Starting phenix.real_space_refine
on Thu Sep 10 22:37:09 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6uwl_20923/09_2026/6uwl_20923.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6uwl_20923/09_2026/6uwl_20923.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.62
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6uwl_20923/09_2026/6uwl_20923.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6uwl_20923/09_2026/6uwl_20923.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6uwl_20923/09_2026/6uwl_20923.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6uwl_20923/09_2026/6uwl_20923.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/6uwl_20923/09_2026/6uwl_20923.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6uwl_20923/09_2026/6uwl_20923.cif"
  }
  resolution = 3.62
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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 1634 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: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      18      5.16       5
     C    1998      2.51       5
     N     479      2.21       5
     O     533      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 3029
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2990
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 402, 2990
          Classifications: {'peptide': 402}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 384}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'FME:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 39
          Unusual residues: {'6OU': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 10
  Time building chain proxies: 1.00, per 1000 atoms: 0.33
  Number of scatterers: 3029
  At special positions: 0
  Unit cell: (67.84, 67.84, 77.38, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      18     16.00
     P       1     15.00
     O     533      8.00
     N     479      7.00
     C    1998      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.33
  Conformation dependent library (CDL) restraints added in 130.5 milliseconds
  

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  724

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 0 sheets defined
      84.3% 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 'A' and resid 2 through 8
      removed outlier: 3.820A  pdb=" N   LYS A   6 " --> pdb=" O   GLY A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 11 through 14
      removed outlier: 3.518A  pdb=" N   GLN A  14 " --> pdb=" O   PRO A  11 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 11 through 14'
    Processing helix  chain 'A' and resid 15 through 32
      removed outlier: 3.931A  pdb=" N   VAL A  26 " --> pdb=" O   LEU A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 43
    Processing helix  chain 'A' and resid 43 through 57
      removed outlier: 3.971A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 70
      removed outlier: 3.590A  pdb=" N   PHE A  63 " --> pdb=" O   MET A  59 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   SER A  65 " --> pdb=" O   ILE A  61 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   LEU A  66 " --> pdb=" O   VAL A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 103
      removed outlier: 3.755A  pdb=" N   TYR A  88 " --> pdb=" O   LYS A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 136
    Processing helix  chain 'A' and resid 143 through 148
    Processing helix  chain 'A' and resid 150 through 169
    Processing helix  chain 'A' and resid 173 through 220
      removed outlier: 3.901A  pdb=" N   TYR A 195 " --> pdb=" O   ALA A 191 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LYS A 196 " --> pdb=" O   GLU A 192 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   TYR A 204 " --> pdb=" O   GLY A 200 " (cutoff:3.500A)
      Proline residue:  A 206  - end of helix
      removed outlier: 3.732A  pdb=" N   GLN A 220 " --> pdb=" O   VAL A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 224
      removed outlier: 3.826A  pdb=" N   VAL A 224 " --> pdb=" O   GLY A 221 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 221 through 224'
    Processing helix  chain 'A' and resid 228 through 254
      removed outlier: 3.884A  pdb=" N   THR A 232 " --> pdb=" O   LEU A 228 " (cutoff:3.500A)
      removed outlier: 4.843A  pdb=" N   PHE A 248 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      removed outlier: 4.807A  pdb=" N   VAL A 249 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   TYR A 254 " --> pdb=" O   LEU A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 276
      removed outlier: 6.153A  pdb=" N   ASP A 267 " --> pdb=" O   LYS A 263 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   ALA A 268 " --> pdb=" O   HIS A 264 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ARG A 276 " --> pdb=" O   ALA A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 293
    Processing helix  chain 'A' and resid 295 through 300
    Processing helix  chain 'A' and resid 301 through 310
      removed outlier: 4.050A  pdb=" N   THR A 308 " --> pdb=" O   PRO A 304 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ASN A 310 " --> pdb=" O   GLY A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 327
      removed outlier: 4.012A  pdb=" N   GLY A 319 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   VAL A 320 " --> pdb=" O   LEU A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 351
      removed outlier: 3.678A  pdb=" N   ILE A 341 " --> pdb=" O   GLN A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 371
      removed outlier: 3.705A  pdb=" N   MET A 362 " --> pdb=" O   ALA A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 415
      removed outlier: 4.016A  pdb=" N   MET A 385 " --> pdb=" O   ALA A 381 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ILE A 386 " --> pdb=" O   ALA A 382 " (cutoff:3.500A)
      removed outlier: 5.282A  pdb=" N   ALA A 391 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   ILE A 392 " --> pdb=" O   GLY A 388 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   LEU A 393 " --> pdb=" O   ILE A 389 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   MET A 395 " --> pdb=" O   ALA A 391 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   GLY A 396 " --> pdb=" O   ILE A 392 " (cutoff:3.500A)

    221 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: 0.48

  Time building geometry restraints manager: 0.39 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 467
        1.31 -     1.43: 749
        1.43 -     1.56: 1819
        1.56 -     1.68: 13
        1.68 -     1.81: 35
  Bond restraints: 3083
  Sorted by residual:
  bond pdb=" C16 6OU A 502 "
       pdb=" O18 6OU A 502 "
    ideal  model  delta    sigma   weight residual
    1.327  1.413 -0.086 2.00e-02 2.50e+03 1.83e+01
  bond pdb=" C31 6OU A 502 "
       pdb=" O30 6OU A 502 "
    ideal  model  delta    sigma   weight residual
    1.331  1.403 -0.072 2.00e-02 2.50e+03 1.30e+01
  bond pdb=" C39 6OU A 502 "
       pdb=" C40 6OU A 502 "
    ideal  model  delta    sigma   weight residual
    1.497  1.565 -0.068 2.00e-02 2.50e+03 1.16e+01
  bond pdb=" C15 6OU A 502 "
       pdb=" C16 6OU A 502 "
    ideal  model  delta    sigma   weight residual
    1.501  1.558 -0.057 2.00e-02 2.50e+03 8.21e+00
  bond pdb=" SD  FME A   1 "
       pdb=" CE  FME A   1 "
    ideal  model  delta    sigma   weight residual
    1.805  1.751  0.054 2.00e-02 2.50e+03 7.33e+00
  ... (remaining 3078 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.26: 4095
        3.26 -     6.51: 77
        6.51 -     9.77: 14
        9.77 -    13.02: 2
       13.02 -    16.28: 2
  Bond angle restraints: 4190
  Sorted by residual:
  angle pdb=" N   ALA A 205 "
        pdb=" CA  ALA A 205 "
        pdb=" C   ALA A 205 "
      ideal   model   delta    sigma   weight residual
     109.81  120.81  -11.00 2.21e+00 2.05e-01 2.48e+01
  angle pdb=" CA  LEU A 228 "
        pdb=" CB  LEU A 228 "
        pdb=" CG  LEU A 228 "
      ideal   model   delta    sigma   weight residual
     116.30  132.58  -16.28 3.50e+00 8.16e-02 2.16e+01
  angle pdb=" O22 6OU A 502 "
        pdb=" P23 6OU A 502 "
        pdb=" O26 6OU A 502 "
      ideal   model   delta    sigma   weight residual
      93.95  107.46  -13.51 3.00e+00 1.11e-01 2.03e+01
  angle pdb=" C   ILE A 294 "
        pdb=" N   SER A 295 "
        pdb=" CA  SER A 295 "
      ideal   model   delta    sigma   weight residual
     121.54  129.72   -8.18 1.91e+00 2.74e-01 1.83e+01
  angle pdb=" CA  TYR A 299 "
        pdb=" CB  TYR A 299 "
        pdb=" CG  TYR A 299 "
      ideal   model   delta    sigma   weight residual
     113.90  121.13   -7.23 1.80e+00 3.09e-01 1.61e+01
  ... (remaining 4185 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.45: 1707
       25.45 -    50.91: 93
       50.91 -    76.36: 12
       76.36 -   101.81: 0
      101.81 -   127.26: 2
  Dihedral angle restraints: 1814
    sinusoidal: 673
      harmonic: 1141
  Sorted by residual:
  dihedral pdb=" CA  ILE A 294 "
           pdb=" C   ILE A 294 "
           pdb=" N   SER A 295 "
           pdb=" CA  SER A 295 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  143.05   36.95     0      5.00e+00 4.00e-02 5.46e+01
  dihedral pdb=" CA  PRO A  75 "
           pdb=" C   PRO A  75 "
           pdb=" N   ALA A  76 "
           pdb=" CA  ALA A  76 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.43  -26.57     0      5.00e+00 4.00e-02 2.82e+01
  dihedral pdb=" CA  SER A  72 "
           pdb=" C   SER A  72 "
           pdb=" N   ILE A  73 "
           pdb=" CA  ILE A  73 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.02   20.98     0      5.00e+00 4.00e-02 1.76e+01
  ... (remaining 1811 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 357
       0.052 -    0.105: 112
       0.105 -    0.157: 45
       0.157 -    0.209: 9
       0.209 -    0.262: 1
  Chirality restraints: 524
  Sorted by residual:
  chirality pdb=" CB  ILE A  73 "
            pdb=" CA  ILE A  73 "
            pdb=" CG1 ILE A  73 "
            pdb=" CG2 ILE A  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" CB  VAL A  62 "
            pdb=" CA  VAL A  62 "
            pdb=" CG1 VAL A  62 "
            pdb=" CG2 VAL A  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CA  ALA A 205 "
            pdb=" N   ALA A 205 "
            pdb=" C   ALA A 205 "
            pdb=" CB  ALA A 205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.29    0.20 2.00e-01 2.50e+01 9.51e-01
  ... (remaining 521 not shown)

  Planarity restraints: 510
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 355 "    0.042 5.00e-02 4.00e+02   6.40e-02 6.56e+00
        pdb=" N   PRO A 356 "   -0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO A 356 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 356 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A  44 "   -0.041 5.00e-02 4.00e+02   6.14e-02 6.03e+00
        pdb=" N   PRO A  45 "    0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO A  45 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A  45 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 243 "   -0.011 2.00e-02 2.50e+03   2.19e-02 4.81e+00
        pdb=" C   ILE A 243 "    0.038 2.00e-02 2.50e+03
        pdb=" O   ILE A 243 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   LEU A 244 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 507 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 926
        2.82 -     3.34: 2992
        3.34 -     3.86: 5003
        3.86 -     4.38: 5617
        4.38 -     4.90: 9689
  Nonbonded interactions: 24227
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 247 "
            pdb=" OD2 ASP A 312 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OH  TYR A 236 "
            pdb=" O   ILE A 392 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" O   THR A 403 "
            pdb=" OG1 THR A 407 "
     model   vdw
     2.326 3.040
  nonbonded pdb=" O   ILE A  61 "
            pdb=" OG  SER A  65 "
     model   vdw
     2.342 3.040
  nonbonded pdb=" O   MET A 311 "
            pdb=" OG  SER A 349 "
     model   vdw
     2.349 3.040
  ... (remaining 24222 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.300
  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:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
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      :  0.008   0.086   3084  Z= 0.356
  Angle     :  1.158  16.279   4190  Z= 0.567
  Chirality :  0.060   0.262    524
  Planarity :  0.009   0.064    510
  Dihedral  : 16.048 127.264   1090
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.58 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 14.01 %
    Favored  : 85.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.71 (0.31), residues: 396
  helix: -2.71 (0.20), residues: 321
  sheet:  None (None), residues: 0
  loop : -3.85 (0.67), residues: 75

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 397 
 TYR   0.028   0.002   TYR A 299 
 PHE   0.017   0.002   PHE A 248 
 HIS   0.005   0.002   HIS A 264 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00808 /  0.36 ( 3083)
  covalent geometry    : angle       1.15805 /  0.57 ( 4190)
  hydrogen bonds       : bond        0.10267 /  5.82 (  221)
  hydrogen bonds       : angle       6.21565 /  4.39 (  663)
  Misc. bond           : bond        0.00007 /  0.00 (    1)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.108 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 TYR cc_start: 0.8103 (m-80) cc_final: 0.7888 (m-80)
REVERT: A  337 GLN cc_start: 0.7419 (mm-40) cc_final: 0.5816 (tt0)
REVERT: A  362 MET cc_start: 0.8500 (mmm) cc_final: 0.8280 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.0592
  time to fit residues: 6.6435
Evaluate side-chains
  70 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0050
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.5194

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  14 GLN
A  40 HIS
A 173 ASN
A 199 ASN
** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.130901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.104811 restraints weight = 5829.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.107148 restraints weight = 3324.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.108641 restraints weight = 2395.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.109549 restraints weight = 1980.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.110171 restraints weight = 1780.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.1787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3084  Z= 0.151
  Angle     :  0.691  10.014   4190  Z= 0.351
  Chirality :  0.042   0.135    524
  Planarity :  0.006   0.054    510
  Dihedral  : 10.498  90.123    452
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.06 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 19.43 %
    Favored  : 77.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.03 (0.40), residues: 396
  helix: -0.75 (0.26), residues: 321
  sheet:  None (None), residues: 0
  loop : -3.44 (0.72), residues: 75

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 105 
 TYR   0.025   0.001   TYR A 299 
 PHE   0.014   0.001   PHE A 324 
 HIS   0.004   0.001   HIS A 332 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.15 ( 3083)
  covalent geometry    : angle       0.69054 /  0.35 ( 4190)
  hydrogen bonds       : bond        0.04251 /  2.61 (  221)
  hydrogen bonds       : angle       4.76209 /  3.27 (  663)
  Misc. bond           : bond        0.00016 /  0.01 (    1)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.071 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 TYR cc_start: 0.8064 (m-80) cc_final: 0.7861 (m-80)
REVERT: A  102 ILE cc_start: 0.8414 (mt) cc_final: 0.8189 (mt)
REVERT: A  227 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7267 (tm-30)
REVERT: A  247 TYR cc_start: 0.7938 (m-80) cc_final: 0.7689 (m-80)
REVERT: A  337 GLN cc_start: 0.7533 (mm-40) cc_final: 0.6425 (tt0)
REVERT: A  406 LEU cc_start: 0.8981 (mm) cc_final: 0.8613 (mp)
  outliers start: 9
  outliers final: 6
  residues processed: 90
  average time/residue: 0.0462
  time to fit residues: 5.3507
Evaluate side-chains
  83 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  275 THR
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  355 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 10 optimal weight:    0.1980
   chunk 6 optimal weight:    0.5980
   chunk 32 optimal weight:    0.3980
   chunk 16 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   chunk 8 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 318 GLN
A 332 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.131442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.105436 restraints weight = 5873.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.107790 restraints weight = 3342.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.109321 restraints weight = 2414.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.110156 restraints weight = 1996.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.110156 restraints weight = 1794.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.2302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3084  Z= 0.139
  Angle     :  0.663  10.257   4190  Z= 0.331
  Chirality :  0.042   0.135    524
  Planarity :  0.005   0.052    510
  Dihedral  :  8.242  64.588    452
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.31 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 21.34 %
    Favored  : 74.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.97 (0.42), residues: 396
  helix:  0.03 (0.28), residues: 324
  sheet:  None (None), residues: 0
  loop : -3.44 (0.73), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 397 
 TYR   0.024   0.001   TYR A 299 
 PHE   0.009   0.001   PHE A 324 
 HIS   0.003   0.001   HIS A  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.14 ( 3083)
  covalent geometry    : angle       0.66251 /  0.33 ( 4190)
  hydrogen bonds       : bond        0.04047 /  2.50 (  221)
  hydrogen bonds       : angle       4.60154 /  3.14 (  663)
  Misc. bond           : bond        0.00008 /  0.00 (    1)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.069 
Fit side-chains
REVERT: A   86 VAL cc_start: 0.9301 (t) cc_final: 0.9063 (m)
REVERT: A  136 ASP cc_start: 0.8059 (t0) cc_final: 0.7831 (t0)
REVERT: A  286 MET cc_start: 0.8672 (mtp) cc_final: 0.8338 (mtp)
REVERT: A  337 GLN cc_start: 0.7487 (mm-40) cc_final: 0.6098 (tt0)
REVERT: A  390 ASP cc_start: 0.8016 (t0) cc_final: 0.7745 (t0)
REVERT: A  406 LEU cc_start: 0.8898 (mm) cc_final: 0.8549 (mt)
  outliers start: 13
  outliers final: 6
  residues processed: 88
  average time/residue: 0.0390
  time to fit residues: 4.3847
Evaluate side-chains
  80 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TYR
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  366 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 1 optimal weight:    0.3980
   chunk 21 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  37 HIS
A 318 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.129875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.103933 restraints weight = 5852.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.106368 restraints weight = 3176.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.107982 restraints weight = 2247.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.108874 restraints weight = 1842.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.109137 restraints weight = 1653.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.2484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3084  Z= 0.177
  Angle     :  0.696  10.487   4190  Z= 0.345
  Chirality :  0.044   0.153    524
  Planarity :  0.005   0.054    510
  Dihedral  :  7.210  49.863    452
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 14.09
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.31 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 24.20 %
    Favored  : 71.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.59 (0.43), residues: 396
  helix:  0.32 (0.29), residues: 323
  sheet:  None (None), residues: 0
  loop : -3.36 (0.73), residues: 73

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 105 
 TYR   0.024   0.001   TYR A 299 
 PHE   0.007   0.001   PHE A 324 
 HIS   0.007   0.001   HIS A  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00425 /  0.18 ( 3083)
  covalent geometry    : angle       0.69615 /  0.34 ( 4190)
  hydrogen bonds       : bond        0.04275 /  2.67 (  221)
  hydrogen bonds       : angle       4.67769 /  3.19 (  663)
  Misc. bond           : bond        0.00005 /  0.00 (    1)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.087 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 VAL cc_start: 0.8489 (m) cc_final: 0.8184 (m)
REVERT: A   86 VAL cc_start: 0.9266 (t) cc_final: 0.9062 (m)
REVERT: A  136 ASP cc_start: 0.8151 (t0) cc_final: 0.7908 (t0)
REVERT: A  227 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7539 (tm-30)
REVERT: A  337 GLN cc_start: 0.7481 (mm-40) cc_final: 0.6069 (tt0)
REVERT: A  397 ARG cc_start: 0.7172 (ttm110) cc_final: 0.6827 (ttm110)
REVERT: A  406 LEU cc_start: 0.9005 (mm) cc_final: 0.8643 (mt)
  outliers start: 14
  outliers final: 11
  residues processed: 83
  average time/residue: 0.0455
  time to fit residues: 4.8367
Evaluate side-chains
  85 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 74
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TYR
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  312 ASP
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  398 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0970
   chunk 15 optimal weight:    0.5980
   chunk 11 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 6 optimal weight:    0.3980
   chunk 36 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.4778

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  37 HIS
A 318 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.131001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.105502 restraints weight = 5770.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.107916 restraints weight = 3227.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.109312 restraints weight = 2307.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 17)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.109945 restraints weight = 1914.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.109945 restraints weight = 1755.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.2701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3084  Z= 0.143
  Angle     :  0.681  10.194   4190  Z= 0.333
  Chirality :  0.043   0.141    524
  Planarity :  0.005   0.054    510
  Dihedral  :  6.740  43.045    452
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.56 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 26.43 %
    Favored  : 70.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.26 (0.43), residues: 396
  helix:  0.57 (0.29), residues: 324
  sheet:  None (None), residues: 0
  loop : -3.44 (0.71), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 105 
 TYR   0.021   0.001   TYR A 299 
 PHE   0.008   0.001   PHE A 324 
 HIS   0.007   0.001   HIS A  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00339 /  0.14 ( 3083)
  covalent geometry    : angle       0.68105 /  0.33 ( 4190)
  hydrogen bonds       : bond        0.03992 /  2.48 (  221)
  hydrogen bonds       : angle       4.54920 /  3.09 (  663)
  Misc. bond           : bond        0.00016 /  0.01 (    1)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 VAL cc_start: 0.8455 (m) cc_final: 0.8139 (m)
REVERT: A   86 VAL cc_start: 0.9261 (t) cc_final: 0.9036 (m)
REVERT: A  136 ASP cc_start: 0.8191 (t0) cc_final: 0.7946 (t0)
REVERT: A  286 MET cc_start: 0.8684 (mtp) cc_final: 0.8322 (mtp)
REVERT: A  337 GLN cc_start: 0.7600 (mm-40) cc_final: 0.6362 (tt0)
REVERT: A  394 ASP cc_start: 0.7470 (m-30) cc_final: 0.7108 (m-30)
REVERT: A  397 ARG cc_start: 0.7150 (ttm110) cc_final: 0.6808 (ttm110)
REVERT: A  406 LEU cc_start: 0.8959 (mm) cc_final: 0.8588 (mt)
  outliers start: 11
  outliers final: 10
  residues processed: 82
  average time/residue: 0.0542
  time to fit residues: 5.5910
Evaluate side-chains
  82 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TYR
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  312 ASP
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  366 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 0 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 1 optimal weight:    0.1980
   chunk 4 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  37 HIS
A 264 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.129910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.104048 restraints weight = 5832.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.106419 restraints weight = 3280.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.107856 restraints weight = 2362.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.108607 restraints weight = 1967.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.109196 restraints weight = 1787.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.2813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3084  Z= 0.162
  Angle     :  0.695  10.114   4190  Z= 0.340
  Chirality :  0.044   0.155    524
  Planarity :  0.005   0.055    510
  Dihedral  :  6.788  46.200    452
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.56 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 25.80 %
    Favored  : 68.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.43), residues: 396
  helix:  0.59 (0.29), residues: 325
  sheet:  None (None), residues: 0
  loop : -3.24 (0.73), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 105 
 TYR   0.020   0.001   TYR A 299 
 PHE   0.007   0.001   PHE A 324 
 HIS   0.007   0.001   HIS A  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00389 /  0.16 ( 3083)
  covalent geometry    : angle       0.69478 /  0.34 ( 4190)
  hydrogen bonds       : bond        0.04134 /  2.57 (  221)
  hydrogen bonds       : angle       4.60008 /  3.14 (  663)
  Misc. bond           : bond        0.00012 /  0.01 (    1)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 VAL cc_start: 0.8536 (m) cc_final: 0.8214 (m)
REVERT: A   86 VAL cc_start: 0.9245 (t) cc_final: 0.9019 (m)
REVERT: A  136 ASP cc_start: 0.8172 (t0) cc_final: 0.7971 (t0)
REVERT: A  247 TYR cc_start: 0.7712 (m-80) cc_final: 0.7448 (m-80)
REVERT: A  337 GLN cc_start: 0.7536 (mm-40) cc_final: 0.6365 (tt0)
  outliers start: 17
  outliers final: 13
  residues processed: 89
  average time/residue: 0.0431
  time to fit residues: 4.8594
Evaluate side-chains
  87 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TYR
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  312 ASP
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  366 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 24 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  37 HIS
A 264 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.129759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.103671 restraints weight = 5882.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.106038 restraints weight = 3301.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.107491 restraints weight = 2375.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.108107 restraints weight = 1974.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.108719 restraints weight = 1813.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3084  Z= 0.167
  Angle     :  0.719  10.602   4190  Z= 0.348
  Chirality :  0.043   0.148    524
  Planarity :  0.005   0.058    510
  Dihedral  :  6.730  45.760    452
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 14.89
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.81 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 24.84 %
    Favored  : 69.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.15 (0.43), residues: 396
  helix:  0.61 (0.29), residues: 330
  sheet:  None (None), residues: 0
  loop : -3.55 (0.71), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 105 
 TYR   0.022   0.001   TYR A 299 
 PHE   0.006   0.001   PHE A 324 
 HIS   0.007   0.001   HIS A  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00399 /  0.17 ( 3083)
  covalent geometry    : angle       0.71860 /  0.35 ( 4190)
  hydrogen bonds       : bond        0.04092 /  2.54 (  221)
  hydrogen bonds       : angle       4.59588 /  3.13 (  663)
  Misc. bond           : bond        0.00012 /  0.01 (    1)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 VAL cc_start: 0.8535 (m) cc_final: 0.8212 (m)
REVERT: A   86 VAL cc_start: 0.9248 (t) cc_final: 0.9034 (m)
REVERT: A  247 TYR cc_start: 0.7755 (m-80) cc_final: 0.7511 (m-80)
REVERT: A  286 MET cc_start: 0.8765 (mtp) cc_final: 0.8462 (mtp)
REVERT: A  337 GLN cc_start: 0.7485 (mm-40) cc_final: 0.6347 (tt0)
REVERT: A  406 LEU cc_start: 0.9008 (mm) cc_final: 0.8579 (mt)
  outliers start: 18
  outliers final: 16
  residues processed: 87
  average time/residue: 0.0522
  time to fit residues: 5.7478
Evaluate side-chains
  88 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TYR
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  312 ASP
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  366 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   chunk 31 optimal weight:    0.4980
   chunk 32 optimal weight:    0.5980
   chunk 6 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0970
   chunk 5 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.4778

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  37 HIS
A 318 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.128697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.100502 restraints weight = 5985.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.102920 restraints weight = 3219.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.104407 restraints weight = 2269.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.105086 restraints weight = 1875.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.105719 restraints weight = 1709.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.3076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3084  Z= 0.147
  Angle     :  0.734  12.560   4190  Z= 0.352
  Chirality :  0.042   0.138    524
  Planarity :  0.005   0.053    510
  Dihedral  :  6.488  41.963    452
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 14.73
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  4.80 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 26.11 %
    Favored  : 68.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.03 (0.43), residues: 396
  helix:  0.69 (0.29), residues: 330
  sheet:  None (None), residues: 0
  loop : -3.49 (0.72), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 397 
 TYR   0.021   0.001   TYR A 299 
 PHE   0.007   0.001   PHE A 324 
 HIS   0.008   0.001   HIS A  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00345 /  0.15 ( 3083)
  covalent geometry    : angle       0.73381 /  0.35 ( 4190)
  hydrogen bonds       : bond        0.03980 /  2.48 (  221)
  hydrogen bonds       : angle       4.51416 /  3.07 (  663)
  Misc. bond           : bond        0.00022 /  0.01 (    1)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 TYR cc_start: 0.7625 (OUTLIER) cc_final: 0.7089 (t80)
REVERT: A   83 VAL cc_start: 0.8440 (m) cc_final: 0.8120 (m)
REVERT: A   86 VAL cc_start: 0.9244 (t) cc_final: 0.9015 (m)
REVERT: A  247 TYR cc_start: 0.7806 (m-80) cc_final: 0.7511 (m-80)
REVERT: A  286 MET cc_start: 0.8588 (mtp) cc_final: 0.8262 (mtp)
REVERT: A  337 GLN cc_start: 0.7411 (mm-40) cc_final: 0.6293 (tt0)
REVERT: A  406 LEU cc_start: 0.8962 (mm) cc_final: 0.8593 (mp)
  outliers start: 16
  outliers final: 12
  residues processed: 89
  average time/residue: 0.0501
  time to fit residues: 5.6989
Evaluate side-chains
  87 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TYR
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  312 ASP
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  366 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 30 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0570
   chunk 10 optimal weight:    0.3980
   chunk 1 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.4698

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  37 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.128842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.100521 restraints weight = 6086.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.102922 restraints weight = 3266.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.104436 restraints weight = 2303.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.105359 restraints weight = 1894.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.105659 restraints weight = 1699.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.3182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   3084  Z= 0.147
  Angle     :  0.738  12.593   4190  Z= 0.354
  Chirality :  0.043   0.148    524
  Planarity :  0.005   0.056    510
  Dihedral  :  6.370  41.712    452
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 14.57
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.05 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 26.43 %
    Favored  : 68.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.43), residues: 396
  helix:  0.71 (0.29), residues: 330
  sheet:  None (None), residues: 0
  loop : -3.56 (0.71), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 397 
 TYR   0.023   0.001   TYR A 299 
 PHE   0.007   0.001   PHE A 324 
 HIS   0.007   0.001   HIS A  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.15 ( 3083)
  covalent geometry    : angle       0.73790 /  0.35 ( 4190)
  hydrogen bonds       : bond        0.03937 /  2.44 (  221)
  hydrogen bonds       : angle       4.54980 /  3.08 (  663)
  Misc. bond           : bond        0.00021 /  0.01 (    1)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 TYR cc_start: 0.7619 (OUTLIER) cc_final: 0.7096 (t80)
REVERT: A   83 VAL cc_start: 0.8283 (m) cc_final: 0.7945 (m)
REVERT: A   86 VAL cc_start: 0.9235 (t) cc_final: 0.9008 (m)
REVERT: A  247 TYR cc_start: 0.7825 (m-80) cc_final: 0.7508 (m-80)
REVERT: A  286 MET cc_start: 0.8617 (mtp) cc_final: 0.8288 (mtp)
REVERT: A  337 GLN cc_start: 0.7375 (mm-40) cc_final: 0.6301 (tt0)
REVERT: A  406 LEU cc_start: 0.8980 (mm) cc_final: 0.8606 (mp)
  outliers start: 17
  outliers final: 13
  residues processed: 86
  average time/residue: 0.0491
  time to fit residues: 5.3799
Evaluate side-chains
  87 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TYR
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  312 ASP
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  355 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 32 optimal weight:    0.6980
   chunk 12 optimal weight:    0.0970
   chunk 37 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 14 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  37 HIS
** A 203 GLN ** 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 = 0.3625 r_free = 0.3625 target = 0.127939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.099594 restraints weight = 5977.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.101934 restraints weight = 3297.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.103341 restraints weight = 2361.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.104052 restraints weight = 1963.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.104673 restraints weight = 1792.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.3154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   3084  Z= 0.167
  Angle     :  0.752  12.788   4190  Z= 0.361
  Chirality :  0.044   0.148    524
  Planarity :  0.006   0.059    510
  Dihedral  :  6.514  43.905    452
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 15.53
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.30 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 27.39 %
    Favored  : 68.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.06 (0.43), residues: 396
  helix:  0.66 (0.29), residues: 330
  sheet:  None (None), residues: 0
  loop : -3.42 (0.71), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 397 
 TYR   0.023   0.001   TYR A 299 
 PHE   0.006   0.001   PHE A 324 
 HIS   0.007   0.001   HIS A  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00403 /  0.17 ( 3083)
  covalent geometry    : angle       0.75185 /  0.36 ( 4190)
  hydrogen bonds       : bond        0.04094 /  2.55 (  221)
  hydrogen bonds       : angle       4.60867 /  3.13 (  663)
  Misc. bond           : bond        0.00015 /  0.01 (    1)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 TYR cc_start: 0.7557 (OUTLIER) cc_final: 0.6979 (t80)
REVERT: A   83 VAL cc_start: 0.8305 (m) cc_final: 0.7987 (m)
REVERT: A   86 VAL cc_start: 0.9251 (t) cc_final: 0.9029 (m)
REVERT: A  247 TYR cc_start: 0.7841 (m-80) cc_final: 0.7564 (m-80)
REVERT: A  286 MET cc_start: 0.8660 (mtp) cc_final: 0.8318 (mtp)
REVERT: A  337 GLN cc_start: 0.7430 (mm-40) cc_final: 0.6301 (tt0)
  outliers start: 14
  outliers final: 13
  residues processed: 82
  average time/residue: 0.0491
  time to fit residues: 5.0926
Evaluate side-chains
  86 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TYR
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  312 ASP
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  355 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 28 optimal weight:    0.2980
   chunk 21 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 6 optimal weight:    0.2980
   chunk 18 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  37 HIS
A 318 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.129264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.100940 restraints weight = 6070.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.103328 restraints weight = 3318.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.104773 restraints weight = 2367.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.105530 restraints weight = 1966.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.105530 restraints weight = 1782.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.3211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   3084  Z= 0.146
  Angle     :  0.736  12.839   4190  Z= 0.350
  Chirality :  0.043   0.146    524
  Planarity :  0.005   0.058    510
  Dihedral  :  6.315  40.320    452
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 14.73
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.30 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 27.71 %
    Favored  : 68.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.43), residues: 396
  helix:  0.70 (0.29), residues: 331
  sheet:  None (None), residues: 0
  loop : -3.32 (0.72), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 397 
 TYR   0.023   0.001   TYR A 299 
 PHE   0.006   0.001   PHE A 324 
 HIS   0.008   0.001   HIS A  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.15 ( 3083)
  covalent geometry    : angle       0.73578 /  0.35 ( 4190)
  hydrogen bonds       : bond        0.03947 /  2.45 (  221)
  hydrogen bonds       : angle       4.54441 /  3.08 (  663)
  Misc. bond           : bond        0.00021 /  0.01 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 711.49 seconds
wall clock time: 12 minutes 50.59 seconds (770.59 seconds total)