: chain C residue  137 ASN
Chi-restraints excluded: chain C residue  341 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 22 optimal weight:    4.9990
   chunk 11 optimal weight:    0.7980
   chunk 4 optimal weight:    0.4980
   chunk 2 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
C  83 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.153855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.119271 restraints weight = 3503.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 2.66
r_work: 0.3345 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.4074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2261  Z= 0.140
  Angle     :  0.601   7.526   3060  Z= 0.297
  Chirality :  0.038   0.112    363
  Planarity :  0.004   0.042    353
  Dihedral  :  6.077  37.737    323
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 22.04 %
    Favored  : 75.92 %
  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 aren not related in a simple way.
  whole:  3.05 (0.50), residues: 258
  helix:  2.66 (0.33), residues: 222
  sheet:  None (None), residues: 0
  loop : -2.48 (0.84), residues: 36

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 110 
 TYR   0.007   0.001   TYR C 139 
 PHE   0.007   0.001   PHE C 134 
 TRP   0.005   0.001   TRP C 120 
 HIS   0.001   0.000   HIS C 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 2260)
  covalent geometry    : angle       0.60126 ( 3058)
  SS BOND              : bond        0.00398 (    1)
  SS BOND              : angle       0.78758 (    2)
  hydrogen bonds       : bond        0.05674 (  163)
  hydrogen bonds       : angle       3.61917 (  489)

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

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

  516 Ramachandran restraints generated.
    258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  516 Ramachandran restraints generated.
    258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.092 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 62
  average time/residue: 0.0607
  time to fit residues: 4.4568
Evaluate side-chains
  57 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  115 ILE
Chi-restraints excluded: chain C residue  137 ASN
Chi-restraints excluded: chain C residue  337 ILE
Chi-restraints excluded: chain C residue  343 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0010
   chunk 7 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 22 optimal weight:    0.0770
   chunk 0 optimal weight:    5.9990
   chunk 12 optimal weight:    0.4980
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.7148

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

Flipped N/Q/H residues before XYZ refinement:
** C 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.154678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.120707 restraints weight = 3603.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 2.64
r_work: 0.3363 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.4194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2261  Z= 0.141
  Angle     :  0.658  13.788   3060  Z= 0.316
  Chirality :  0.039   0.137    363
  Planarity :  0.004   0.042    353
  Dihedral  :  6.023  35.963    323
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 23.67 %
    Favored  : 74.29 %
  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 aren not related in a simple way.
  whole:  3.00 (0.51), residues: 258
  helix:  2.60 (0.33), residues: 223
  sheet:  None (None), residues: 0
  loop : -2.46 (0.84), residues: 35

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 110 
 TYR   0.023   0.001   TYR C 238 
 PHE   0.008   0.001   PHE C 205 
 TRP   0.005   0.001   TRP C 120 
 HIS   0.001   0.000   HIS C 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 2260)
  covalent geometry    : angle       0.65838 ( 3058)
  SS BOND              : bond        0.00107 (    1)
  SS BOND              : angle       0.24659 (    2)
  hydrogen bonds       : bond        0.05574 (  163)
  hydrogen bonds       : angle       3.73187 (  489)

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

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

  516 Ramachandran restraints generated.
    258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  516 Ramachandran restraints generated.
    258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
REVERT: C  195 LYS cc_start: 0.4312 (mptt) cc_final: 0.3124 (tppt)
REVERT: C  269 PHE cc_start: 0.7484 (m-10) cc_final: 0.7162 (m-10)
  outliers start: 5
  outliers final: 5
  residues processed: 59
  average time/residue: 0.0635
  time to fit residues: 4.4045
Evaluate side-chains
  61 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  115 ILE
Chi-restraints excluded: chain C residue  136 MET
Chi-restraints excluded: chain C residue  137 ASN
Chi-restraints excluded: chain C residue  337 ILE
Chi-restraints excluded: chain C residue  343 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 14 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 15 optimal weight:    9.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
C  83 HIS
** C 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.151898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.116580 restraints weight = 3600.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 2.74
r_work: 0.3306 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.4312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2261  Z= 0.157
  Angle     :  0.634   7.074   3060  Z= 0.311
  Chirality :  0.039   0.132    363
  Planarity :  0.004   0.041    353
  Dihedral  :  5.982  34.161    323
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 24.08 %
    Favored  : 73.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.05 (0.51), residues: 258
  helix:  2.65 (0.33), residues: 223
  sheet:  None (None), residues: 0
  loop : -2.54 (0.82), residues: 35

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 110 
 TYR   0.016   0.001   TYR C 238 
 PHE   0.011   0.001   PHE C 205 
 TRP   0.006   0.001   TRP C 120 
 HIS   0.002   0.001   HIS C 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 2260)
  covalent geometry    : angle       0.63429 ( 3058)
  SS BOND              : bond        0.00126 (    1)
  SS BOND              : angle       0.70452 (    2)
  hydrogen bonds       : bond        0.06067 (  163)
  hydrogen bonds       : angle       3.72199 (  489)

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

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

  516 Ramachandran restraints generated.
    258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  516 Ramachandran restraints generated.
    258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.052 
Fit side-chains
   revert: symmetry clash
REVERT: C  195 LYS cc_start: 0.4359 (mptt) cc_final: 0.3180 (tppt)
  outliers start: 6
  outliers final: 4
  residues processed: 61
  average time/residue: 0.0558
  time to fit residues: 4.0233
Evaluate side-chains
  58 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 54
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  115 ILE
Chi-restraints excluded: chain C residue  137 ASN
Chi-restraints excluded: chain C residue  337 ILE
Chi-restraints excluded: chain C residue  341 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 11 optimal weight:    0.0770
   chunk 16 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 4 optimal weight:    0.2980
   chunk 22 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.5538

-------------------------------------------------------------------------------
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 = 0.4000 r_free = 0.4000 target = 0.155239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.121676 restraints weight = 3669.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 2.70
r_work: 0.3366 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.4425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2261  Z= 0.133
  Angle     :  0.662  15.536   3060  Z= 0.313
  Chirality :  0.038   0.115    363
  Planarity :  0.003   0.042    353
  Dihedral  :  5.906  36.928    323
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 25.31 %
    Favored  : 72.65 %
  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 aren not related in a simple way.
  whole:  3.01 (0.51), residues: 258
  helix:  2.64 (0.33), residues: 223
  sheet:  None (None), residues: 0
  loop : -2.66 (0.81), residues: 35

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 110 
 TYR   0.015   0.001   TYR C 238 
 PHE   0.007   0.001   PHE C 134 
 TRP   0.004   0.001   TRP C 120 
 HIS   0.001   0.000   HIS C 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 2260)
  covalent geometry    : angle       0.66192 ( 3058)
  SS BOND              : bond        0.00214 (    1)
  SS BOND              : angle       0.05576 (    2)
  hydrogen bonds       : bond        0.05247 (  163)
  hydrogen bonds       : angle       3.69591 (  489)

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

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

  516 Ramachandran restraints generated.
    258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  516 Ramachandran restraints generated.
    258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.072 
Fit side-chains
REVERT: C  173 TYR cc_start: 0.7474 (m-10) cc_final: 0.7269 (m-10)
REVERT: C  195 LYS cc_start: 0.4443 (mptt) cc_final: 0.3303 (tppt)
REVERT: C  214 LYS cc_start: 0.7694 (mttt) cc_final: 0.6988 (pttm)
  outliers start: 5
  outliers final: 4
  residues processed: 62
  average time/residue: 0.0625
  time to fit residues: 4.5583
Evaluate side-chains
  60 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  115 ILE
Chi-restraints excluded: chain C residue  136 MET
Chi-restraints excluded: chain C residue  137 ASN
Chi-restraints excluded: chain C residue  341 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 10 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 0 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
C  83 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.153148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.118719 restraints weight = 3636.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 2.76
r_work: 0.3339 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.4508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2261  Z= 0.143
  Angle     :  0.662  14.604   3060  Z= 0.312
  Chirality :  0.039   0.159    363
  Planarity :  0.003   0.041    353
  Dihedral  :  5.929  38.758    323
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 26.12 %
    Favored  : 71.84 %
  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 aren not related in a simple way.
  whole:  2.93 (0.51), residues: 258
  helix:  2.59 (0.33), residues: 223
  sheet:  None (None), residues: 0
  loop : -2.77 (0.80), residues: 35

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 110 
 TYR   0.013   0.001   TYR C 238 
 PHE   0.009   0.001   PHE C 205 
 TRP   0.006   0.001   TRP C 228 
 HIS   0.003   0.001   HIS C  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 2260)
  covalent geometry    : angle       0.66254 ( 3058)
  SS BOND              : bond        0.00110 (    1)
  SS BOND              : angle       0.43737 (    2)
  hydrogen bonds       : bond        0.05669 (  163)
  hydrogen bonds       : angle       3.77044 (  489)

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

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

  516 Ramachandran restraints generated.
    258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  516 Ramachandran restraints generated.
    258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.107 
Fit side-chains
REVERT: C  173 TYR cc_start: 0.7463 (m-10) cc_final: 0.7238 (m-10)
REVERT: C  195 LYS cc_start: 0.4473 (mptt) cc_final: 0.3385 (tppt)
  outliers start: 5
  outliers final: 4
  residues processed: 56
  average time/residue: 0.0632
  time to fit residues: 4.1637
Evaluate side-chains
  56 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 52
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  115 ILE
Chi-restraints excluded: chain C residue  136 MET
Chi-restraints excluded: chain C residue  137 ASN
Chi-restraints excluded: chain C residue  341 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 26
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 7 optimal weight:    0.5980
   chunk 13 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.154281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.120009 restraints weight = 3701.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3547 rms_B_bonded: 2.76
r_work: 0.3353 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.4539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2261  Z= 0.138
  Angle     :  0.615   8.313   3060  Z= 0.299
  Chirality :  0.038   0.128    363
  Planarity :  0.003   0.042    353
  Dihedral  :  5.873  39.555    323
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 24.08 %
    Favored  : 73.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.96 (0.51), residues: 258
  helix:  2.64 (0.33), residues: 222
  sheet:  None (None), residues: 0
  loop : -2.85 (0.78), residues: 36

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 110 
 TYR   0.010   0.001   TYR C 238 
 PHE   0.007   0.001   PHE C 134 
 TRP   0.005   0.001   TRP C 120 
 HIS   0.001   0.000   HIS C 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 2260)
  covalent geometry    : angle       0.61423 ( 3058)
  SS BOND              : bond        0.00284 (    1)
  SS BOND              : angle       1.00646 (    2)
  hydrogen bonds       : bond        0.05505 (  163)
  hydrogen bonds       : angle       3.72825 (  489)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 767.27 seconds
wall clock time: 15 minutes 11.77 seconds (911.77 seconds total)