Starting phenix.real_space_refine
on Sat May  2 12:38:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9uw3_64544/05_2026/9uw3_64544.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9uw3_64544/05_2026/9uw3_64544.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9uw3_64544/05_2026/9uw3_64544.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9uw3_64544/05_2026/9uw3_64544.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9uw3_64544/05_2026/9uw3_64544.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9uw3_64544/05_2026/9uw3_64544.map"
  }
  resolution = 3.36
  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=   0.104
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: 6
    Type Number    sf(0)   Gaussians
     P       9      5.49       5
     Mg      1      5.21       5
     S      30      5.16       5
     C    3304      2.51       5
     N     889      2.21       5
     O     971      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5204
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2298
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 295, 2298
          Classifications: {'peptide': 295}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 19, 'TRANS': 275}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "B"
      Number of atoms: 2843
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 348, 2843
          Classifications: {'peptide': 348}
          Link IDs: {'PTRANS': 18, 'TRANS': 329}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'PTR:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ANP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.46, per 1000 atoms: 0.28
  Number of scatterers: 5204
  At special positions: 0
  Unit cell: (64.638, 82.9521, 99.1116, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      30     16.00
     P       9     15.00
     Mg      1     11.99
     O     971      8.00
     N     889      7.00
     C    3304      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=0, symmetry=0
  Time building additional restraints: 0.42
  Conformation dependent library (CDL) restraints added in 204.5 milliseconds
  

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1212

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 5 sheets defined
      41.7% alpha, 10.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 64 through 66
      No H-bonds generated for 'chain 'A' and resid 64 through 66'
    Processing helix  chain 'A' and resid 104 through 112
      removed outlier: 4.833A  pdb=" N   GLN A 110 " --> pdb=" O   ALA A 106 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ILE A 111 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ILE A 112 " --> pdb=" O   ARG A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 119
      removed outlier: 3.859A  pdb=" N   LEU A 118 " --> pdb=" O   GLU A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 159
    Processing helix  chain 'A' and resid 162 through 185
      removed outlier: 3.673A  pdb=" N   LYS A 168 " --> pdb=" O   GLN A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 194
      No H-bonds generated for 'chain 'A' and resid 192 through 194'
    Processing helix  chain 'A' and resid 226 through 230
      removed outlier: 3.936A  pdb=" N   MET A 230 " --> pdb=" O   ARG A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 236
      removed outlier: 3.798A  pdb=" N   GLN A 236 " --> pdb=" O   PRO A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 259
    Processing helix  chain 'A' and resid 267 through 275
      removed outlier: 3.598A  pdb=" N   LEU A 271 " --> pdb=" O   ASP A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 319
      removed outlier: 3.548A  pdb=" N   ASP A 315 " --> pdb=" O   PHE A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 341
    Processing helix  chain 'A' and resid 351 through 357
      removed outlier: 3.537A  pdb=" N   VAL A 357 " --> pdb=" O   LYS A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 366
    Processing helix  chain 'B' and resid 78 through 93
    Processing helix  chain 'B' and resid 129 through 135
      removed outlier: 3.863A  pdb=" N   SER B 135 " --> pdb=" O   LYS B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 158
    Processing helix  chain 'B' and resid 212 through 218
      removed outlier: 4.124A  pdb=" N   MET B 216 " --> pdb=" O   ALA B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 226
      removed outlier: 3.861A  pdb=" N   ILE B 226 " --> pdb=" O   THR B 223 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 223 through 226'
    Processing helix  chain 'B' and resid 227 through 241
    Processing helix  chain 'B' and resid 249 through 262
      removed outlier: 3.705A  pdb=" N   LEU B 254 " --> pdb=" O   TYR B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 270
    Processing helix  chain 'B' and resid 275 through 283
      removed outlier: 3.586A  pdb=" N   ASN B 279 " --> pdb=" O   MET B 275 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   TYR B 280 " --> pdb=" O   LYS B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 296
      removed outlier: 3.730A  pdb=" N   LEU B 295 " --> pdb=" O   ALA B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 300 through 310
    Processing helix  chain 'B' and resid 320 through 326
    Processing helix  chain 'B' and resid 327 through 331
    Processing helix  chain 'B' and resid 358 through 368
      removed outlier: 3.904A  pdb=" N   GLU B 362 " --> pdb=" O   GLU B 358 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 76
      removed outlier: 3.687A  pdb=" N   GLU A  69 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   LYS A  84 " --> pdb=" O   ILE A  71 " (cutoff:3.500A)
      removed outlier: 5.644A  pdb=" N   GLU A  73 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   VAL A  82 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 7.183A  pdb=" N   GLY A  75 " --> pdb=" O   GLY A  80 " (cutoff:3.500A)
      removed outlier: 7.408A  pdb=" N   GLY A  80 " --> pdb=" O   GLY A  75 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   VAL A  81 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   GLY A 131 " --> pdb=" O   CYS A 142 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 150
    Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 187
    Processing sheet with id=AA4, first strand: chain 'B' and resid 42 through 47
      removed outlier: 4.163A  pdb=" N   LEU B  45 " --> pdb=" O   SER B  58 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   SER B  58 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ILE B 120 " --> pdb=" O   LYS B  71 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ILE B  73 " --> pdb=" O   VAL B 118 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 127 through 128

    181 hydrogen bonds defined for protein.
    516 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: 0.74

  Time building geometry restraints manager: 0.56 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 854
        1.32 -     1.44: 1342
        1.44 -     1.56: 3059
        1.56 -     1.69: 13
        1.69 -     1.81: 50
  Bond restraints: 5318
  Sorted by residual:
  bond pdb=" OH  PTR B 204 "
       pdb=" P   PTR B 204 "
    ideal  model  delta    sigma   weight residual
    1.769  1.579  0.190 2.00e-02 2.50e+03 9.07e+01
  bond pdb=" N3B ANP B 402 "
       pdb=" PG  ANP B 402 "
    ideal  model  delta    sigma   weight residual
    1.795  1.627  0.168 2.00e-02 2.50e+03 7.04e+01
  bond pdb=" N3B ANP A 501 "
       pdb=" PG  ANP A 501 "
    ideal  model  delta    sigma   weight residual
    1.795  1.639  0.156 2.00e-02 2.50e+03 6.12e+01
  bond pdb=" O3A ANP A 501 "
       pdb=" PB  ANP A 501 "
    ideal  model  delta    sigma   weight residual
    1.700  1.580  0.120 2.00e-02 2.50e+03 3.61e+01
  bond pdb=" O2P SEP A 222 "
       pdb=" P   SEP A 222 "
    ideal  model  delta    sigma   weight residual
    1.610  1.500  0.110 2.00e-02 2.50e+03 3.00e+01
  ... (remaining 5313 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 6999
        2.27 -     4.54: 159
        4.54 -     6.82: 32
        6.82 -     9.09: 8
        9.09 -    11.36: 5
  Bond angle restraints: 7203
  Sorted by residual:
  angle pdb=" N   GLU A 312 "
        pdb=" CA  GLU A 312 "
        pdb=" C   GLU A 312 "
      ideal   model   delta    sigma   weight residual
     112.45  106.69    5.76 1.39e+00 5.18e-01 1.72e+01
  angle pdb=" N   LEU A 313 "
        pdb=" CA  LEU A 313 "
        pdb=" C   LEU A 313 "
      ideal   model   delta    sigma   weight residual
     111.14  106.77    4.37 1.08e+00 8.57e-01 1.64e+01
  angle pdb=" N3B ANP A 501 "
        pdb=" PG  ANP A 501 "
        pdb=" O2G ANP A 501 "
      ideal   model   delta    sigma   weight residual
     101.05  112.41  -11.36 3.00e+00 1.11e-01 1.43e+01
  angle pdb=" C   TYR A 316 "
        pdb=" N   ILE A 317 "
        pdb=" CA  ILE A 317 "
      ideal   model   delta    sigma   weight residual
     120.53  115.27    5.26 1.41e+00 5.03e-01 1.39e+01
  angle pdb=" N   GLU B 194 "
        pdb=" CA  GLU B 194 "
        pdb=" C   GLU B 194 "
      ideal   model   delta    sigma   weight residual
     114.56  109.98    4.58 1.27e+00 6.20e-01 1.30e+01
  ... (remaining 7198 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.69: 3014
       29.69 -    59.38: 245
       59.38 -    89.07: 26
       89.07 -   118.76: 1
      118.76 -   148.44: 1
  Dihedral angle restraints: 3287
    sinusoidal: 1412
      harmonic: 1875
  Sorted by residual:
  dihedral pdb=" CA  ARG A 113 "
           pdb=" C   ARG A 113 "
           pdb=" N   GLU A 114 "
           pdb=" CA  GLU A 114 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.76   22.24     0      5.00e+00 4.00e-02 1.98e+01
  dihedral pdb=" O1B ANP B 402 "
           pdb=" N3B ANP B 402 "
           pdb=" PB  ANP B 402 "
           pdb=" PG  ANP B 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
      35.15 -176.41 -148.44     1      3.00e+01 1.11e-03 1.98e+01
  dihedral pdb=" CA  LYS A   5 "
           pdb=" C   LYS A   5 "
           pdb=" N   PRO A   6 "
           pdb=" CA  PRO A   6 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.58  -19.42     0      5.00e+00 4.00e-02 1.51e+01
  ... (remaining 3284 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 712
       0.076 -    0.152: 71
       0.152 -    0.228: 4
       0.228 -    0.304: 3
       0.304 -    0.380: 2
  Chirality restraints: 792
  Sorted by residual:
  chirality pdb=" C3' ANP B 402 "
            pdb=" C2' ANP B 402 "
            pdb=" C4' ANP B 402 "
            pdb=" O3' ANP B 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.74    0.38 2.00e-01 2.50e+01 3.60e+00
  chirality pdb=" C3' ANP A 501 "
            pdb=" C2' ANP A 501 "
            pdb=" C4' ANP A 501 "
            pdb=" O3' ANP A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.68    0.33 2.00e-01 2.50e+01 2.67e+00
  chirality pdb=" CA  ILE A 310 "
            pdb=" N   ILE A 310 "
            pdb=" C   ILE A 310 "
            pdb=" CB  ILE A 310 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.68   -0.25 2.00e-01 2.50e+01 1.54e+00
  ... (remaining 789 not shown)

  Planarity restraints: 911
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SEP A 218 "   -0.010 2.00e-02 2.50e+03   2.18e-02 4.76e+00
        pdb=" C   SEP A 218 "    0.038 2.00e-02 2.50e+03
        pdb=" O   SEP A 218 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   MET A 219 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 320 "    0.028 5.00e-02 4.00e+02   4.27e-02 2.92e+00
        pdb=" N   PRO A 321 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 321 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 321 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 249 "   -0.008 2.00e-02 2.50e+03   1.69e-02 2.86e+00
        pdb=" C   MET A 249 "    0.029 2.00e-02 2.50e+03
        pdb=" O   MET A 249 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   GLY A 250 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 908 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 14
        2.57 -     3.15: 4009
        3.15 -     3.74: 7722
        3.74 -     4.32: 10368
        4.32 -     4.90: 17424
  Nonbonded interactions: 39537
  Sorted by model distance:
  nonbonded pdb="MG    MG B 401 "
            pdb=" O1G ANP B 402 "
     model   vdw
     1.989 2.170
  nonbonded pdb=" OD2 ASP B 184 "
            pdb="MG    MG B 401 "
     model   vdw
     2.021 2.170
  nonbonded pdb=" OD1 ASN B 171 "
            pdb="MG    MG B 401 "
     model   vdw
     2.085 2.170
  nonbonded pdb=" O   GLU A 233 "
            pdb=" OG1 THR A 238 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   MET A 249 "
            pdb=" OG  SER A 252 "
     model   vdw
     2.440 3.040
  ... (remaining 39532 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:             0.480
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     6.840
  Find NCS groups from input model:        0.030
  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:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.190   5318  Z= 0.387
  Angle     :  0.846  11.362   7203  Z= 0.425
  Chirality :  0.050   0.380    792
  Planarity :  0.004   0.043    911
  Dihedral  : 19.877 148.444   2075
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  : 27.22 %
    Favored  : 72.60 %
  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: -0.87 (0.35), residues: 624
  helix:  0.44 (0.37), residues: 229
  sheet:  0.83 (0.62), residues: 83
  loop : -1.82 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 108 
 TYR   0.013   0.001   TYR A 316 
 PHE   0.011   0.001   PHE A 311 
 TRP   0.013   0.001   TRP A 247 
 HIS   0.002   0.000   HIS A 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00745 ( 5318)
  covalent geometry    : angle       0.84642 ( 7203)
  hydrogen bonds       : bond        0.15934 (  181)
  hydrogen bonds       : angle       6.68886 (  516)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A   93 VAL cc_start: 0.9167 (t) cc_final: 0.8844 (p)
REVERT: A  116 GLN cc_start: 0.8679 (tp40) cc_final: 0.8265 (tp40)
REVERT: A  146 MET cc_start: 0.7445 (mmt) cc_final: 0.7132 (mmm)
REVERT: A  165 ILE cc_start: 0.7989 (mm) cc_final: 0.7702 (mt)
REVERT: A  245 ASP cc_start: 0.8165 (m-30) cc_final: 0.7850 (m-30)
REVERT: A  320 GLU cc_start: 0.8225 (tp30) cc_final: 0.7967 (tp30)
REVERT: A  354 GLN cc_start: 0.8576 (mt0) cc_final: 0.7899 (mt0)
REVERT: B  147 LEU cc_start: 0.8133 (tp) cc_final: 0.7845 (tp)
REVERT: B  179 ASP cc_start: 0.8196 (m-30) cc_final: 0.7814 (m-30)
REVERT: B  275 MET cc_start: 0.8844 (tpp) cc_final: 0.8559 (tpt)
  outliers start: 1
  outliers final: 0
  residues processed: 105
  average time/residue: 0.0675
  time to fit residues: 9.6185
Evaluate side-chains
  97 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    0.1980
   chunk 56 optimal weight:    5.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9990
   chunk 61 optimal weight:    4.9990
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 110 GLN
A 195 ASN
A 339 ASN
B 140 ASN
B 314 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.149526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.124017 restraints weight = 7546.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 3.03
r_work: 0.3393 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.0805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5318  Z= 0.116
  Angle     :  0.535   6.193   7203  Z= 0.270
  Chirality :  0.042   0.193    792
  Planarity :  0.003   0.039    911
  Dihedral  : 12.299 151.335    777
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 26.16 %
    Favored  : 70.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.76 (0.35), residues: 624
  helix:  0.71 (0.37), residues: 235
  sheet:  0.30 (0.64), residues: 78
  loop : -1.73 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 227 
 TYR   0.007   0.001   TYR B 156 
 PHE   0.008   0.001   PHE B  76 
 TRP   0.007   0.001   TRP A 247 
 HIS   0.003   0.001   HIS B 327 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 5318)
  covalent geometry    : angle       0.53485 ( 7203)
  hydrogen bonds       : bond        0.03564 (  181)
  hydrogen bonds       : angle       5.16817 (  516)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.189 
Fit side-chains
REVERT: A  116 GLN cc_start: 0.8609 (tp40) cc_final: 0.8161 (tp40)
REVERT: A  146 MET cc_start: 0.7434 (mmt) cc_final: 0.7167 (mmm)
REVERT: A  165 ILE cc_start: 0.8015 (mm) cc_final: 0.7752 (mt)
REVERT: A  219 MET cc_start: 0.7770 (mtt) cc_final: 0.7441 (mtp)
REVERT: A  245 ASP cc_start: 0.8169 (m-30) cc_final: 0.7895 (m-30)
REVERT: A  308 MET cc_start: 0.7821 (ttm) cc_final: 0.7454 (ttm)
REVERT: A  354 GLN cc_start: 0.8628 (mt0) cc_final: 0.7925 (mt0)
REVERT: B  147 LEU cc_start: 0.8159 (tp) cc_final: 0.7873 (tp)
REVERT: B  251 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8331 (mp)
REVERT: B  275 MET cc_start: 0.8819 (tpp) cc_final: 0.8568 (tpt)
  outliers start: 17
  outliers final: 10
  residues processed: 109
  average time/residue: 0.0667
  time to fit residues: 9.7789
Evaluate side-chains
  99 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 GLN
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   98 GLU
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  310 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   chunk 7 optimal weight:    6.9990
   chunk 18 optimal weight:    4.9990
   chunk 48 optimal weight:    5.9990
   chunk 20 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0980
   chunk 50 optimal weight:    0.0370
   overall best weight:    0.7460

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

Flipped N/Q/H residues before XYZ refinement:
A 110 GLN
** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 319 ASN
A 339 ASN
** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 314 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.149117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.123157 restraints weight = 7544.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 3.07
r_work: 0.3381 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.1115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5318  Z= 0.108
  Angle     :  0.515   5.881   7203  Z= 0.259
  Chirality :  0.042   0.206    792
  Planarity :  0.004   0.053    911
  Dihedral  : 11.032 145.817    777
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 26.87 %
    Favored  : 71.00 %
  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: -0.62 (0.35), residues: 624
  helix:  0.83 (0.36), residues: 235
  sheet:  0.55 (0.61), residues: 88
  loop : -1.78 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 189 
 TYR   0.007   0.001   TYR B 156 
 PHE   0.007   0.001   PHE B  76 
 TRP   0.007   0.001   TRP A 247 
 HIS   0.006   0.001   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 5318)
  covalent geometry    : angle       0.51524 ( 7203)
  hydrogen bonds       : bond        0.03162 (  181)
  hydrogen bonds       : angle       4.80134 (  516)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
REVERT: A  116 GLN cc_start: 0.8622 (tp40) cc_final: 0.8192 (tp40)
REVERT: A  146 MET cc_start: 0.7549 (mmt) cc_final: 0.7240 (mmm)
REVERT: A  165 ILE cc_start: 0.8045 (mm) cc_final: 0.7775 (mt)
REVERT: A  219 MET cc_start: 0.7828 (mtt) cc_final: 0.7491 (mtp)
REVERT: A  245 ASP cc_start: 0.8226 (m-30) cc_final: 0.7896 (m-30)
REVERT: A  308 MET cc_start: 0.7669 (ttm) cc_final: 0.7239 (ttm)
REVERT: A  320 GLU cc_start: 0.8317 (tp30) cc_final: 0.7946 (tp30)
REVERT: B  147 LEU cc_start: 0.8175 (tp) cc_final: 0.7892 (tp)
REVERT: B  275 MET cc_start: 0.8824 (tpp) cc_final: 0.8562 (tpt)
  outliers start: 12
  outliers final: 9
  residues processed: 103
  average time/residue: 0.0683
  time to fit residues: 9.4202
Evaluate side-chains
  94 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  153 GLN
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain B residue   98 GLU
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  310 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 58 optimal weight:    5.9990
   chunk 57 optimal weight:    0.7980
   chunk 26 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   chunk 11 optimal weight:    6.9990
   chunk 22 optimal weight:    0.4980
   chunk 29 optimal weight:    9.9990
   chunk 51 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 37 optimal weight:    6.9990
   chunk 60 optimal weight:    4.9990
   overall best weight:    1.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 110 GLN
** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 214 GLN
A 339 ASN
B  99 ASN
** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 314 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.144176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.117765 restraints weight = 7647.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 3.14
r_work: 0.3301 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.1529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   5318  Z= 0.207
  Angle     :  0.608   5.242   7203  Z= 0.306
  Chirality :  0.045   0.165    792
  Planarity :  0.004   0.051    911
  Dihedral  : 11.076 142.195    777
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 25.44 %
    Favored  : 70.11 %
  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: -0.80 (0.35), residues: 624
  helix:  0.63 (0.36), residues: 237
  sheet:  0.46 (0.62), residues: 88
  loop : -1.86 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 189 
 TYR   0.009   0.001   TYR A 240 
 PHE   0.011   0.002   PHE B  76 
 TRP   0.007   0.002   TRP A 247 
 HIS   0.005   0.001   HIS B 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 ( 5318)
  covalent geometry    : angle       0.60781 ( 7203)
  hydrogen bonds       : bond        0.03828 (  181)
  hydrogen bonds       : angle       4.86854 (  516)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 88
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
REVERT: A  116 GLN cc_start: 0.8747 (tp40) cc_final: 0.8346 (tp40)
REVERT: A  146 MET cc_start: 0.7607 (mmt) cc_final: 0.7356 (mmm)
REVERT: A  165 ILE cc_start: 0.8155 (mm) cc_final: 0.7840 (mt)
REVERT: A  320 GLU cc_start: 0.8305 (tp30) cc_final: 0.8001 (tp30)
REVERT: A  354 GLN cc_start: 0.8689 (mt0) cc_final: 0.8006 (mt0)
REVERT: B  107 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8174 (mt)
REVERT: B  147 LEU cc_start: 0.8388 (tp) cc_final: 0.7996 (tp)
REVERT: B  237 GLU cc_start: 0.8478 (tt0) cc_final: 0.8045 (tp30)
REVERT: B  275 MET cc_start: 0.8856 (tpp) cc_final: 0.8583 (tpt)
REVERT: B  316 ASN cc_start: 0.8813 (OUTLIER) cc_final: 0.8603 (t0)
  outliers start: 25
  outliers final: 20
  residues processed: 105
  average time/residue: 0.0597
  time to fit residues: 8.7025
Evaluate side-chains
  103 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 81
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 SER
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  119 HIS
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  153 GLN
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   98 GLU
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  215 ILE
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  310 MET
Chi-restraints excluded: chain B residue  316 ASN
Chi-restraints excluded: chain B residue  364 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 7 optimal weight:    0.4980
   chunk 54 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 110 GLN
A 195 ASN
A 339 ASN
** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.146751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.120350 restraints weight = 7709.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 3.13
r_work: 0.3336 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.1550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5318  Z= 0.127
  Angle     :  0.534   5.423   7203  Z= 0.272
  Chirality :  0.043   0.217    792
  Planarity :  0.004   0.050    911
  Dihedral  : 10.811 140.087    777
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 26.87 %
    Favored  : 69.75 %
  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: -0.67 (0.35), residues: 624
  helix:  0.80 (0.36), residues: 237
  sheet:  0.45 (0.62), residues: 88
  loop : -1.82 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 234 
 TYR   0.009   0.001   TYR A 240 
 PHE   0.009   0.001   PHE B  76 
 TRP   0.006   0.001   TRP A 247 
 HIS   0.003   0.001   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 5318)
  covalent geometry    : angle       0.53354 ( 7203)
  hydrogen bonds       : bond        0.03209 (  181)
  hydrogen bonds       : angle       4.70501 (  516)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
REVERT: A  116 GLN cc_start: 0.8692 (tp40) cc_final: 0.8318 (tp40)
REVERT: A  146 MET cc_start: 0.7558 (mmt) cc_final: 0.7300 (mmm)
REVERT: A  165 ILE cc_start: 0.8091 (mm) cc_final: 0.7792 (mt)
REVERT: A  219 MET cc_start: 0.7822 (mtt) cc_final: 0.7476 (mtp)
REVERT: A  320 GLU cc_start: 0.8233 (tp30) cc_final: 0.7887 (tp30)
REVERT: B  147 LEU cc_start: 0.8301 (tp) cc_final: 0.8002 (tp)
REVERT: B  275 MET cc_start: 0.8853 (tpp) cc_final: 0.8597 (tpt)
  outliers start: 19
  outliers final: 13
  residues processed: 99
  average time/residue: 0.0610
  time to fit residues: 8.3431
Evaluate side-chains
  95 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 SER
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  153 GLN
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  195 ASN
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   98 GLU
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  310 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 50 optimal weight:    0.6980
   chunk 60 optimal weight:   10.0000
   chunk 11 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0970
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 339 ASN
** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 314 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.147338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.121170 restraints weight = 7666.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 3.11
r_work: 0.3347 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5318  Z= 0.104
  Angle     :  0.516   7.016   7203  Z= 0.262
  Chirality :  0.042   0.190    792
  Planarity :  0.003   0.048    911
  Dihedral  : 10.680 138.297    777
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 27.40 %
    Favored  : 69.93 %
  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: -0.68 (0.35), residues: 624
  helix:  0.79 (0.36), residues: 237
  sheet:  0.45 (0.62), residues: 88
  loop : -1.81 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 227 
 TYR   0.008   0.001   TYR A 240 
 PHE   0.007   0.001   PHE B  76 
 TRP   0.006   0.001   TRP A 247 
 HIS   0.003   0.001   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 5318)
  covalent geometry    : angle       0.51619 ( 7203)
  hydrogen bonds       : bond        0.02945 (  181)
  hydrogen bonds       : angle       4.60546 (  516)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 GLN cc_start: 0.8692 (tp40) cc_final: 0.8317 (tp40)
REVERT: A  146 MET cc_start: 0.7569 (mmt) cc_final: 0.7312 (mmm)
REVERT: A  165 ILE cc_start: 0.8056 (mm) cc_final: 0.7760 (mt)
REVERT: A  219 MET cc_start: 0.7882 (mtt) cc_final: 0.7536 (mtp)
REVERT: A  245 ASP cc_start: 0.8262 (m-30) cc_final: 0.7939 (m-30)
REVERT: A  308 MET cc_start: 0.7547 (ttm) cc_final: 0.7266 (ttm)
REVERT: A  320 GLU cc_start: 0.8279 (tp30) cc_final: 0.7953 (tp30)
REVERT: B  147 LEU cc_start: 0.8358 (tp) cc_final: 0.8106 (tp)
REVERT: B  275 MET cc_start: 0.8843 (tpp) cc_final: 0.8587 (tpt)
REVERT: B  284 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8527 (mp)
  outliers start: 15
  outliers final: 13
  residues processed: 96
  average time/residue: 0.0591
  time to fit residues: 7.9384
Evaluate side-chains
  93 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 SER
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  153 GLN
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   98 GLU
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  310 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 25 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 11 optimal weight:    4.9990
   chunk 57 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0060
   chunk 8 optimal weight:    0.3980
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
A 339 ASN
** B 249 HIS ** 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 = 0.3831 r_free = 0.3831 target = 0.148341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.122485 restraints weight = 7605.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3525 rms_B_bonded: 3.06
r_work: 0.3369 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.1591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   5318  Z= 0.100
  Angle     :  0.511   7.017   7203  Z= 0.261
  Chirality :  0.042   0.179    792
  Planarity :  0.003   0.047    911
  Dihedral  : 10.551 136.528    777
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 28.11 %
    Favored  : 69.57 %
  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 are not related in a simple way.
  whole: -0.60 (0.35), residues: 624
  helix:  0.87 (0.36), residues: 237
  sheet:  0.43 (0.62), residues: 88
  loop : -1.77 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 227 
 TYR   0.007   0.001   TYR B 156 
 PHE   0.008   0.001   PHE A  68 
 TRP   0.006   0.001   TRP A 247 
 HIS   0.003   0.001   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 5318)
  covalent geometry    : angle       0.51086 ( 7203)
  hydrogen bonds       : bond        0.02790 (  181)
  hydrogen bonds       : angle       4.52178 (  516)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
REVERT: A  116 GLN cc_start: 0.8681 (tp40) cc_final: 0.8289 (tp40)
REVERT: A  146 MET cc_start: 0.7565 (mmt) cc_final: 0.7300 (mmm)
REVERT: A  165 ILE cc_start: 0.8030 (mm) cc_final: 0.7757 (mt)
REVERT: A  219 MET cc_start: 0.7921 (mtt) cc_final: 0.7600 (mtp)
REVERT: A  245 ASP cc_start: 0.8261 (m-30) cc_final: 0.7943 (m-30)
REVERT: A  320 GLU cc_start: 0.8262 (tp30) cc_final: 0.7921 (tp30)
REVERT: A  354 GLN cc_start: 0.8643 (mt0) cc_final: 0.7874 (mt0)
REVERT: B  120 ILE cc_start: 0.8332 (mt) cc_final: 0.8018 (mm)
REVERT: B  147 LEU cc_start: 0.8270 (tp) cc_final: 0.8030 (tp)
REVERT: B  275 MET cc_start: 0.8843 (tpp) cc_final: 0.8582 (tpt)
REVERT: B  284 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8522 (mp)
  outliers start: 13
  outliers final: 12
  residues processed: 97
  average time/residue: 0.0546
  time to fit residues: 7.4208
Evaluate side-chains
  94 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 SER
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  153 GLN
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   98 GLU
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  310 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 56 optimal weight:    6.9990
   chunk 17 optimal weight:    4.9990
   chunk 31 optimal weight:    0.0970
   chunk 11 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 18 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 13 optimal weight:    0.4980
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
A 339 ASN
B 249 HIS
B 314 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.145873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.119373 restraints weight = 7673.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 3.17
r_work: 0.3322 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.1707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5318  Z= 0.149
  Angle     :  0.552   6.885   7203  Z= 0.279
  Chirality :  0.043   0.172    792
  Planarity :  0.003   0.045    911
  Dihedral  : 10.599 136.072    777
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 28.11 %
    Favored  : 69.04 %
  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: -0.65 (0.35), residues: 624
  helix:  0.81 (0.36), residues: 237
  sheet:  0.38 (0.62), residues: 88
  loop : -1.78 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 227 
 TYR   0.008   0.001   TYR B 156 
 PHE   0.009   0.001   PHE A  68 
 TRP   0.005   0.001   TRP A 247 
 HIS   0.004   0.001   HIS B 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 5318)
  covalent geometry    : angle       0.55211 ( 7203)
  hydrogen bonds       : bond        0.03253 (  181)
  hydrogen bonds       : angle       4.56166 (  516)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 GLN cc_start: 0.8742 (tp40) cc_final: 0.8359 (tp40)
REVERT: A  146 MET cc_start: 0.7583 (mmt) cc_final: 0.7358 (mmm)
REVERT: A  165 ILE cc_start: 0.8093 (mm) cc_final: 0.7794 (mt)
REVERT: A  219 MET cc_start: 0.7937 (mtt) cc_final: 0.7575 (mtp)
REVERT: A  245 ASP cc_start: 0.8283 (m-30) cc_final: 0.7952 (m-30)
REVERT: A  320 GLU cc_start: 0.8317 (tp30) cc_final: 0.7969 (tp30)
REVERT: B  147 LEU cc_start: 0.8342 (tp) cc_final: 0.8023 (tp)
REVERT: B  275 MET cc_start: 0.8861 (tpp) cc_final: 0.8597 (tpt)
REVERT: B  284 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8573 (mp)
  outliers start: 16
  outliers final: 14
  residues processed: 96
  average time/residue: 0.0574
  time to fit residues: 7.7040
Evaluate side-chains
  93 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 SER
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  153 GLN
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain B residue   98 GLU
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  310 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9980
   chunk 55 optimal weight:    0.1980
   chunk 46 optimal weight:    5.9990
   chunk 42 optimal weight:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 23 optimal weight:    0.4980
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN
A 339 ASN
B 314 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.147841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.121928 restraints weight = 7567.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 3.03
r_work: 0.3366 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.1689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   5318  Z= 0.104
  Angle     :  0.537   7.065   7203  Z= 0.275
  Chirality :  0.042   0.255    792
  Planarity :  0.003   0.046    911
  Dihedral  : 10.467 134.713    777
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 29.00 %
    Favored  : 68.68 %
  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: -0.56 (0.35), residues: 624
  helix:  0.91 (0.37), residues: 237
  sheet:  0.42 (0.62), residues: 88
  loop : -1.74 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 189 
 TYR   0.007   0.001   TYR B 156 
 PHE   0.008   0.001   PHE A  68 
 TRP   0.005   0.001   TRP A 247 
 HIS   0.002   0.000   HIS A 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 5318)
  covalent geometry    : angle       0.53666 ( 7203)
  hydrogen bonds       : bond        0.02816 (  181)
  hydrogen bonds       : angle       4.50796 (  516)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
REVERT: A  116 GLN cc_start: 0.8706 (tp40) cc_final: 0.8296 (tp40)
REVERT: A  146 MET cc_start: 0.7505 (mmt) cc_final: 0.7254 (mmm)
REVERT: A  165 ILE cc_start: 0.8028 (mm) cc_final: 0.7752 (mt)
REVERT: A  219 MET cc_start: 0.7977 (mtt) cc_final: 0.7619 (mtp)
REVERT: A  245 ASP cc_start: 0.8235 (m-30) cc_final: 0.7925 (m-30)
REVERT: A  320 GLU cc_start: 0.8355 (tp30) cc_final: 0.8025 (tp30)
REVERT: A  354 GLN cc_start: 0.8644 (mt0) cc_final: 0.7879 (mt0)
REVERT: B  147 LEU cc_start: 0.8270 (tp) cc_final: 0.8027 (tp)
REVERT: B  275 MET cc_start: 0.8822 (tpp) cc_final: 0.8568 (tpt)
REVERT: B  284 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8515 (mp)
  outliers start: 13
  outliers final: 12
  residues processed: 93
  average time/residue: 0.0605
  time to fit residues: 7.6978
Evaluate side-chains
  93 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  153 GLN
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   98 GLU
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  310 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 57 optimal weight:    0.2980
   chunk 52 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 42 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 1 optimal weight:    9.9990
   chunk 48 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0770
   chunk 41 optimal weight:    1.9990
   chunk 45 optimal weight:    9.9990
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
A 339 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.148426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.122658 restraints weight = 7598.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 3.03
r_work: 0.3371 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   5318  Z= 0.104
  Angle     :  0.526   7.037   7203  Z= 0.268
  Chirality :  0.042   0.241    792
  Planarity :  0.003   0.046    911
  Dihedral  : 10.394 133.217    777
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 28.65 %
    Favored  : 69.04 %
  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: -0.51 (0.36), residues: 624
  helix:  0.94 (0.37), residues: 238
  sheet:  0.43 (0.62), residues: 88
  loop : -1.71 (0.36), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 189 
 TYR   0.008   0.001   TYR B 156 
 PHE   0.006   0.001   PHE B  76 
 TRP   0.005   0.001   TRP A 247 
 HIS   0.003   0.000   HIS A 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 5318)
  covalent geometry    : angle       0.52556 ( 7203)
  hydrogen bonds       : bond        0.02738 (  181)
  hydrogen bonds       : angle       4.45825 (  516)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
REVERT: A  116 GLN cc_start: 0.8715 (tp40) cc_final: 0.8319 (tp40)
REVERT: A  146 MET cc_start: 0.7548 (mmt) cc_final: 0.7299 (mmm)
REVERT: A  165 ILE cc_start: 0.8046 (mm) cc_final: 0.7784 (mt)
REVERT: A  219 MET cc_start: 0.7978 (mtt) cc_final: 0.7647 (mtp)
REVERT: A  245 ASP cc_start: 0.8217 (m-30) cc_final: 0.7888 (m-30)
REVERT: A  320 GLU cc_start: 0.8324 (tp30) cc_final: 0.7987 (tp30)
REVERT: A  354 GLN cc_start: 0.8623 (mt0) cc_final: 0.7871 (mt0)
REVERT: B  120 ILE cc_start: 0.8298 (mt) cc_final: 0.8022 (mm)
REVERT: B  147 LEU cc_start: 0.8266 (tp) cc_final: 0.8025 (tp)
REVERT: B  275 MET cc_start: 0.8819 (tpp) cc_final: 0.8563 (tpt)
REVERT: B  284 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8497 (mp)
  outliers start: 13
  outliers final: 12
  residues processed: 94
  average time/residue: 0.0522
  time to fit residues: 6.9366
Evaluate side-chains
  96 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 SER
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  153 GLN
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   98 GLU
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  310 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 50 optimal weight:    0.0060
   chunk 34 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 3 optimal weight:    8.9990
   chunk 10 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 1 optimal weight:    9.9990
   chunk 30 optimal weight:    3.9990
   chunk 48 optimal weight:    5.9990
   overall best weight:    0.9600

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.147260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.121095 restraints weight = 7745.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 3.09
r_work: 0.3352 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5318  Z= 0.125
  Angle     :  0.542   6.921   7203  Z= 0.276
  Chirality :  0.043   0.239    792
  Planarity :  0.003   0.045    911
  Dihedral  : 10.407 132.920    777
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 29.00 %
    Favored  : 68.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.35), residues: 624
  helix:  0.94 (0.36), residues: 237
  sheet:  0.42 (0.62), residues: 88
  loop : -1.70 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 227 
 TYR   0.007   0.001   TYR B 156 
 PHE   0.007   0.001   PHE A 311 
 TRP   0.005   0.001   TRP A 247 
 HIS   0.003   0.001   HIS B 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 5318)
  covalent geometry    : angle       0.54174 ( 7203)
  hydrogen bonds       : bond        0.02903 (  181)
  hydrogen bonds       : angle       4.47925 (  516)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1168.22 seconds
wall clock time: 20 minutes 35.99 seconds (1235.99 seconds total)