Starting phenix.real_space_refine
on Fri May  9 20:39:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jj8_36342/05_2025/8jj8_36342.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jj8_36342/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jj8_36342/05_2025/8jj8_36342.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jj8_36342/05_2025/8jj8_36342.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jj8_36342/05_2025/8jj8_36342.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jj8_36342/05_2025/8jj8_36342.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.113
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 2.78, per 1000 atoms: 0.92
  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: 0.81
  Conformation dependent library (CDL) restraints added in 361.7 milliseconds
  

  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: 0.28
  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: 0.81

  Time building geometry restraints manager: 0.94 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:                  0.010
  Normalize map: mean=0, sd=1:             1.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.510
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.140
-------------------------------------------------------------------------------
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 : 14.28
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  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
 TRP   0.011   0.001   TRP F 237 
 HIS   0.002   0.000   HIS F 363 
 PHE   0.021   0.002   PHE F 284 
 TYR   0.020   0.002   TYR F 328 
 ARG   0.007   0.001   ARG F 400 

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

*********************** 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  : 0.337 
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: 0.1262
  time to fit residues: 12.2229
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  : 0.329 
-------------------------------------------------------------------------------
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 31 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0370
   chunk 9 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 11 optimal weight:   10.0000
   chunk 17 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.6058

-------------------------------------------------------------------------------
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 = 0.4204 r_free = 0.4204 target = 0.190750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.150283 restraints weight = 3693.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3797 rms_B_bonded: 2.63
r_work: 0.3620 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7133
moved from start:          0.1391

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= 0.152
  Angle     :  0.606   5.687   4200  Z= 0.324
  Chirality :  0.041   0.157    489
  Planarity :  0.003   0.025    515
  Dihedral  :  9.892  71.789    422
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  7.43 %
    Favored  : 90.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.44), residues: 371
  helix:  1.47 (0.29), residues: 312
  sheet:  None (None), residues: 0
  loop : -3.83 (0.71), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP F 237 
 HIS   0.002   0.001   HIS F 178 
 PHE   0.016   0.001   PHE F 284 
 TYR   0.019   0.002   TYR F 328 
 ARG   0.006   0.000   ARG F 400 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05414 (  247)
  hydrogen bonds       : angle       4.20166 (  738)
  SS BOND              : bond        0.00164 (    2)
  SS BOND              : angle       0.52914 (    4)
  covalent geometry    : bond        0.00323 ( 3091)
  covalent geometry    : angle       0.60651 ( 4196)

*********************** 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  : 0.315 
Fit side-chains
REVERT: F  122 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8082 (mm-30)
REVERT: F  230 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6926 (tp)
REVERT: F  269 ASP cc_start: 0.7960 (m-30) cc_final: 0.7561 (m-30)
REVERT: F  360 ASN cc_start: 0.8101 (t0) cc_final: 0.7734 (m-40)
  outliers start: 6
  outliers final: 3
  residues processed: 68
  average time/residue: 0.0946
  time to fit residues: 8.4866
Evaluate side-chains
  53 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 49
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
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 2 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 32 optimal weight:    0.0980
   chunk 23 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.4200 r_free = 0.4200 target = 0.191593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.151451 restraints weight = 3648.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.3801 rms_B_bonded: 2.56
r_work: 0.3630 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7111
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3093  Z= 0.144
  Angle     :  0.582   6.823   4200  Z= 0.307
  Chirality :  0.040   0.163    489
  Planarity :  0.003   0.023    515
  Dihedral  :  8.806  64.570    415
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  :  9.60 %
    Favored  : 87.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.44), residues: 371
  helix:  1.73 (0.29), residues: 310
  sheet:  None (None), residues: 0
  loop : -3.64 (0.69), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP F 237 
 HIS   0.002   0.000   HIS F 363 
 PHE   0.014   0.001   PHE F 284 
 TYR   0.013   0.002   TYR F 324 
 ARG   0.003   0.000   ARG F 400 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04918 (  247)
  hydrogen bonds       : angle       4.08838 (  738)
  SS BOND              : bond        0.00225 (    2)
  SS BOND              : angle       0.64380 (    4)
  covalent geometry    : bond        0.00309 ( 3091)
  covalent geometry    : angle       0.58225 ( 4196)

*********************** 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
  63 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.309 
Fit side-chains
REVERT: F  122 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7990 (mm-30)
REVERT: F  230 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6592 (tp)
REVERT: F  234 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7064 (mt-10)
  outliers start: 9
  outliers final: 3
  residues processed: 60
  average time/residue: 0.0904
  time to fit residues: 7.3856
Evaluate side-chains
  55 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 51
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
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 10 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 17 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:   20.0000
   chunk 11 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 30 optimal weight:    6.9990
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.4173 r_free = 0.4173 target = 0.188919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.152710 restraints weight = 3777.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3788 rms_B_bonded: 2.45
r_work: 0.3574 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
moved from start:          0.2011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3093  Z= 0.168
  Angle     :  0.595   6.931   4200  Z= 0.315
  Chirality :  0.040   0.123    489
  Planarity :  0.003   0.020    515
  Dihedral  :  8.224  65.420    415
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 13.62 %
    Favored  : 84.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.44), residues: 371
  helix:  1.67 (0.29), residues: 310
  sheet:  None (None), residues: 0
  loop : -3.63 (0.68), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP F 237 
 HIS   0.002   0.001   HIS F 363 
 PHE   0.013   0.002   PHE F 284 
 TYR   0.014   0.002   TYR F 174 
 ARG   0.002   0.000   ARG F 400 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05073 (  247)
  hydrogen bonds       : angle       4.16504 (  738)
  SS BOND              : bond        0.00227 (    2)
  SS BOND              : angle       0.63542 (    4)
  covalent geometry    : bond        0.00382 ( 3091)
  covalent geometry    : angle       0.59477 ( 4196)

*********************** 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
  57 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.311 
Fit side-chains
REVERT: F  122 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8033 (mm-30)
REVERT: F  230 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.7054 (tp)
  outliers start: 7
  outliers final: 5
  residues processed: 53
  average time/residue: 0.0919
  time to fit residues: 6.7491
Evaluate side-chains
  55 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   82 MET
Chi-restraints excluded: chain F residue  130 ASP
Chi-restraints excluded: chain F residue  230 LEU
Chi-restraints excluded: chain F residue  233 LEU
Chi-restraints excluded: chain F residue  238 GLU
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 20 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   chunk 6 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0980
   chunk 9 optimal weight:    0.6980
   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 = 0.4188 r_free = 0.4188 target = 0.190671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.149976 restraints weight = 3751.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.3778 rms_B_bonded: 2.60
r_work: 0.3605 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7158
moved from start:          0.2104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3093  Z= 0.137
  Angle     :  0.558   7.100   4200  Z= 0.294
  Chirality :  0.039   0.113    489
  Planarity :  0.003   0.020    515
  Dihedral  :  7.877  65.169    414
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 16.10 %
    Favored  : 81.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.45), residues: 371
  helix:  1.85 (0.29), residues: 310
  sheet:  None (None), residues: 0
  loop : -3.61 (0.68), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP F 237 
 HIS   0.002   0.000   HIS F 363 
 PHE   0.014   0.001   PHE F 284 
 TYR   0.013   0.002   TYR F 174 
 ARG   0.002   0.000   ARG F 400 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04702 (  247)
  hydrogen bonds       : angle       4.05411 (  738)
  SS BOND              : bond        0.00319 (    2)
  SS BOND              : angle       1.03195 (    4)
  covalent geometry    : bond        0.00296 ( 3091)
  covalent geometry    : angle       0.55763 ( 4196)

*********************** 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
  60 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.323 
Fit side-chains
REVERT: F  122 GLU cc_start: 0.8270 (mm-30) cc_final: 0.8042 (mm-30)
REVERT: F  243 ASN cc_start: 0.8209 (m-40) cc_final: 0.7897 (m110)
REVERT: F  342 LEU cc_start: 0.6676 (OUTLIER) cc_final: 0.5679 (mp)
  outliers start: 8
  outliers final: 4
  residues processed: 56
  average time/residue: 0.0924
  time to fit residues: 7.0649
Evaluate side-chains
  53 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 48
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
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  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 20 optimal weight:    0.8980
   chunk 30 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 6 optimal weight:    0.0020
   chunk 2 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.6788

-------------------------------------------------------------------------------
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 = 0.4188 r_free = 0.4188 target = 0.190524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.154138 restraints weight = 3815.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.3808 rms_B_bonded: 2.50
r_work: 0.3595 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7119
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3093  Z= 0.140
  Angle     :  0.560   7.378   4200  Z= 0.294
  Chirality :  0.039   0.114    489
  Planarity :  0.003   0.019    515
  Dihedral  :  7.378  65.111    412
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 17.65 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.45), residues: 371
  helix:  1.89 (0.29), residues: 309
  sheet:  None (None), residues: 0
  loop : -3.69 (0.67), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP F 237 
 HIS   0.002   0.000   HIS F 363 
 PHE   0.014   0.001   PHE F 284 
 TYR   0.027   0.002   TYR F 324 
 ARG   0.002   0.000   ARG F 400 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04648 (  247)
  hydrogen bonds       : angle       4.01564 (  738)
  SS BOND              : bond        0.00283 (    2)
  SS BOND              : angle       0.90055 (    4)
  covalent geometry    : bond        0.00310 ( 3091)
  covalent geometry    : angle       0.55935 ( 4196)

*********************** 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: 7
    poor density    : 49
  time to evaluate  : 0.328 
Fit side-chains
REVERT: F  243 ASN cc_start: 0.8153 (m-40) cc_final: 0.7837 (m110)
REVERT: F  296 ASP cc_start: 0.7898 (m-30) cc_final: 0.7690 (m-30)
REVERT: F  342 LEU cc_start: 0.6512 (OUTLIER) cc_final: 0.5542 (mp)
  outliers start: 7
  outliers final: 4
  residues processed: 53
  average time/residue: 0.0995
  time to fit residues: 7.1683
Evaluate side-chains
  53 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 48
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
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  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 19 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0870
   chunk 31 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.7960

-------------------------------------------------------------------------------
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 = 0.4162 r_free = 0.4162 target = 0.188529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.152452 restraints weight = 3785.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.3783 rms_B_bonded: 2.50
r_work: 0.3562 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7149
moved from start:          0.2364

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= 0.148
  Angle     :  0.568   7.869   4200  Z= 0.297
  Chirality :  0.039   0.117    489
  Planarity :  0.003   0.019    515
  Dihedral  :  7.381  65.301    412
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 17.65 %
    Favored  : 80.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.45), residues: 371
  helix:  1.93 (0.29), residues: 307
  sheet:  None (None), residues: 0
  loop : -3.42 (0.72), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP F 237 
 HIS   0.002   0.000   HIS F 363 
 PHE   0.016   0.001   PHE F 284 
 TYR   0.025   0.002   TYR F 324 
 ARG   0.002   0.000   ARG F 400 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04716 (  247)
  hydrogen bonds       : angle       4.00323 (  738)
  SS BOND              : bond        0.00221 (    2)
  SS BOND              : angle       0.70109 (    4)
  covalent geometry    : bond        0.00335 ( 3091)
  covalent geometry    : angle       0.56829 ( 4196)

*********************** 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
  53 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.310 
Fit side-chains
REVERT: F  243 ASN cc_start: 0.8155 (m-40) cc_final: 0.7676 (m110)
REVERT: F  251 ASP cc_start: 0.7527 (t0) cc_final: 0.7236 (t0)
REVERT: F  296 ASP cc_start: 0.7983 (m-30) cc_final: 0.7770 (m-30)
REVERT: F  342 LEU cc_start: 0.6544 (OUTLIER) cc_final: 0.5550 (mp)
  outliers start: 6
  outliers final: 4
  residues processed: 50
  average time/residue: 0.0939
  time to fit residues: 6.4795
Evaluate side-chains
  51 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
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  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 2 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 14 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0670
   chunk 11 optimal weight:    6.9990
   chunk 5 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.6518

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.190279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.149039 restraints weight = 3785.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3756 rms_B_bonded: 2.67
r_work: 0.3581 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7143
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3093  Z= 0.137
  Angle     :  0.566   8.040   4200  Z= 0.295
  Chirality :  0.039   0.121    489
  Planarity :  0.003   0.019    515
  Dihedral  :  7.320  65.118    412
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 19.20 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.45), residues: 371
  helix:  1.99 (0.29), residues: 307
  sheet:  None (None), residues: 0
  loop : -3.33 (0.74), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP F 237 
 HIS   0.002   0.000   HIS F 363 
 PHE   0.018   0.001   PHE F 284 
 TYR   0.028   0.002   TYR F 324 
 ARG   0.002   0.000   ARG F 400 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04597 (  247)
  hydrogen bonds       : angle       3.95827 (  738)
  SS BOND              : bond        0.00275 (    2)
  SS BOND              : angle       0.78646 (    4)
  covalent geometry    : bond        0.00303 ( 3091)
  covalent geometry    : angle       0.56618 ( 4196)

*********************** 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
  48 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.300 
Fit side-chains
REVERT: F  243 ASN cc_start: 0.8175 (m-40) cc_final: 0.7864 (m110)
REVERT: F  251 ASP cc_start: 0.7483 (t0) cc_final: 0.7251 (t0)
REVERT: F  296 ASP cc_start: 0.7983 (m-30) cc_final: 0.7723 (m-30)
REVERT: F  342 LEU cc_start: 0.6559 (OUTLIER) cc_final: 0.5664 (mp)
  outliers start: 5
  outliers final: 4
  residues processed: 46
  average time/residue: 0.0990
  time to fit residues: 6.2824
Evaluate side-chains
  49 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
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  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 32 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 27 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.189515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.148291 restraints weight = 3766.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3745 rms_B_bonded: 2.65
r_work: 0.3569 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7168
moved from start:          0.2482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3093  Z= 0.147
  Angle     :  0.588   8.241   4200  Z= 0.303
  Chirality :  0.039   0.125    489
  Planarity :  0.003   0.019    515
  Dihedral  :  7.335  65.147    412
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 19.20 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.45), residues: 371
  helix:  1.97 (0.29), residues: 307
  sheet:  None (None), residues: 0
  loop : -3.28 (0.75), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP F 237 
 HIS   0.002   0.000   HIS F 363 
 PHE   0.018   0.001   PHE F 284 
 TYR   0.029   0.002   TYR F 324 
 ARG   0.001   0.000   ARG F 400 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04689 (  247)
  hydrogen bonds       : angle       3.96519 (  738)
  SS BOND              : bond        0.00247 (    2)
  SS BOND              : angle       0.73262 (    4)
  covalent geometry    : bond        0.00330 ( 3091)
  covalent geometry    : angle       0.58775 ( 4196)

*********************** 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
  49 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.333 
Fit side-chains
REVERT: F  243 ASN cc_start: 0.8180 (m-40) cc_final: 0.7877 (m110)
REVERT: F  251 ASP cc_start: 0.7575 (t0) cc_final: 0.7339 (t0)
REVERT: F  296 ASP cc_start: 0.7949 (m-30) cc_final: 0.7696 (m-30)
REVERT: F  342 LEU cc_start: 0.6609 (OUTLIER) cc_final: 0.5690 (mp)
  outliers start: 6
  outliers final: 5
  residues processed: 46
  average time/residue: 0.1016
  time to fit residues: 6.5439
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  : 0.350 
-------------------------------------------------------------------------------
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 35 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0570
   chunk 33 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0040
   chunk 11 optimal weight:    0.0670
   chunk 5 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.3448

-------------------------------------------------------------------------------
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 = 0.4210 r_free = 0.4210 target = 0.193153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.153200 restraints weight = 3699.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3816 rms_B_bonded: 2.60
r_work: 0.3641 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7107
moved from start:          0.2551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   3093  Z= 0.120
  Angle     :  0.557   7.889   4200  Z= 0.286
  Chirality :  0.038   0.124    489
  Planarity :  0.003   0.020    515
  Dihedral  :  7.126  63.908    412
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 19.50 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.89 (0.46), residues: 371
  helix:  2.08 (0.30), residues: 309
  sheet:  None (None), residues: 0
  loop : -3.26 (0.78), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP F 237 
 HIS   0.002   0.000   HIS F 363 
 PHE   0.020   0.001   PHE F 284 
 TYR   0.034   0.002   TYR F 324 
 ARG   0.002   0.000   ARG F 400 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04237 (  247)
  hydrogen bonds       : angle       3.86289 (  738)
  SS BOND              : bond        0.00279 (    2)
  SS BOND              : angle       0.66475 (    4)
  covalent geometry    : bond        0.00243 ( 3091)
  covalent geometry    : angle       0.55664 ( 4196)

********************** 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  : 0.335 
Fit side-chains
REVERT: F   99 TRP cc_start: 0.8165 (t-100) cc_final: 0.7510 (t-100)
REVERT: F  122 GLU cc_start: 0.8238 (mm-30) cc_final: 0.8035 (mm-30)
REVERT: F  243 ASN cc_start: 0.7905 (m-40) cc_final: 0.7653 (m110)
REVERT: F  296 ASP cc_start: 0.7897 (m-30) cc_final: 0.7647 (m-30)
REVERT: F  342 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6157 (mp)
  outliers start: 6
  outliers final: 4
  residues processed: 48
  average time/residue: 0.1010
  time to fit residues: 6.7483
Evaluate side-chains
  46 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
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 9 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 22 optimal weight:    0.4980
   chunk 1 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 13 optimal weight:    0.4980
   chunk 7 optimal weight:    0.5980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4180 r_free = 0.4180 target = 0.190318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.149874 restraints weight = 3723.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.3773 rms_B_bonded: 2.61
r_work: 0.3598 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7143
moved from start:          0.2570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3093  Z= 0.136
  Angle     :  0.584   8.097   4200  Z= 0.300
  Chirality :  0.039   0.123    489
  Planarity :  0.003   0.020    515
  Dihedral  :  7.186  63.456    412
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 20.74 %
    Favored  : 77.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.46), residues: 371
  helix:  2.08 (0.30), residues: 307
  sheet:  None (None), residues: 0
  loop : -3.27 (0.76), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP F 237 
 HIS   0.002   0.000   HIS F 363 
 PHE   0.017   0.001   PHE F 284 
 TYR   0.020   0.002   TYR F 324 
 ARG   0.001   0.000   ARG F 400 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04445 (  247)
  hydrogen bonds       : angle       3.88526 (  738)
  SS BOND              : bond        0.00214 (    2)
  SS BOND              : angle       0.68252 (    4)
  covalent geometry    : bond        0.00298 ( 3091)
  covalent geometry    : angle       0.58340 ( 4196)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1819.52 seconds
wall clock time: 32 minutes 9.04 seconds (1929.04 seconds total)