Starting phenix.real_space_refine
on Fri Aug 22 13:12:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jjo_36361/08_2025/8jjo_36361_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jjo_36361/08_2025/8jjo_36361.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jjo_36361/08_2025/8jjo_36361_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jjo_36361/08_2025/8jjo_36361_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jjo_36361/08_2025/8jjo_36361.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jjo_36361/08_2025/8jjo_36361.map"
  }
  resolution = 3.4
  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=  -0.002 sd=   0.158
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    1980      2.51       5
     N     487      2.21       5
     O     529      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 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: 3016
  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: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 18
          Unusual residues: {'JTZ': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.81, per 1000 atoms: 0.27
  Number of scatterers: 3016
  At special positions: 0
  Unit cell: (54.57, 81.32, 107, 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     529      8.00
     N     487      7.00
     C    1980      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: 0.25
  Conformation dependent library (CDL) restraints added in 92.0 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:
      15 helices and 0 sheets defined
      82.1% 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 29 through 61
      removed outlier: 3.703A  pdb=" N   VAL F  34 " --> pdb=" O   GLU F  30 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   GLY F  37 " --> pdb=" O   VAL F  33 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 66 through 86
    Processing helix  chain 'F' and resid 86 through 96
    Processing helix  chain 'F' and resid 106 through 134
    Processing helix  chain 'F' and resid 146 through 170
      removed outlier: 4.093A  pdb=" N   LEU F 167 " --> pdb=" O   LEU F 163 " (cutoff:3.500A)
      Proline residue:  F 168  - end of helix
    Processing helix  chain 'F' and resid 180 through 186
      removed outlier: 3.816A  pdb=" N   ASN F 183 " --> pdb=" O   GLU F 180 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ALA F 186 " --> pdb=" O   ASN F 183 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 196 through 207
    Processing helix  chain 'F' and resid 210 through 237
      removed outlier: 3.560A  pdb=" N   VAL F 216 " --> pdb=" O   LEU F 212 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LYS F 227 " --> pdb=" O   PHE F 223 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ARG F 228 " --> pdb=" O   GLN F 224 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 240 through 247
    Processing helix  chain 'F' and resid 252 through 273
    Processing helix  chain 'F' and resid 279 through 300
    Processing helix  chain 'F' and resid 309 through 366
      removed outlier: 4.393A  pdb=" N   GLN F 326 " --> pdb=" O   ASN F 322 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   LYS F 327 " --> pdb=" O   ALA F 323 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LYS F 340 " --> pdb=" O   HIS F 336 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   THR F 350 " --> pdb=" O   MET F 346 " (cutoff:3.500A)
      Proline residue:  F 355  - end of helix
      removed outlier: 3.506A  pdb=" N   VAL F 359 " --> pdb=" O   PRO F 355 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ILE F 361 " --> pdb=" O   PHE F 357 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   VAL F 362 " --> pdb=" O   ILE F 358 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   VAL F 364 " --> pdb=" O   ASN F 360 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 373 through 386
      removed outlier: 3.909A  pdb=" N   GLY F 382 " --> pdb=" O   LEU F 378 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   SER F 386 " --> pdb=" O   GLY F 382 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 387 through 394
      removed outlier: 4.366A  pdb=" N   LEU F 391 " --> pdb=" O   GLY F 387 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 396 through 405
      removed outlier: 3.525A  pdb=" N   ALA F 402 " --> pdb=" O   ASP F 398 " (cutoff:3.500A)

    223 hydrogen bonds defined for protein.
    663 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: 0.43

  Time building geometry restraints manager: 0.32 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 930
        1.34 -     1.46: 738
        1.46 -     1.58: 1384
        1.58 -     1.70: 0
        1.70 -     1.82: 31
  Bond restraints: 3083
  Sorted by residual:
  bond pdb=" C12 JTZ F 501 "
       pdb=" C7  JTZ F 501 "
    ideal  model  delta    sigma   weight residual
    1.403  1.353  0.050 2.00e-02 2.50e+03 6.22e+00
  bond pdb=" C2  JTZ F 501 "
       pdb=" N1  JTZ F 501 "
    ideal  model  delta    sigma   weight residual
    1.458  1.417  0.041 2.00e-02 2.50e+03 4.14e+00
  bond pdb=" C8  JTZ F 501 "
       pdb=" C9  JTZ F 501 "
    ideal  model  delta    sigma   weight residual
    1.390  1.352  0.038 2.00e-02 2.50e+03 3.62e+00
  bond pdb=" C7  JTZ F 501 "
       pdb=" C8  JTZ F 501 "
    ideal  model  delta    sigma   weight residual
    1.393  1.357  0.036 2.00e-02 2.50e+03 3.25e+00
  bond pdb=" C10 JTZ F 501 "
       pdb=" C9  JTZ F 501 "
    ideal  model  delta    sigma   weight residual
    1.385  1.351  0.034 2.00e-02 2.50e+03 2.88e+00
  ... (remaining 3078 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 4105
        1.78 -     3.56: 58
        3.56 -     5.35: 11
        5.35 -     7.13: 6
        7.13 -     8.91: 4
  Bond angle restraints: 4184
  Sorted by residual:
  angle pdb=" C1  JTZ F 501 "
        pdb=" C2  JTZ F 501 "
        pdb=" N1  JTZ F 501 "
      ideal   model   delta    sigma   weight residual
     114.33  105.42    8.91 3.00e+00 1.11e-01 8.83e+00
  angle pdb=" C2  JTZ F 501 "
        pdb=" N1  JTZ F 501 "
        pdb=" C4  JTZ F 501 "
      ideal   model   delta    sigma   weight residual
     115.12  106.67    8.45 3.00e+00 1.11e-01 7.93e+00
  angle pdb=" N   TRP F 105 "
        pdb=" CA  TRP F 105 "
        pdb=" C   TRP F 105 "
      ideal   model   delta    sigma   weight residual
     113.38  110.14    3.24 1.17e+00 7.31e-01 7.69e+00
  angle pdb=" C   ASP F 367 "
        pdb=" N   ASN F 368 "
        pdb=" CA  ASN F 368 "
      ideal   model   delta    sigma   weight residual
     121.54  126.63   -5.09 1.91e+00 2.74e-01 7.09e+00
  angle pdb=" C6  JTZ F 501 "
        pdb=" C5  JTZ F 501 "
        pdb=" O1  JTZ F 501 "
      ideal   model   delta    sigma   weight residual
     112.06  104.46    7.60 3.00e+00 1.11e-01 6.42e+00
  ... (remaining 4179 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.27: 1729
       31.27 -    62.54: 83
       62.54 -    93.82: 8
       93.82 -   125.09: 0
      125.09 -   156.36: 1
  Dihedral angle restraints: 1821
    sinusoidal: 713
      harmonic: 1108
  Sorted by residual:
  dihedral pdb=" CB  CYS F 184 "
           pdb=" SG  CYS F 184 "
           pdb=" SG  CYS F 190 "
           pdb=" CB  CYS F 190 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00    0.68  -86.68     1      1.00e+01 1.00e-02 9.04e+01
  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 -162.86   76.86     1      1.00e+01 1.00e-02 7.42e+01
  dihedral pdb=" C4  JTZ F 501 "
           pdb=" C5  JTZ F 501 "
           pdb=" C6  JTZ F 501 "
           pdb=" O2  JTZ F 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     181.12   24.76  156.36     1      3.00e+01 1.11e-03 2.04e+01
  ... (remaining 1818 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 430
       0.060 -    0.120: 56
       0.120 -    0.181: 1
       0.181 -    0.241: 0
       0.241 -    0.301: 1
  Chirality restraints: 488
  Sorted by residual:
  chirality pdb=" C5  JTZ F 501 "
            pdb=" C4  JTZ F 501 "
            pdb=" C6  JTZ F 501 "
            pdb=" O1  JTZ F 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.63    0.30 2.00e-01 2.50e+01 2.27e+00
  chirality pdb=" CB  ILE F 370 "
            pdb=" CA  ILE F 370 "
            pdb=" CG1 ILE F 370 "
            pdb=" CG2 ILE F 370 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.52    0.12 2.00e-01 2.50e+01 3.86e-01
  chirality pdb=" CA  ASN F 368 "
            pdb=" N   ASN F 368 "
            pdb=" C   ASN F 368 "
            pdb=" CB  ASN F 368 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.40    0.11 2.00e-01 2.50e+01 3.22e-01
  ... (remaining 485 not shown)

  Planarity restraints: 513
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP F 237 "    0.003 2.00e-02 2.50e+03   8.53e-03 1.82e+00
        pdb=" CG  TRP F 237 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD1 TRP F 237 "    0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP F 237 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP F 237 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE2 TRP F 237 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP F 237 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP F 237 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP F 237 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP F 237 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN F 385 "    0.006 2.00e-02 2.50e+03   1.10e-02 1.22e+00
        pdb=" C   ASN F 385 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   ASN F 385 "    0.007 2.00e-02 2.50e+03
        pdb=" N   SER F 386 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU F 354 "   -0.018 5.00e-02 4.00e+02   2.67e-02 1.14e+00
        pdb=" N   PRO F 355 "    0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO F 355 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO F 355 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 510 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 140
        2.73 -     3.27: 3211
        3.27 -     3.81: 5027
        3.81 -     4.36: 5604
        4.36 -     4.90: 9744
  Nonbonded interactions: 23726
  Sorted by model distance:
  nonbonded pdb=" OH  TYR F 219 "
            pdb=" O   LEU F 339 "
     model   vdw
     2.184 3.040
  nonbonded pdb=" OD2 ASP F 113 "
            pdb=" OH  TYR F 383 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" OG1 THR F 118 "
            pdb=" OG  SER F 207 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O   ALA F 119 "
            pdb=" OG1 THR F 123 "
     model   vdw
     2.377 3.040
  nonbonded pdb=" C4  JTZ F 501 "
            pdb=" O2  JTZ F 501 "
     model   vdw
     2.378 2.752
  ... (remaining 23721 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.100
  Find NCS groups from input model:        0.010
  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:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6849
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      :  0.003   0.050   3085  Z= 0.166
  Angle     :  0.637   8.912   4188  Z= 0.327
  Chirality :  0.041   0.301    488
  Planarity :  0.003   0.027    513
  Dihedral  : 17.699 156.361   1093
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 17.96 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.44), residues: 371
  helix:  0.85 (0.31), residues: 293
  sheet:  None (None), residues: 0
  loop : -3.64 (0.54), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 371 
 TYR   0.010   0.001   TYR F 383 
 PHE   0.007   0.001   PHE F 193 
 TRP   0.018   0.001   TRP F 237 
 HIS   0.006   0.001   HIS F 286 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 3083)
  covalent geometry    : angle       0.63689 ( 4184)
  SS BOND              : bond        0.00042 (    2)
  SS BOND              : angle       0.49378 (    4)
  hydrogen bonds       : bond        0.18224 (  223)
  hydrogen bonds       : angle       6.40887 (  663)

*********************** 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
  54 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.068 
Fit side-chains
REVERT: F  171 MET cc_start: 0.6084 (ppp) cc_final: 0.5567 (ppp)
  outliers start: 1
  outliers final: 1
  residues processed: 53
  average time/residue: 0.0366
  time to fit residues: 2.5750
Evaluate side-chains
  54 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  223 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
F  65 GLN
F 360 ASN
** F 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4570 r_free = 0.4570 target = 0.214356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.169100 restraints weight = 3442.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.4224 rms_B_bonded: 2.65
r_work: 0.3979 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.3979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6950
moved from start:          0.1078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3085  Z= 0.138
  Angle     :  0.531   5.731   4188  Z= 0.283
  Chirality :  0.039   0.130    488
  Planarity :  0.003   0.027    513
  Dihedral  :  8.811 121.262    409
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 17.34 %
    Favored  : 79.57 %
  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:  0.57 (0.45), residues: 371
  helix:  1.18 (0.31), residues: 305
  sheet:  None (None), residues: 0
  loop : -3.47 (0.64), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 371 
 TYR   0.020   0.002   TYR F 383 
 PHE   0.009   0.001   PHE F 356 
 TRP   0.008   0.001   TRP F 237 
 HIS   0.003   0.001   HIS F 286 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 3083)
  covalent geometry    : angle       0.53105 ( 4184)
  SS BOND              : bond        0.00057 (    2)
  SS BOND              : angle       0.72121 (    4)
  hydrogen bonds       : bond        0.04468 (  223)
  hydrogen bonds       : angle       4.42098 (  663)

*********************** 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: 10
    poor density    : 59
  time to evaluate  : 0.109 
Fit side-chains
  outliers start: 10
  outliers final: 6
  residues processed: 66
  average time/residue: 0.0317
  time to fit residues: 2.8734
Evaluate side-chains
  58 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   38 ILE
Chi-restraints excluded: chain F residue   65 GLN
Chi-restraints excluded: chain F residue  203 SER
Chi-restraints excluded: chain F residue  223 PHE
Chi-restraints excluded: chain F residue  325 ILE
Chi-restraints excluded: chain F residue  386 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 17 optimal weight:    0.3980
   chunk 31 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 6 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
F 255 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4552 r_free = 0.4552 target = 0.206748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.164409 restraints weight = 3368.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.4236 rms_B_bonded: 2.27
r_work: 0.4009 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.4009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6955
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3085  Z= 0.124
  Angle     :  0.500   6.945   4188  Z= 0.266
  Chirality :  0.038   0.117    488
  Planarity :  0.003   0.029    513
  Dihedral  :  8.465 112.693    409
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 19.81 %
    Favored  : 76.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.74 (0.46), residues: 371
  helix:  1.31 (0.31), residues: 305
  sheet:  None (None), residues: 0
  loop : -3.45 (0.64), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 371 
 TYR   0.010   0.001   TYR F 383 
 PHE   0.006   0.001   PHE F 356 
 TRP   0.005   0.001   TRP F 380 
 HIS   0.003   0.001   HIS F 286 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 3083)
  covalent geometry    : angle       0.49985 ( 4184)
  SS BOND              : bond        0.00020 (    2)
  SS BOND              : angle       0.64577 (    4)
  hydrogen bonds       : bond        0.04037 (  223)
  hydrogen bonds       : angle       4.20746 (  663)

*********************** 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
  65 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 54
  time to evaluate  : 0.090 
Fit side-chains
  outliers start: 11
  outliers final: 6
  residues processed: 62
  average time/residue: 0.0290
  time to fit residues: 2.4802
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  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  100 THR
Chi-restraints excluded: chain F residue  155 LEU
Chi-restraints excluded: chain F residue  203 SER
Chi-restraints excluded: chain F residue  223 PHE
Chi-restraints excluded: chain F residue  325 ILE
Chi-restraints excluded: chain F residue  374 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 11 optimal weight:    7.9990
   chunk 17 optimal weight:    1.9990
   chunk 23 optimal weight:    7.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
F 252 ASN
F 363 HIS
** F 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.211413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.165928 restraints weight = 3524.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.4184 rms_B_bonded: 2.45
r_work: 0.3955 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7016
moved from start:          0.1628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3085  Z= 0.154
  Angle     :  0.546   9.466   4188  Z= 0.281
  Chirality :  0.039   0.117    488
  Planarity :  0.003   0.028    513
  Dihedral  :  8.347 109.579    409
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 21.36 %
    Favored  : 75.54 %
  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:  0.56 (0.45), residues: 371
  helix:  1.23 (0.31), residues: 301
  sheet:  None (None), residues: 0
  loop : -3.47 (0.59), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 371 
 TYR   0.023   0.002   TYR F 174 
 PHE   0.009   0.001   PHE F 288 
 TRP   0.005   0.001   TRP F 380 
 HIS   0.003   0.001   HIS F 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 3083)
  covalent geometry    : angle       0.54573 ( 4184)
  SS BOND              : bond        0.00034 (    2)
  SS BOND              : angle       0.62602 (    4)
  hydrogen bonds       : bond        0.04030 (  223)
  hydrogen bonds       : angle       4.17089 (  663)

*********************** 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
  68 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.145 
Fit side-chains
REVERT: F  215 MET cc_start: 0.5910 (ttp) cc_final: 0.5707 (tmm)
  outliers start: 10
  outliers final: 9
  residues processed: 65
  average time/residue: 0.0319
  time to fit residues: 2.8552
Evaluate side-chains
  61 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   42 LEU
Chi-restraints excluded: chain F residue  100 THR
Chi-restraints excluded: chain F residue  155 LEU
Chi-restraints excluded: chain F residue  203 SER
Chi-restraints excluded: chain F residue  223 PHE
Chi-restraints excluded: chain F residue  325 ILE
Chi-restraints excluded: chain F residue  341 THR
Chi-restraints excluded: chain F residue  363 HIS
Chi-restraints excluded: chain F residue  374 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0970
   chunk 24 optimal weight:    0.2980
   chunk 18 optimal weight:    0.9980
   chunk 5 optimal weight:    0.2980
   chunk 28 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 7 optimal weight:   10.0000
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
** F 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4586 r_free = 0.4586 target = 0.215389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.169367 restraints weight = 3483.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.4159 rms_B_bonded: 2.47
r_work: 0.3980 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6993
moved from start:          0.1801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   3085  Z= 0.114
  Angle     :  0.496   9.083   4188  Z= 0.259
  Chirality :  0.037   0.111    488
  Planarity :  0.003   0.029    513
  Dihedral  :  8.142 104.600    409
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 23.84 %
    Favored  : 73.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.71 (0.46), residues: 371
  helix:  1.31 (0.31), residues: 305
  sheet:  None (None), residues: 0
  loop : -3.61 (0.57), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 371 
 TYR   0.021   0.001   TYR F 174 
 PHE   0.009   0.001   PHE F  49 
 TRP   0.006   0.001   TRP F 237 
 HIS   0.009   0.001   HIS F 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 3083)
  covalent geometry    : angle       0.49546 ( 4184)
  SS BOND              : bond        0.00016 (    2)
  SS BOND              : angle       0.60986 (    4)
  hydrogen bonds       : bond        0.03710 (  223)
  hydrogen bonds       : angle       4.01593 (  663)

*********************** 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
  62 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.126 
Fit side-chains
REVERT: F  236 ASN cc_start: 0.8042 (t0) cc_final: 0.7794 (t0)
REVERT: F  373 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6845 (mm-30)
  outliers start: 10
  outliers final: 7
  residues processed: 60
  average time/residue: 0.0422
  time to fit residues: 3.4390
Evaluate side-chains
  58 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   42 LEU
Chi-restraints excluded: chain F residue   53 LEU
Chi-restraints excluded: chain F residue  100 THR
Chi-restraints excluded: chain F residue  155 LEU
Chi-restraints excluded: chain F residue  203 SER
Chi-restraints excluded: chain F residue  223 PHE
Chi-restraints excluded: chain F residue  325 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0870
   chunk 12 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 10 optimal weight:    0.3980
   chunk 0 optimal weight:   20.0000
   chunk 11 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 3 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 5 optimal weight:    0.3980
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
F 368 ASN
** F 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4587 r_free = 0.4587 target = 0.216100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.172149 restraints weight = 3463.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.4252 rms_B_bonded: 2.69
r_work: 0.4006 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.4006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6938
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   3085  Z= 0.108
  Angle     :  0.484   8.891   4188  Z= 0.252
  Chirality :  0.037   0.105    488
  Planarity :  0.003   0.029    513
  Dihedral  :  8.100 100.260    409
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 24.77 %
    Favored  : 71.83 %
  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:  0.84 (0.46), residues: 371
  helix:  1.40 (0.31), residues: 305
  sheet:  None (None), residues: 0
  loop : -3.57 (0.58), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 371 
 TYR   0.019   0.002   TYR F 174 
 PHE   0.008   0.001   PHE F  49 
 TRP   0.005   0.001   TRP F 380 
 HIS   0.002   0.001   HIS F 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 3083)
  covalent geometry    : angle       0.48350 ( 4184)
  SS BOND              : bond        0.00033 (    2)
  SS BOND              : angle       0.54777 (    4)
  hydrogen bonds       : bond        0.03555 (  223)
  hydrogen bonds       : angle       3.96213 (  663)

*********************** 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
  65 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 54
  time to evaluate  : 0.112 
Fit side-chains
REVERT: F  236 ASN cc_start: 0.8208 (t0) cc_final: 0.7700 (t0)
REVERT: F  245 LYS cc_start: 0.7856 (ttpp) cc_final: 0.7063 (tppt)
  outliers start: 11
  outliers final: 11
  residues processed: 62
  average time/residue: 0.0434
  time to fit residues: 3.5713
Evaluate side-chains
  61 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 50
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   42 LEU
Chi-restraints excluded: chain F residue   53 LEU
Chi-restraints excluded: chain F residue  100 THR
Chi-restraints excluded: chain F residue  126 VAL
Chi-restraints excluded: chain F residue  155 LEU
Chi-restraints excluded: chain F residue  203 SER
Chi-restraints excluded: chain F residue  223 PHE
Chi-restraints excluded: chain F residue  235 ASP
Chi-restraints excluded: chain F residue  325 ILE
Chi-restraints excluded: chain F residue  368 ASN
Chi-restraints excluded: chain F residue  374 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 24 optimal weight:    0.2980
   chunk 21 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 14 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
F  65 GLN
F 368 ASN
** F 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4559 r_free = 0.4559 target = 0.213371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.167902 restraints weight = 3490.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.4209 rms_B_bonded: 2.43
r_work: 0.3985 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6989
moved from start:          0.2139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3085  Z= 0.130
  Angle     :  0.523  10.848   4188  Z= 0.268
  Chirality :  0.039   0.155    488
  Planarity :  0.003   0.028    513
  Dihedral  :  8.196  98.165    409
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 24.77 %
    Favored  : 71.52 %
  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:  0.60 (0.45), residues: 371
  helix:  1.24 (0.31), residues: 305
  sheet:  None (None), residues: 0
  loop : -3.67 (0.56), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 371 
 TYR   0.016   0.002   TYR F 174 
 PHE   0.009   0.001   PHE F 288 
 TRP   0.006   0.001   TRP F 237 
 HIS   0.002   0.001   HIS F 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 3083)
  covalent geometry    : angle       0.52333 ( 4184)
  SS BOND              : bond        0.00035 (    2)
  SS BOND              : angle       0.52062 (    4)
  hydrogen bonds       : bond        0.03629 (  223)
  hydrogen bonds       : angle       3.98489 (  663)

*********************** 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
  67 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 0.074 
Fit side-chains
REVERT: F  236 ASN cc_start: 0.8205 (t0) cc_final: 0.7746 (t0)
REVERT: F  245 LYS cc_start: 0.7855 (ttpp) cc_final: 0.6964 (tppt)
  outliers start: 12
  outliers final: 10
  residues processed: 64
  average time/residue: 0.0509
  time to fit residues: 4.1995
Evaluate side-chains
  61 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   42 LEU
Chi-restraints excluded: chain F residue   65 GLN
Chi-restraints excluded: chain F residue  100 THR
Chi-restraints excluded: chain F residue  126 VAL
Chi-restraints excluded: chain F residue  155 LEU
Chi-restraints excluded: chain F residue  203 SER
Chi-restraints excluded: chain F residue  223 PHE
Chi-restraints excluded: chain F residue  325 ILE
Chi-restraints excluded: chain F residue  368 ASN
Chi-restraints excluded: chain F residue  374 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 36 optimal weight:    0.1980
   chunk 25 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 3 optimal weight:    0.8980
   chunk 0 optimal weight:   20.0000
   chunk 4 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
F 368 ASN
** F 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4582 r_free = 0.4582 target = 0.215741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.170285 restraints weight = 3516.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.4243 rms_B_bonded: 2.80
r_work: 0.3987 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6965
moved from start:          0.2194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3085  Z= 0.115
  Angle     :  0.523  10.857   4188  Z= 0.267
  Chirality :  0.038   0.146    488
  Planarity :  0.003   0.030    513
  Dihedral  :  7.836  95.011    409
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 24.77 %
    Favored  : 71.52 %
  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:  0.83 (0.45), residues: 371
  helix:  1.43 (0.31), residues: 299
  sheet:  None (None), residues: 0
  loop : -3.29 (0.55), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 371 
 TYR   0.016   0.001   TYR F 174 
 PHE   0.008   0.001   PHE F  49 
 TRP   0.005   0.001   TRP F 380 
 HIS   0.001   0.001   HIS F 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 3083)
  covalent geometry    : angle       0.52244 ( 4184)
  SS BOND              : bond        0.00019 (    2)
  SS BOND              : angle       0.75093 (    4)
  hydrogen bonds       : bond        0.03499 (  223)
  hydrogen bonds       : angle       3.94413 (  663)

*********************** 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
  61 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.081 
Fit side-chains
REVERT: F  236 ASN cc_start: 0.8205 (t0) cc_final: 0.7734 (t0)
REVERT: F  245 LYS cc_start: 0.7744 (ttpp) cc_final: 0.6914 (tppt)
  outliers start: 12
  outliers final: 11
  residues processed: 58
  average time/residue: 0.0407
  time to fit residues: 3.1153
Evaluate side-chains
  59 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   42 LEU
Chi-restraints excluded: chain F residue   53 LEU
Chi-restraints excluded: chain F residue  100 THR
Chi-restraints excluded: chain F residue  126 VAL
Chi-restraints excluded: chain F residue  155 LEU
Chi-restraints excluded: chain F residue  203 SER
Chi-restraints excluded: chain F residue  223 PHE
Chi-restraints excluded: chain F residue  235 ASP
Chi-restraints excluded: chain F residue  325 ILE
Chi-restraints excluded: chain F residue  368 ASN
Chi-restraints excluded: chain F residue  374 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0970
   chunk 20 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0170
   chunk 36 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0970
   chunk 1 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.3214

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

Flipped N/Q/H residues before XYZ refinement:
** F 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4599 r_free = 0.4599 target = 0.218230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.172785 restraints weight = 3527.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.4216 rms_B_bonded: 2.51
r_work: 0.4027 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.4027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6914
moved from start:          0.2315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   3085  Z= 0.106
  Angle     :  0.513  10.438   4188  Z= 0.262
  Chirality :  0.038   0.137    488
  Planarity :  0.003   0.031    513
  Dihedral  :  7.621  93.125    409
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 25.70 %
    Favored  : 71.52 %
  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:  1.00 (0.45), residues: 371
  helix:  1.52 (0.32), residues: 299
  sheet:  None (None), residues: 0
  loop : -3.12 (0.56), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 371 
 TYR   0.017   0.001   TYR F 174 
 PHE   0.008   0.001   PHE F  49 
 TRP   0.006   0.001   TRP F 380 
 HIS   0.001   0.000   HIS F 286 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 3083)
  covalent geometry    : angle       0.51263 ( 4184)
  SS BOND              : bond        0.00025 (    2)
  SS BOND              : angle       0.67520 (    4)
  hydrogen bonds       : bond        0.03426 (  223)
  hydrogen bonds       : angle       3.92188 (  663)

*********************** 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
  61 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.076 
Fit side-chains
REVERT: F  236 ASN cc_start: 0.8159 (t0) cc_final: 0.7786 (t0)
REVERT: F  245 LYS cc_start: 0.7765 (ttpp) cc_final: 0.7037 (tppt)
  outliers start: 9
  outliers final: 7
  residues processed: 58
  average time/residue: 0.0423
  time to fit residues: 3.2635
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  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   42 LEU
Chi-restraints excluded: chain F residue   53 LEU
Chi-restraints excluded: chain F residue  155 LEU
Chi-restraints excluded: chain F residue  203 SER
Chi-restraints excluded: chain F residue  223 PHE
Chi-restraints excluded: chain F residue  235 ASP
Chi-restraints excluded: chain F residue  374 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 17 optimal weight:    7.9990
   chunk 35 optimal weight:    2.9990
   chunk 26 optimal weight:    0.1980
   chunk 13 optimal weight:    0.0970
   chunk 11 optimal weight:    0.9990
   chunk 20 optimal weight:    9.9990
   chunk 3 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   chunk 36 optimal weight:    0.5980
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.4578

-------------------------------------------------------------------------------
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 = 0.4598 r_free = 0.4598 target = 0.217953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.173189 restraints weight = 3481.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.4265 rms_B_bonded: 2.47
r_work: 0.4041 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.4041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6902
moved from start:          0.2393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   3085  Z= 0.106
  Angle     :  0.508   8.602   4188  Z= 0.262
  Chirality :  0.038   0.162    488
  Planarity :  0.003   0.030    513
  Dihedral  :  7.526  92.309    409
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 26.63 %
    Favored  : 71.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.20 (0.45), residues: 371
  helix:  1.75 (0.32), residues: 292
  sheet:  None (None), residues: 0
  loop : -3.01 (0.55), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 371 
 TYR   0.017   0.001   TYR F 174 
 PHE   0.012   0.001   PHE F  49 
 TRP   0.006   0.001   TRP F 380 
 HIS   0.001   0.001   HIS F 286 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 3083)
  covalent geometry    : angle       0.50789 ( 4184)
  SS BOND              : bond        0.00018 (    2)
  SS BOND              : angle       0.65130 (    4)
  hydrogen bonds       : bond        0.03409 (  223)
  hydrogen bonds       : angle       3.90392 (  663)

********************** 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
  59 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.092 
Fit side-chains
REVERT: F   79 ASP cc_start: 0.7258 (m-30) cc_final: 0.6975 (t70)
REVERT: F  236 ASN cc_start: 0.8145 (t0) cc_final: 0.7746 (t0)
REVERT: F  245 LYS cc_start: 0.7730 (ttpp) cc_final: 0.6996 (tppt)
  outliers start: 7
  outliers final: 7
  residues processed: 57
  average time/residue: 0.0442
  time to fit residues: 3.3233
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  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   42 LEU
Chi-restraints excluded: chain F residue   53 LEU
Chi-restraints excluded: chain F residue  126 VAL
Chi-restraints excluded: chain F residue  155 LEU
Chi-restraints excluded: chain F residue  203 SER
Chi-restraints excluded: chain F residue  223 PHE
Chi-restraints excluded: chain F residue  235 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 24 optimal weight:    0.1980
   chunk 16 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 2 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   chunk 0 optimal weight:   20.0000
   chunk 20 optimal weight:    8.9990
   chunk 9 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.4572 r_free = 0.4572 target = 0.214760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.169841 restraints weight = 3480.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.4225 rms_B_bonded: 2.43
r_work: 0.4002 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6966
moved from start:          0.2386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3085  Z= 0.134
  Angle     :  0.561   8.653   4188  Z= 0.291
  Chirality :  0.040   0.184    488
  Planarity :  0.003   0.032    513
  Dihedral  :  7.617  92.968    409
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 26.93 %
    Favored  : 70.28 %
  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:  1.05 (0.45), residues: 371
  helix:  1.64 (0.31), residues: 291
  sheet:  None (None), residues: 0
  loop : -3.02 (0.55), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 371 
 TYR   0.015   0.001   TYR F 174 
 PHE   0.011   0.001   PHE F  49 
 TRP   0.005   0.001   TRP F 237 
 HIS   0.001   0.001   HIS F 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 3083)
  covalent geometry    : angle       0.56065 ( 4184)
  SS BOND              : bond        0.00016 (    2)
  SS BOND              : angle       0.63041 (    4)
  hydrogen bonds       : bond        0.03566 (  223)
  hydrogen bonds       : angle       3.95771 (  663)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 820.26 seconds
wall clock time: 14 minutes 43.68 seconds (883.68 seconds total)