Starting phenix.real_space_refine
on Fri Aug 22 14:01:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jj8_36342/08_2025/8jj8_36342.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jj8_36342/08_2025/8jj8_36342.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jj8_36342/08_2025/8jj8_36342.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jj8_36342/08_2025/8jj8_36342.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jj8_36342/08_2025/8jj8_36342.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jj8_36342/08_2025/8jj8_36342.map"
  }
  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=   0.113
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 707 atoms to isotropic.
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      20      5.16       5
     C    1984      2.51       5
     N     488      2.21       5
     O     531      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 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: 3023
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "F"
      Number of atoms: 2998
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 375, 2998
          Classifications: {'peptide': 375}
          Link IDs: {'PTRANS': 8, 'TRANS': 366}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'H98': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.99, per 1000 atoms: 0.33
  Number of scatterers: 3023
  At special positions: 0
  Unit cell: (57.78, 103.79, 82.39, 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      20     16.00
     O     531      8.00
     N     488      7.00
     C    1984      6.00
    sf(0) = scattering factor at diffraction angle 0.

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

  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: 0.16
  Conformation dependent library (CDL) restraints added in 111.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  722

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 0 sheets defined
      90.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'F' and resid 30 through 56
      removed outlier: 4.023A  pdb=" N   MET F  36 " --> pdb=" O   TRP F  32 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   ILE F  38 " --> pdb=" O   VAL F  34 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   VAL F  39 " --> pdb=" O   GLY F  35 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 66 through 93
      removed outlier: 3.531A  pdb=" N   PHE F  71 " --> pdb=" O   VAL F  67 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   VAL F  87 " --> pdb=" O   GLY F  83 " (cutoff:3.500A)
      Proline residue:  F  88  - end of helix
    Processing helix  chain 'F' and resid 102 through 136
    Processing helix  chain 'F' and resid 137 through 143
      removed outlier: 4.230A  pdb=" N   SER F 143 " --> pdb=" O   PHE F 139 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 146 through 166
    Processing helix  chain 'F' and resid 166 through 171
      removed outlier: 4.261A  pdb=" N   MET F 171 " --> pdb=" O   LEU F 167 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 178 through 186
      removed outlier: 3.780A  pdb=" N   ASN F 183 " --> pdb=" O   GLN F 179 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   CYS F 184 " --> pdb=" O   GLU F 180 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 196 through 208
    Processing helix  chain 'F' and resid 208 through 249
      removed outlier: 3.608A  pdb=" N   LYS F 249 " --> pdb=" O   LYS F 245 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 252 through 273
      removed outlier: 3.682A  pdb=" N   VAL F 256 " --> pdb=" O   ASN F 252 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 279 through 305
    Processing helix  chain 'F' and resid 306 through 365
      removed outlier: 4.741A  pdb=" N   GLN F 326 " --> pdb=" O   ASN F 322 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   LYS F 327 " --> pdb=" O   ALA F 323 " (cutoff:3.500A)
      removed outlier: 5.396A  pdb=" N   LEU F 329 " --> pdb=" O   ILE F 325 " (cutoff:3.500A)
      Proline residue:  F 355  - end of helix
      removed outlier: 3.920A  pdb=" N   ILE F 361 " --> pdb=" O   PHE F 357 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 366 through 370
      removed outlier: 3.517A  pdb=" N   ILE F 370 " --> pdb=" O   ASP F 367 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 371 through 384
    Processing helix  chain 'F' and resid 384 through 389
      removed outlier: 3.606A  pdb=" N   PHE F 388 " --> pdb=" O   VAL F 384 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 389 through 394
    Processing helix  chain 'F' and resid 396 through 407
      removed outlier: 3.590A  pdb=" N   GLN F 404 " --> pdb=" O   ARG F 400 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   GLU F 405 " --> pdb=" O   ILE F 401 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   LEU F 406 " --> pdb=" O   ALA F 402 " (cutoff:3.500A)

    247 hydrogen bonds defined for protein.
    738 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: 0.45

  Time building geometry restraints manager: 0.25 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 478
        1.29 -     1.42: 820
        1.42 -     1.55: 1760
        1.55 -     1.68: 2
        1.68 -     1.81: 31
  Bond restraints: 3091
  Sorted by residual:
  bond pdb=" C   TYR F 328 "
       pdb=" O   TYR F 328 "
    ideal  model  delta    sigma   weight residual
    1.236  1.161  0.076 1.26e-02 6.30e+03 3.61e+01
  bond pdb=" C   LYS F 327 "
       pdb=" O   LYS F 327 "
    ideal  model  delta    sigma   weight residual
    1.237  1.190  0.047 1.16e-02 7.43e+03 1.61e+01
  bond pdb=" C   GLN F 326 "
       pdb=" O   GLN F 326 "
    ideal  model  delta    sigma   weight residual
    1.235  1.286 -0.050 1.26e-02 6.30e+03 1.60e+01
  bond pdb=" C   LEU F 342 "
       pdb=" O   LEU F 342 "
    ideal  model  delta    sigma   weight residual
    1.235  1.190  0.045 1.26e-02 6.30e+03 1.27e+01
  bond pdb=" C   ALA F 338 "
       pdb=" O   ALA F 338 "
    ideal  model  delta    sigma   weight residual
    1.236  1.281 -0.045 1.29e-02 6.01e+03 1.22e+01
  ... (remaining 3086 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.48: 4144
        3.48 -     6.97: 46
        6.97 -    10.45: 5
       10.45 -    13.93: 0
       13.93 -    17.42: 1
  Bond angle restraints: 4196
  Sorted by residual:
  angle pdb=" O   ILE F 325 "
        pdb=" C   ILE F 325 "
        pdb=" N   GLN F 326 "
      ideal   model   delta    sigma   weight residual
     121.96  130.61   -8.65 8.40e-01 1.42e+00 1.06e+02
  angle pdb=" CA  ILE F 325 "
        pdb=" C   ILE F 325 "
        pdb=" N   GLN F 326 "
      ideal   model   delta    sigma   weight residual
     115.25  106.83    8.42 9.50e-01 1.11e+00 7.85e+01
  angle pdb=" N   LYS F 340 "
        pdb=" CA  LYS F 340 "
        pdb=" C   LYS F 340 "
      ideal   model   delta    sigma   weight residual
     111.28  102.34    8.94 1.09e+00 8.42e-01 6.73e+01
  angle pdb=" N   GLN F 326 "
        pdb=" CA  GLN F 326 "
        pdb=" C   GLN F 326 "
      ideal   model   delta    sigma   weight residual
     110.80   93.38   17.42 2.13e+00 2.20e-01 6.69e+01
  angle pdb=" N   LEU F 329 "
        pdb=" CA  LEU F 329 "
        pdb=" C   LEU F 329 "
      ideal   model   delta    sigma   weight residual
     111.07  103.97    7.10 1.07e+00 8.73e-01 4.41e+01
  ... (remaining 4191 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 1615
       17.82 -    35.64: 168
       35.64 -    53.46: 33
       53.46 -    71.28: 4
       71.28 -    89.10: 6
  Dihedral angle restraints: 1826
    sinusoidal: 718
      harmonic: 1108
  Sorted by residual:
  dihedral pdb=" CB  CYS F 106 "
           pdb=" SG  CYS F 106 "
           pdb=" SG  CYS F 191 "
           pdb=" CB  CYS F 191 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -175.10   89.10     1      1.00e+01 1.00e-02 9.45e+01
  dihedral pdb=" CA  MET F  96 "
           pdb=" C   MET F  96 "
           pdb=" N   LYS F  97 "
           pdb=" CA  LYS F  97 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.15  -18.85     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" N   GLN F 326 "
           pdb=" C   GLN F 326 "
           pdb=" CA  GLN F 326 "
           pdb=" CB  GLN F 326 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  114.83    7.97     0      2.50e+00 1.60e-01 1.02e+01
  ... (remaining 1823 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 399
       0.060 -    0.120: 80
       0.120 -    0.180: 6
       0.180 -    0.240: 2
       0.240 -    0.300: 2
  Chirality restraints: 489
  Sorted by residual:
  chirality pdb=" CA  GLN F 326 "
            pdb=" N   GLN F 326 "
            pdb=" C   GLN F 326 "
            pdb=" CB  GLN F 326 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.81   -0.30 2.00e-01 2.50e+01 2.26e+00
  chirality pdb=" CA  LYS F 340 "
            pdb=" N   LYS F 340 "
            pdb=" C   LYS F 340 "
            pdb=" CB  LYS F 340 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" CA  LEU F 339 "
            pdb=" N   LEU F 339 "
            pdb=" C   LEU F 339 "
            pdb=" CB  LEU F 339 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.24e-01
  ... (remaining 486 not shown)

  Planarity restraints: 515
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN F 326 "    0.021 2.00e-02 2.50e+03   4.23e-02 1.79e+01
        pdb=" C   GLN F 326 "   -0.073 2.00e-02 2.50e+03
        pdb=" O   GLN F 326 "    0.027 2.00e-02 2.50e+03
        pdb=" N   LYS F 327 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU F 329 "   -0.017 2.00e-02 2.50e+03   3.42e-02 1.17e+01
        pdb=" C   LEU F 329 "    0.059 2.00e-02 2.50e+03
        pdb=" O   LEU F 329 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   LYS F 330 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN F 236 "    0.013 2.00e-02 2.50e+03   2.66e-02 7.06e+00
        pdb=" C   ASN F 236 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   ASN F 236 "    0.017 2.00e-02 2.50e+03
        pdb=" N   TRP F 237 "    0.016 2.00e-02 2.50e+03
  ... (remaining 512 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 57
        2.67 -     3.22: 3111
        3.22 -     3.78: 4782
        3.78 -     4.34: 6157
        4.34 -     4.90: 10166
  Nonbonded interactions: 24273
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU F 187 "
            pdb=" OG1 THR F 189 "
     model   vdw
     2.107 3.040
  nonbonded pdb=" OG  SER F 203 "
            pdb=" O2  H98 F 501 "
     model   vdw
     2.191 3.040
  nonbonded pdb=" O   THR F 341 "
            pdb=" C   LEU F 342 "
     model   vdw
     2.229 3.270
  nonbonded pdb=" O   THR F 239 "
            pdb=" ND2 ASN F 243 "
     model   vdw
     2.315 3.120
  nonbonded pdb=" OD2 ASP F 113 "
            pdb=" OH  TYR F 383 "
     model   vdw
     2.323 3.040
  ... (remaining 24268 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:             1.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.010
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     4.490
  Find NCS groups from input model:        0.020
  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:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7208
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   0.076   3093  Z= 0.351
  Angle     :  0.898  17.416   4200  Z= 0.611
  Chirality :  0.050   0.300    489
  Planarity :  0.005   0.042    515
  Dihedral  : 15.213  81.138   1098
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 14.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  1.55 %
    Favored  : 96.59 %
  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:  0.54 (0.45), residues: 371
  helix:  1.06 (0.30), residues: 311
  sheet:  None (None), residues: 0
  loop : -3.25 (0.85), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F 400 
 TYR   0.020   0.002   TYR F 328 
 PHE   0.021   0.002   PHE F 284 
 TRP   0.011   0.001   TRP F 237 
 HIS   0.002   0.000   HIS F 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00530 ( 3091)
  covalent geometry    : angle       0.89806 ( 4196)
  SS BOND              : bond        0.00176 (    2)
  SS BOND              : angle       0.50549 (    4)
  hydrogen bonds       : bond        0.13688 (  247)
  hydrogen bonds       : angle       5.56686 (  738)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.073 
Fit side-chains
REVERT: F  230 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7669 (tp)
REVERT: F  269 ASP cc_start: 0.7008 (m-30) cc_final: 0.6792 (m-30)
REVERT: F  331 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.6948 (t80)
  outliers start: 6
  outliers final: 4
  residues processed: 78
  average time/residue: 0.0482
  time to fit residues: 4.7174
Evaluate side-chains
  63 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  230 LEU
Chi-restraints excluded: chain F residue  329 LEU
Chi-restraints excluded: chain F residue  331 PHE
Chi-restraints excluded: chain F residue  332 CYS
Chi-restraints excluded: chain F residue  341 THR
Chi-restraints excluded: chain F residue  342 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
F 379 ASN
F 404 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.189487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.148044 restraints weight = 3699.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.3749 rms_B_bonded: 2.67
r_work: 0.3576 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7147
moved from start:          0.1451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   3093  Z= 0.167
  Angle     :  0.625   5.824   4200  Z= 0.333
  Chirality :  0.042   0.169    489
  Planarity :  0.003   0.025    515
  Dihedral  :  9.840  69.334    422
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  6.81 %
    Favored  : 91.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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:  0.93 (0.44), residues: 371
  helix:  1.43 (0.29), residues: 310
  sheet:  None (None), residues: 0
  loop : -3.72 (0.69), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F 400 
 TYR   0.020   0.002   TYR F 328 
 PHE   0.015   0.002   PHE F 284 
 TRP   0.017   0.001   TRP F 237 
 HIS   0.002   0.000   HIS F 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 3091)
  covalent geometry    : angle       0.62483 ( 4196)
  SS BOND              : bond        0.00175 (    2)
  SS BOND              : angle       0.53747 (    4)
  hydrogen bonds       : bond        0.05511 (  247)
  hydrogen bonds       : angle       4.23593 (  738)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 63
  time to evaluate  : 0.132 
Fit side-chains
REVERT: F  122 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8019 (mm-30)
REVERT: F  230 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6892 (tp)
REVERT: F  269 ASP cc_start: 0.7975 (m-30) cc_final: 0.7613 (m-30)
  outliers start: 6
  outliers final: 3
  residues processed: 68
  average time/residue: 0.0395
  time to fit residues: 3.6087
Evaluate side-chains
  52 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  230 LEU
Chi-restraints excluded: chain F residue  233 LEU
Chi-restraints excluded: chain F residue  244 LEU
Chi-restraints excluded: chain F residue  341 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 21 optimal weight:    0.0980
   chunk 17 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 10 optimal weight:    5.9990
   chunk 6 optimal weight:    0.0970
   chunk 32 optimal weight:    0.1980
   chunk 16 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.3778

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

Flipped N/Q/H residues before XYZ refinement:
F 379 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.193129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.153554 restraints weight = 3740.044|
|-----------------------------------------------------------------------------|
r_work (start): 0.3825 rms_B_bonded: 2.58
r_work: 0.3654 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7076
moved from start:          0.1804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3093  Z= 0.130
  Angle     :  0.567   6.546   4200  Z= 0.300
  Chirality :  0.039   0.142    489
  Planarity :  0.003   0.022    515
  Dihedral  :  8.679  64.789    415
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 10.53 %
    Favored  : 87.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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:  1.43 (0.44), residues: 371
  helix:  1.78 (0.29), residues: 310
  sheet:  None (None), residues: 0
  loop : -3.65 (0.69), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 400 
 TYR   0.023   0.002   TYR F 324 
 PHE   0.016   0.001   PHE F 284 
 TRP   0.025   0.001   TRP F 237 
 HIS   0.002   0.000   HIS F 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 3091)
  covalent geometry    : angle       0.56705 ( 4196)
  SS BOND              : bond        0.00242 (    2)
  SS BOND              : angle       0.72218 (    4)
  hydrogen bonds       : bond        0.04708 (  247)
  hydrogen bonds       : angle       4.04403 (  738)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.072 
Fit side-chains
REVERT: F  230 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6864 (tp)
REVERT: F  243 ASN cc_start: 0.8270 (m-40) cc_final: 0.7807 (m110)
REVERT: F  269 ASP cc_start: 0.7966 (m-30) cc_final: 0.7572 (m-30)
REVERT: F  360 ASN cc_start: 0.7927 (t0) cc_final: 0.7648 (m-40)
  outliers start: 8
  outliers final: 3
  residues processed: 62
  average time/residue: 0.0307
  time to fit residues: 2.6747
Evaluate side-chains
  61 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  230 LEU
Chi-restraints excluded: chain F residue  233 LEU
Chi-restraints excluded: chain F residue  244 LEU
Chi-restraints excluded: chain F residue  341 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0030
   chunk 26 optimal weight:    0.5980
   chunk 16 optimal weight:    0.2980
   chunk 21 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.5190

-------------------------------------------------------------------------------
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 = 0.4209 r_free = 0.4209 target = 0.192751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.152605 restraints weight = 3728.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.3796 rms_B_bonded: 2.58
r_work: 0.3625 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7116
moved from start:          0.2045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3093  Z= 0.133
  Angle     :  0.555   6.293   4200  Z= 0.294
  Chirality :  0.039   0.122    489
  Planarity :  0.003   0.020    515
  Dihedral  :  7.998  64.310    415
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 12.38 %
    Favored  : 85.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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:  1.55 (0.45), residues: 371
  helix:  1.86 (0.29), residues: 310
  sheet:  None (None), residues: 0
  loop : -3.58 (0.70), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 400 
 TYR   0.016   0.002   TYR F 324 
 PHE   0.013   0.001   PHE F 284 
 TRP   0.024   0.001   TRP F 237 
 HIS   0.002   0.000   HIS F 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 3091)
  covalent geometry    : angle       0.55378 ( 4196)
  SS BOND              : bond        0.00308 (    2)
  SS BOND              : angle       1.12096 (    4)
  hydrogen bonds       : bond        0.04597 (  247)
  hydrogen bonds       : angle       4.02587 (  738)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.111 
Fit side-chains
REVERT: F   48 VAL cc_start: 0.7304 (t) cc_final: 0.6995 (m)
REVERT: F  243 ASN cc_start: 0.8253 (m-40) cc_final: 0.7968 (m110)
REVERT: F  251 ASP cc_start: 0.7598 (t0) cc_final: 0.7341 (t0)
REVERT: F  269 ASP cc_start: 0.7965 (m-30) cc_final: 0.7569 (m-30)
REVERT: F  330 LYS cc_start: 0.6977 (mtpt) cc_final: 0.6707 (ttmt)
REVERT: F  360 ASN cc_start: 0.7956 (t0) cc_final: 0.7681 (m-40)
  outliers start: 7
  outliers final: 3
  residues processed: 64
  average time/residue: 0.0421
  time to fit residues: 3.6493
Evaluate side-chains
  56 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 53
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  233 LEU
Chi-restraints excluded: chain F residue  244 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 36 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
F  51 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.190308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.149380 restraints weight = 3729.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.3748 rms_B_bonded: 2.62
r_work: 0.3582 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7143
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3093  Z= 0.157
  Angle     :  0.573   6.741   4200  Z= 0.305
  Chirality :  0.040   0.119    489
  Planarity :  0.003   0.020    515
  Dihedral  :  7.466  65.138    412
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 15.48 %
    Favored  : 82.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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:  1.45 (0.45), residues: 371
  helix:  1.82 (0.29), residues: 309
  sheet:  None (None), residues: 0
  loop : -3.69 (0.69), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 400 
 TYR   0.020   0.002   TYR F 324 
 PHE   0.013   0.001   PHE F 284 
 TRP   0.026   0.002   TRP F 237 
 HIS   0.001   0.000   HIS F 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 3091)
  covalent geometry    : angle       0.57227 ( 4196)
  SS BOND              : bond        0.00223 (    2)
  SS BOND              : angle       0.90013 (    4)
  hydrogen bonds       : bond        0.04828 (  247)
  hydrogen bonds       : angle       4.05063 (  738)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.117 
Fit side-chains
REVERT: F  243 ASN cc_start: 0.8249 (m-40) cc_final: 0.7931 (m110)
REVERT: F  330 LYS cc_start: 0.6949 (mtpt) cc_final: 0.6678 (ttmt)
REVERT: F  342 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.5509 (mp)
  outliers start: 6
  outliers final: 5
  residues processed: 54
  average time/residue: 0.0473
  time to fit residues: 3.3866
Evaluate side-chains
  54 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  233 LEU
Chi-restraints excluded: chain F residue  238 GLU
Chi-restraints excluded: chain F residue  244 LEU
Chi-restraints excluded: chain F residue  342 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0060
   chunk 26 optimal weight:    0.6980
   chunk 30 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 15 optimal weight:    8.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.6796

-------------------------------------------------------------------------------
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 = 0.190969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.150096 restraints weight = 3730.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.3784 rms_B_bonded: 2.61
r_work: 0.3615 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7110
moved from start:          0.2286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3093  Z= 0.139
  Angle     :  0.553   6.995   4200  Z= 0.295
  Chirality :  0.039   0.116    489
  Planarity :  0.003   0.024    515
  Dihedral  :  7.380  65.268    412
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.77 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 16.72 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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:  1.54 (0.45), residues: 371
  helix:  1.89 (0.29), residues: 309
  sheet:  None (None), residues: 0
  loop : -3.68 (0.69), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 400 
 TYR   0.020   0.002   TYR F 324 
 PHE   0.014   0.001   PHE F 284 
 TRP   0.025   0.002   TRP F 237 
 HIS   0.002   0.000   HIS F 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 3091)
  covalent geometry    : angle       0.55239 ( 4196)
  SS BOND              : bond        0.00325 (    2)
  SS BOND              : angle       0.94483 (    4)
  hydrogen bonds       : bond        0.04634 (  247)
  hydrogen bonds       : angle       3.99850 (  738)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.120 
Fit side-chains
REVERT: F  243 ASN cc_start: 0.8160 (m-40) cc_final: 0.7703 (m110)
REVERT: F  330 LYS cc_start: 0.6885 (mtpt) cc_final: 0.6627 (ttmt)
REVERT: F  342 LEU cc_start: 0.6560 (OUTLIER) cc_final: 0.5623 (mp)
  outliers start: 8
  outliers final: 5
  residues processed: 52
  average time/residue: 0.0403
  time to fit residues: 2.8758
Evaluate side-chains
  54 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   82 MET
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  233 LEU
Chi-restraints excluded: chain F residue  244 LEU
Chi-restraints excluded: chain F residue  342 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 6 optimal weight:    0.3980
   chunk 3 optimal weight:    3.9990
   chunk 32 optimal weight:    0.5980
   chunk 17 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.190916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.150271 restraints weight = 3716.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3788 rms_B_bonded: 2.58
r_work: 0.3616 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7162
moved from start:          0.2384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3093  Z= 0.141
  Angle     :  0.564   7.297   4200  Z= 0.299
  Chirality :  0.039   0.118    489
  Planarity :  0.003   0.019    515
  Dihedral  :  7.360  65.320    412
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.77 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 16.72 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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:  1.60 (0.45), residues: 371
  helix:  1.91 (0.29), residues: 307
  sheet:  None (None), residues: 0
  loop : -3.39 (0.74), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 400 
 TYR   0.026   0.002   TYR F 324 
 PHE   0.016   0.001   PHE F 284 
 TRP   0.033   0.002   TRP F 237 
 HIS   0.002   0.000   HIS F 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 3091)
  covalent geometry    : angle       0.56355 ( 4196)
  SS BOND              : bond        0.00232 (    2)
  SS BOND              : angle       0.71890 (    4)
  hydrogen bonds       : bond        0.04649 (  247)
  hydrogen bonds       : angle       4.01386 (  738)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.077 
Fit side-chains
REVERT: F  234 GLU cc_start: 0.7880 (mt-10) cc_final: 0.6971 (mt-10)
REVERT: F  243 ASN cc_start: 0.8128 (m-40) cc_final: 0.7818 (m110)
REVERT: F  251 ASP cc_start: 0.7505 (t0) cc_final: 0.7284 (t0)
REVERT: F  330 LYS cc_start: 0.6887 (mtpt) cc_final: 0.6630 (ttmt)
REVERT: F  342 LEU cc_start: 0.6581 (OUTLIER) cc_final: 0.5696 (mp)
  outliers start: 7
  outliers final: 5
  residues processed: 50
  average time/residue: 0.0443
  time to fit residues: 2.9939
Evaluate side-chains
  50 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   82 MET
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  233 LEU
Chi-restraints excluded: chain F residue  244 LEU
Chi-restraints excluded: chain F residue  342 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 16 optimal weight:    0.3980
   chunk 29 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 35 optimal weight:    0.4980
   chunk 23 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 7 optimal weight:    0.3980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.191251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.150474 restraints weight = 3805.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.3791 rms_B_bonded: 2.61
r_work: 0.3618 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7146
moved from start:          0.2429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3093  Z= 0.136
  Angle     :  0.560   7.699   4200  Z= 0.297
  Chirality :  0.039   0.123    489
  Planarity :  0.003   0.019    515
  Dihedral  :  7.312  65.234    412
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.50 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 17.34 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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:  1.72 (0.45), residues: 371
  helix:  1.98 (0.29), residues: 307
  sheet:  None (None), residues: 0
  loop : -3.25 (0.76), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 400 
 TYR   0.027   0.002   TYR F 324 
 PHE   0.017   0.001   PHE F 284 
 TRP   0.037   0.002   TRP F 237 
 HIS   0.002   0.000   HIS F 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 3091)
  covalent geometry    : angle       0.55935 ( 4196)
  SS BOND              : bond        0.00271 (    2)
  SS BOND              : angle       0.77226 (    4)
  hydrogen bonds       : bond        0.04539 (  247)
  hydrogen bonds       : angle       3.97124 (  738)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.116 
Fit side-chains
REVERT: F  234 GLU cc_start: 0.7821 (mt-10) cc_final: 0.6912 (mt-10)
REVERT: F  243 ASN cc_start: 0.8069 (m-40) cc_final: 0.7747 (m110)
REVERT: F  330 LYS cc_start: 0.6890 (mtpt) cc_final: 0.6641 (ttmt)
REVERT: F  342 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.5662 (mp)
  outliers start: 6
  outliers final: 5
  residues processed: 47
  average time/residue: 0.0441
  time to fit residues: 2.8120
Evaluate side-chains
  49 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   82 MET
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  233 LEU
Chi-restraints excluded: chain F residue  244 LEU
Chi-restraints excluded: chain F residue  342 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 26 optimal weight:    0.5980
   chunk 11 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0670
   chunk 28 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.6318

-------------------------------------------------------------------------------
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 = 0.4197 r_free = 0.4197 target = 0.191158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.150367 restraints weight = 3808.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.3791 rms_B_bonded: 2.62
r_work: 0.3615 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7163
moved from start:          0.2487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3093  Z= 0.138
  Angle     :  0.572   7.754   4200  Z= 0.302
  Chirality :  0.039   0.126    489
  Planarity :  0.003   0.019    515
  Dihedral  :  7.303  65.103    412
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.23 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 17.96 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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:  1.76 (0.45), residues: 371
  helix:  2.00 (0.29), residues: 307
  sheet:  None (None), residues: 0
  loop : -3.19 (0.78), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 400 
 TYR   0.030   0.002   TYR F 324 
 PHE   0.018   0.001   PHE F 284 
 TRP   0.040   0.002   TRP F 237 
 HIS   0.002   0.000   HIS F 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 3091)
  covalent geometry    : angle       0.57162 ( 4196)
  SS BOND              : bond        0.00261 (    2)
  SS BOND              : angle       0.73555 (    4)
  hydrogen bonds       : bond        0.04517 (  247)
  hydrogen bonds       : angle       3.95535 (  738)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.116 
Fit side-chains
REVERT: F  234 GLU cc_start: 0.7935 (mt-10) cc_final: 0.6996 (mt-10)
REVERT: F  243 ASN cc_start: 0.8134 (m-40) cc_final: 0.7822 (m110)
REVERT: F  330 LYS cc_start: 0.6853 (mtpt) cc_final: 0.6629 (ttmt)
REVERT: F  342 LEU cc_start: 0.6644 (OUTLIER) cc_final: 0.5815 (mp)
  outliers start: 6
  outliers final: 5
  residues processed: 47
  average time/residue: 0.0430
  time to fit residues: 2.7470
Evaluate side-chains
  49 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   82 MET
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  233 LEU
Chi-restraints excluded: chain F residue  244 LEU
Chi-restraints excluded: chain F residue  342 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0670
   chunk 14 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 6 optimal weight:    0.4980
   chunk 29 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0030
   overall best weight:    0.3728

-------------------------------------------------------------------------------
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 = 0.4218 r_free = 0.4218 target = 0.193357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.153379 restraints weight = 3743.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.3817 rms_B_bonded: 2.59
r_work: 0.3649 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7094
moved from start:          0.2554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3093  Z= 0.125
  Angle     :  0.556   7.712   4200  Z= 0.295
  Chirality :  0.038   0.123    489
  Planarity :  0.003   0.019    515
  Dihedral  :  7.179  64.177    412
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.23 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 18.89 %
    Favored  : 79.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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:  1.90 (0.46), residues: 371
  helix:  2.09 (0.30), residues: 307
  sheet:  None (None), residues: 0
  loop : -3.11 (0.80), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 400 
 TYR   0.029   0.002   TYR F 324 
 PHE   0.018   0.001   PHE F 284 
 TRP   0.039   0.002   TRP F 237 
 HIS   0.002   0.000   HIS F 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 3091)
  covalent geometry    : angle       0.55599 ( 4196)
  SS BOND              : bond        0.00265 (    2)
  SS BOND              : angle       0.69697 (    4)
  hydrogen bonds       : bond        0.04290 (  247)
  hydrogen bonds       : angle       3.90092 (  738)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.085 
Fit side-chains
REVERT: F   99 TRP cc_start: 0.8140 (t-100) cc_final: 0.7631 (t-100)
REVERT: F  122 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8130 (mm-30)
REVERT: F  234 GLU cc_start: 0.7914 (mt-10) cc_final: 0.6941 (mt-10)
REVERT: F  243 ASN cc_start: 0.8010 (m-40) cc_final: 0.7631 (m110)
REVERT: F  342 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.5968 (mp)
  outliers start: 6
  outliers final: 4
  residues processed: 48
  average time/residue: 0.0439
  time to fit residues: 2.8171
Evaluate side-chains
  44 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   82 MET
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue  233 LEU
Chi-restraints excluded: chain F residue  244 LEU
Chi-restraints excluded: chain F residue  342 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 5 optimal weight:    0.0070
   chunk 3 optimal weight:    0.2980
   chunk 1 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0060
   chunk 22 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0010
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.2020

-------------------------------------------------------------------------------
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 = 0.4255 r_free = 0.4255 target = 0.197266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.157985 restraints weight = 3755.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3865 rms_B_bonded: 2.60
r_work: 0.3699 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7041
moved from start:          0.2715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3093  Z= 0.118
  Angle     :  0.555   7.376   4200  Z= 0.293
  Chirality :  0.038   0.124    489
  Planarity :  0.003   0.024    515
  Dihedral  :  6.992  61.734    412
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.77 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 19.50 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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:  2.04 (0.46), residues: 371
  helix:  2.16 (0.30), residues: 310
  sheet:  None (None), residues: 0
  loop : -3.18 (0.83), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 400 
 TYR   0.020   0.001   TYR F 324 
 PHE   0.017   0.001   PHE F 284 
 TRP   0.029   0.002   TRP F 237 
 HIS   0.003   0.001   HIS F 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 3091)
  covalent geometry    : angle       0.55521 ( 4196)
  SS BOND              : bond        0.00248 (    2)
  SS BOND              : angle       0.60349 (    4)
  hydrogen bonds       : bond        0.03973 (  247)
  hydrogen bonds       : angle       3.82135 (  738)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 905.98 seconds
wall clock time: 16 minutes 10.21 seconds (970.21 seconds total)