Starting phenix.real_space_refine
on Sat May  2 12:47:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9uux_64519/05_2026/9uux_64519.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9uux_64519/05_2026/9uux_64519.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9uux_64519/05_2026/9uux_64519.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9uux_64519/05_2026/9uux_64519.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9uux_64519/05_2026/9uux_64519.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9uux_64519/05_2026/9uux_64519.map"
  }
  resolution = 3.12
  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=  -0.001 sd=   0.159
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      31      5.16       5
     C    3372      2.51       5
     N     904      2.21       5
     O     993      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 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: 5310
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2397
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 2397
          Classifications: {'peptide': 308}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 20, 'TRANS': 287}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 23
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 12
    Chain: "B"
      Number of atoms: 2850
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 349, 2850
          Classifications: {'peptide': 349}
          Link IDs: {'PTRANS': 18, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'TPO:plan-1': 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: 1.62, per 1000 atoms: 0.31
  Number of scatterers: 5310
  At special positions: 0
  Unit cell: (64.638, 80.7975, 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      31     16.00
     P       9     15.00
     Mg      1     11.99
     O     993      8.00
     N     904      7.00
     C    3372      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: 0.35
  Conformation dependent library (CDL) restraints added in 148.8 milliseconds
  

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1238

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 6 sheets defined
      40.3% alpha, 10.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  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 107 through 112
    Processing helix  chain 'A' and resid 114 through 119
    Processing helix  chain 'A' and resid 150 through 159
    Processing helix  chain 'A' and resid 162 through 185
      removed outlier: 3.801A  pdb=" N   LYS A 168 " --> pdb=" O   GLN A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 230
      removed outlier: 3.790A  pdb=" N   MET A 230 " --> pdb=" O   ARG A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 236
      removed outlier: 3.893A  pdb=" N   GLN A 236 " --> pdb=" O   PRO A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 257
      removed outlier: 4.262A  pdb=" N   ASP A 245 " --> pdb=" O   SER A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 275
    Processing helix  chain 'A' and resid 309 through 319
    Processing helix  chain 'A' and resid 332 through 341
    Processing helix  chain 'A' and resid 351 through 357
    Processing helix  chain 'A' and resid 358 through 366
    Processing helix  chain 'A' and resid 370 through 378
      removed outlier: 3.676A  pdb=" N   TRP A 374 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   LEU A 375 " --> pdb=" O   PHE A 371 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   CYS A 376 " --> pdb=" O   ALA A 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 93
    Processing helix  chain 'B' and resid 129 through 133
    Processing helix  chain 'B' and resid 139 through 158
    Processing helix  chain 'B' and resid 212 through 218
      removed outlier: 4.028A  pdb=" N   MET B 216 " --> pdb=" O   ALA B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 241
    Processing helix  chain 'B' and resid 249 through 262
    Processing helix  chain 'B' and resid 265 through 270
    Processing helix  chain 'B' and resid 276 through 283
    Processing helix  chain 'B' and resid 291 through 296
      removed outlier: 3.531A  pdb=" N   PHE B 296 " --> pdb=" O   TRP B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 300 through 308
    Processing helix  chain 'B' and resid 320 through 326
      removed outlier: 3.677A  pdb=" N   ALA B 326 " --> pdb=" O   GLU B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 331
    Processing helix  chain 'B' and resid 335 through 339
      removed outlier: 4.131A  pdb=" N   GLU B 339 " --> pdb=" O   PRO B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 359 through 368
    Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 75
      removed outlier: 7.504A  pdb=" N   ILE A  71 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
      removed outlier: 8.430A  pdb=" N   SER A  86 " --> pdb=" O   ILE A  71 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   GLU A  73 " --> pdb=" O   LYS A  84 " (cutoff:3.500A)
      removed outlier: 5.648A  pdb=" N   LYS A  84 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLY A  75 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   VAL A  81 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   LEU A  92 " --> pdb=" O   HIS A  87 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLY A 131 " --> pdb=" O   CYS A 142 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 187
    Processing sheet with id=AA3, first strand: chain 'A' and resid 196 through 198
    Processing sheet with id=AA4, first strand: chain 'B' and resid 29 through 30
      removed outlier: 3.912A  pdb=" N   GLU B  29 " --> pdb=" O   PHE B  36 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   PHE B  36 " --> pdb=" O   GLU B  29 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 42 through 47
      removed outlier: 4.180A  pdb=" N   LEU B  45 " --> pdb=" O   SER B  58 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   SER B  58 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   TYR B 119 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   ILE B 106 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   VAL B 121 " --> pdb=" O   ARG B 104 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 127 through 128

    185 hydrogen bonds defined for protein.
    528 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: 0.80

  Time building geometry restraints manager: 0.51 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 870
        1.30 -     1.43: 1348
        1.43 -     1.56: 3145
        1.56 -     1.68: 13
        1.68 -     1.81: 51
  Bond restraints: 5427
  Sorted by residual:
  bond pdb=" N3B ANP B 402 "
       pdb=" PG  ANP B 402 "
    ideal  model  delta    sigma   weight residual
    1.795  1.604  0.191 2.00e-02 2.50e+03 9.13e+01
  bond pdb=" N3B ANP A 501 "
       pdb=" PG  ANP A 501 "
    ideal  model  delta    sigma   weight residual
    1.795  1.631  0.164 2.00e-02 2.50e+03 6.69e+01
  bond pdb=" O3A ANP A 501 "
       pdb=" PB  ANP A 501 "
    ideal  model  delta    sigma   weight residual
    1.700  1.558  0.142 2.00e-02 2.50e+03 5.04e+01
  bond pdb=" O1P SEP A 222 "
       pdb=" P   SEP A 222 "
    ideal  model  delta    sigma   weight residual
    1.610  1.485  0.125 2.00e-02 2.50e+03 3.89e+01
  bond pdb=" O2P SEP A 222 "
       pdb=" P   SEP A 222 "
    ideal  model  delta    sigma   weight residual
    1.610  1.489  0.121 2.00e-02 2.50e+03 3.68e+01
  ... (remaining 5422 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.87: 7226
        2.87 -     5.75: 97
        5.75 -     8.62: 22
        8.62 -    11.49: 5
       11.49 -    14.36: 4
  Bond angle restraints: 7354
  Sorted by residual:
  angle pdb=" C   SEP A 222 "
        pdb=" N   PHE A 223 "
        pdb=" CA  PHE A 223 "
      ideal   model   delta    sigma   weight residual
     121.70  130.91   -9.21 1.80e+00 3.09e-01 2.62e+01
  angle pdb=" N3B ANP A 501 "
        pdb=" PG  ANP A 501 "
        pdb=" O3G ANP A 501 "
      ideal   model   delta    sigma   weight residual
     105.24  119.60  -14.36 3.00e+00 1.11e-01 2.29e+01
  angle pdb=" O2G ANP A 501 "
        pdb=" PG  ANP A 501 "
        pdb=" O3G ANP A 501 "
      ideal   model   delta    sigma   weight residual
     114.34  100.02   14.32 3.00e+00 1.11e-01 2.28e+01
  angle pdb=" N   GLN A  34 "
        pdb=" CA  GLN A  34 "
        pdb=" C   GLN A  34 "
      ideal   model   delta    sigma   weight residual
     113.43  107.47    5.96 1.26e+00 6.30e-01 2.23e+01
  angle pdb=" C   LYS A   5 "
        pdb=" CA  LYS A   5 "
        pdb=" CB  LYS A   5 "
      ideal   model   delta    sigma   weight residual
     110.31  101.77    8.54 2.06e+00 2.36e-01 1.72e+01
  ... (remaining 7349 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.93: 2978
       24.93 -    49.87: 311
       49.87 -    74.80: 40
       74.80 -    99.73: 8
       99.73 -   124.66: 1
  Dihedral angle restraints: 3338
    sinusoidal: 1422
      harmonic: 1916
  Sorted by residual:
  dihedral pdb=" C   LYS A   5 "
           pdb=" N   LYS A   5 "
           pdb=" CA  LYS A   5 "
           pdb=" CB  LYS A   5 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -108.83  -13.77     0      2.50e+00 1.60e-01 3.03e+01
  dihedral pdb=" N   LYS A   5 "
           pdb=" C   LYS A   5 "
           pdb=" CA  LYS A   5 "
           pdb=" CB  LYS A   5 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  111.32   11.48     0      2.50e+00 1.60e-01 2.11e+01
  dihedral pdb=" O1A ANP A 501 "
           pdb=" O3A ANP A 501 "
           pdb=" PA  ANP A 501 "
           pdb=" PB  ANP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      83.11  -41.55  124.66     1      3.00e+01 1.11e-03 1.67e+01
  ... (remaining 3335 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.083: 739
       0.083 -    0.167: 63
       0.167 -    0.250: 3
       0.250 -    0.334: 1
       0.334 -    0.417: 3
  Chirality restraints: 809
  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   -2.77    0.42 2.00e-01 2.50e+01 4.35e+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   -2.70    0.34 2.00e-01 2.50e+01 2.86e+00
  chirality pdb=" CA  LYS A   5 "
            pdb=" N   LYS A   5 "
            pdb=" C   LYS A   5 "
            pdb=" CB  LYS A   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.85   -0.34 2.00e-01 2.50e+01 2.83e+00
  ... (remaining 806 not shown)

  Planarity restraints: 931
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 158 "    0.023 2.00e-02 2.50e+03   4.75e-02 2.26e+01
        pdb=" C   ALA A 158 "   -0.082 2.00e-02 2.50e+03
        pdb=" O   ALA A 158 "    0.031 2.00e-02 2.50e+03
        pdb=" N   GLY A 159 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 109 "    0.016 2.00e-02 2.50e+03   3.16e-02 1.00e+01
        pdb=" C   ASN A 109 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   ASN A 109 "    0.020 2.00e-02 2.50e+03
        pdb=" N   GLN A 110 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 201 "    0.015 2.00e-02 2.50e+03   3.07e-02 9.41e+00
        pdb=" C   LEU B 201 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   LEU B 201 "    0.020 2.00e-02 2.50e+03
        pdb=" N   TPO B 202 "    0.018 2.00e-02 2.50e+03
  ... (remaining 928 not shown)

  Histogram of nonbonded interaction distances:
        1.86 -     2.47: 7
        2.47 -     3.08: 3377
        3.08 -     3.68: 7589
        3.68 -     4.29: 11279
        4.29 -     4.90: 19287
  Nonbonded interactions: 41539
  Sorted by model distance:
  nonbonded pdb="MG    MG B 401 "
            pdb=" O1B ANP B 402 "
     model   vdw
     1.861 2.170
  nonbonded pdb=" OD1 ASN B 171 "
            pdb="MG    MG B 401 "
     model   vdw
     1.941 2.170
  nonbonded pdb=" OD2 ASP B 184 "
            pdb="MG    MG B 401 "
     model   vdw
     1.990 2.170
  nonbonded pdb=" N3B ANP A 501 "
            pdb=" O1A ANP A 501 "
     model   vdw
     2.359 3.120
  nonbonded pdb=" N   SEP A 218 "
            pdb=" OG  SEP A 218 "
     model   vdw
     2.390 2.496
  ... (remaining 41534 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:             0.910
  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:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.350
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:1.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
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   0.191   5427  Z= 0.411
  Angle     :  0.888  14.365   7354  Z= 0.441
  Chirality :  0.052   0.417    809
  Planarity :  0.005   0.066    931
  Dihedral  : 19.076 124.663   2100
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.31 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  : 27.75 %
    Favored  : 71.90 %
  Cbeta Deviations :  0.16 %
  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: -0.86 (0.34), residues: 638
  helix:  0.57 (0.36), residues: 229
  sheet: -0.33 (0.65), residues: 72
  loop : -1.46 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  96 
 TYR   0.016   0.001   TYR B  53 
 PHE   0.008   0.001   PHE B 348 
 TRP   0.004   0.001   TRP A 247 
 HIS   0.003   0.001   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00787 ( 5427)
  covalent geometry    : angle       0.88791 ( 7354)
  hydrogen bonds       : bond        0.15513 (  185)
  hydrogen bonds       : angle       6.74629 (  528)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 78
  time to evaluate  : 0.177 
Fit side-chains
REVERT: A  233 GLU cc_start: 0.8361 (pm20) cc_final: 0.8138 (pm20)
REVERT: B  104 ARG cc_start: 0.8040 (mtp85) cc_final: 0.7764 (mtp85)
REVERT: B  273 ILE cc_start: 0.7956 (tp) cc_final: 0.7482 (mm)
REVERT: B  338 ASP cc_start: 0.8107 (t0) cc_final: 0.7694 (t0)
  outliers start: 2
  outliers final: 1
  residues processed: 80
  average time/residue: 0.0950
  time to fit residues: 9.5731
Evaluate side-chains
  74 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 73
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 49 optimal weight:    0.0470
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   overall best weight:    0.8880

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

Flipped N/Q/H residues before XYZ refinement:
A 110 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.167448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.138782 restraints weight = 5967.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3664 rms_B_bonded: 2.33
r_work: 0.3478 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.0612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5427  Z= 0.130
  Angle     :  0.528   5.794   7354  Z= 0.271
  Chirality :  0.042   0.134    809
  Planarity :  0.003   0.032    931
  Dihedral  : 11.341 124.170    786
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 23.91 %
    Favored  : 72.25 %
  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: -0.83 (0.35), residues: 638
  helix:  0.52 (0.36), residues: 239
  sheet: -0.29 (0.66), residues: 72
  loop : -1.46 (0.35), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  96 
 TYR   0.010   0.001   TYR B 145 
 PHE   0.008   0.001   PHE A 337 
 TRP   0.011   0.001   TRP A 374 
 HIS   0.002   0.000   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 5427)
  covalent geometry    : angle       0.52797 ( 7354)
  hydrogen bonds       : bond        0.03584 (  185)
  hydrogen bonds       : angle       4.89484 (  528)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 79
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 MET cc_start: 0.7289 (mmt) cc_final: 0.6975 (mmt)
REVERT: A  230 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8714 (mtt)
REVERT: A  233 GLU cc_start: 0.8389 (pm20) cc_final: 0.8186 (pm20)
REVERT: A  336 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.7185 (m-30)
REVERT: B  104 ARG cc_start: 0.8119 (mtp85) cc_final: 0.7885 (mtp85)
REVERT: B  115 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8172 (ttm)
REVERT: B  273 ILE cc_start: 0.7966 (tp) cc_final: 0.7488 (mm)
REVERT: B  338 ASP cc_start: 0.7933 (t0) cc_final: 0.7454 (t0)
  outliers start: 22
  outliers final: 11
  residues processed: 91
  average time/residue: 0.0743
  time to fit residues: 8.8437
Evaluate side-chains
  90 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  120 GLU
Chi-restraints excluded: chain A residue  217 ASP
Chi-restraints excluded: chain A residue  230 MET
Chi-restraints excluded: chain A residue  308 MET
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  115 MET
Chi-restraints excluded: chain B residue  122 GLN
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain B residue  355 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 32 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 13 optimal weight:    0.6980
   chunk 54 optimal weight:    0.3980
   chunk 45 optimal weight:    0.7980
   chunk 22 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.168755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.141101 restraints weight = 5854.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.3683 rms_B_bonded: 2.26
r_work: 0.3491 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.0795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5427  Z= 0.111
  Angle     :  0.503   6.577   7354  Z= 0.257
  Chirality :  0.041   0.136    809
  Planarity :  0.003   0.032    931
  Dihedral  :  9.437 123.363    782
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.68 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 24.08 %
    Favored  : 71.20 %
  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: -0.70 (0.35), residues: 638
  helix:  0.71 (0.36), residues: 240
  sheet: -0.15 (0.67), residues: 72
  loop : -1.47 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  96 
 TYR   0.010   0.001   TYR A 134 
 PHE   0.007   0.001   PHE A 337 
 TRP   0.006   0.001   TRP A 247 
 HIS   0.002   0.000   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 5427)
  covalent geometry    : angle       0.50348 ( 7354)
  hydrogen bonds       : bond        0.03223 (  185)
  hydrogen bonds       : angle       4.58967 (  528)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 79
  time to evaluate  : 0.214 
Fit side-chains
REVERT: A  110 GLN cc_start: 0.7038 (mt0) cc_final: 0.6719 (tt0)
REVERT: A  164 GLN cc_start: 0.8100 (mp10) cc_final: 0.7340 (mp10)
REVERT: A  230 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8626 (mtt)
REVERT: A  233 GLU cc_start: 0.8400 (pm20) cc_final: 0.8159 (pm20)
REVERT: A  320 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.6418 (mp0)
REVERT: A  336 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7183 (m-30)
REVERT: B  104 ARG cc_start: 0.8091 (mtp85) cc_final: 0.7868 (mtp85)
REVERT: B  115 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8154 (ttp)
REVERT: B  273 ILE cc_start: 0.7829 (tp) cc_final: 0.7389 (mm)
REVERT: B  338 ASP cc_start: 0.7866 (t0) cc_final: 0.7369 (t0)
  outliers start: 27
  outliers final: 15
  residues processed: 94
  average time/residue: 0.0696
  time to fit residues: 8.5220
Evaluate side-chains
  96 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 GLU
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  214 GLN
Chi-restraints excluded: chain A residue  217 ASP
Chi-restraints excluded: chain A residue  230 MET
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  308 MET
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  115 MET
Chi-restraints excluded: chain B residue  122 GLN
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  355 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 46 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0010
   chunk 45 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   chunk 61 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   overall best weight:    1.3190

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.165577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.137538 restraints weight = 5908.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 2.27
r_work: 0.3443 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.0962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5427  Z= 0.168
  Angle     :  0.552   7.282   7354  Z= 0.281
  Chirality :  0.042   0.141    809
  Planarity :  0.004   0.032    931
  Dihedral  :  8.986 123.676    782
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 24.43 %
    Favored  : 70.68 %
  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: -0.84 (0.34), residues: 638
  helix:  0.61 (0.35), residues: 239
  sheet: -0.17 (0.67), residues: 72
  loop : -1.57 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  96 
 TYR   0.008   0.001   TYR A 179 
 PHE   0.011   0.001   PHE A 337 
 TRP   0.010   0.001   TRP A 247 
 HIS   0.003   0.001   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 5427)
  covalent geometry    : angle       0.55193 ( 7354)
  hydrogen bonds       : bond        0.03668 (  185)
  hydrogen bonds       : angle       4.62996 (  528)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 78
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 LYS cc_start: 0.8519 (mttm) cc_final: 0.8313 (mttp)
REVERT: A  110 GLN cc_start: 0.7093 (mt0) cc_final: 0.6797 (tt0)
REVERT: A  160 ARG cc_start: 0.7431 (ptt90) cc_final: 0.7094 (ptp90)
REVERT: A  163 GLU cc_start: 0.7680 (pm20) cc_final: 0.7347 (pm20)
REVERT: A  164 GLN cc_start: 0.8042 (mp10) cc_final: 0.7448 (mp10)
REVERT: A  230 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8639 (mtm)
REVERT: A  233 GLU cc_start: 0.8422 (pm20) cc_final: 0.8167 (pm20)
REVERT: A  320 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.6508 (mp0)
REVERT: A  336 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7328 (m-30)
REVERT: B  104 ARG cc_start: 0.8139 (mtp85) cc_final: 0.7858 (mtp85)
REVERT: B  115 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8095 (ttp)
REVERT: B  273 ILE cc_start: 0.7902 (tp) cc_final: 0.7441 (mm)
REVERT: B  338 ASP cc_start: 0.7872 (t0) cc_final: 0.7400 (t0)
  outliers start: 28
  outliers final: 18
  residues processed: 92
  average time/residue: 0.0811
  time to fit residues: 9.5637
Evaluate side-chains
  99 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 77
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  120 GLU
Chi-restraints excluded: chain A residue  214 GLN
Chi-restraints excluded: chain A residue  230 MET
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain B residue   53 TYR
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  115 MET
Chi-restraints excluded: chain B residue  122 GLN
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  216 MET
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  272 ILE
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain B residue  331 GLU
Chi-restraints excluded: chain B residue  355 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 23 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0020
   overall best weight:    1.5794

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.165813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.135120 restraints weight = 6086.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 2.46
r_work: 0.3411 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.1129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   5427  Z= 0.190
  Angle     :  0.576   8.802   7354  Z= 0.293
  Chirality :  0.043   0.141    809
  Planarity :  0.004   0.034    931
  Dihedral  :  8.874 123.534    782
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.46 %
    Favored  : 91.54 %
  Rotamer:
    Outliers :  5.76 %
    Allowed  : 24.78 %
    Favored  : 69.46 %
  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: -0.99 (0.34), residues: 638
  helix:  0.48 (0.34), residues: 239
  sheet: -0.24 (0.67), residues: 72
  loop : -1.66 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  96 
 TYR   0.008   0.001   TYR A 179 
 PHE   0.013   0.001   PHE A 337 
 TRP   0.010   0.001   TRP A 247 
 HIS   0.003   0.001   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 5427)
  covalent geometry    : angle       0.57565 ( 7354)
  hydrogen bonds       : bond        0.03972 (  185)
  hydrogen bonds       : angle       4.66177 (  528)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 79
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 LYS cc_start: 0.8543 (mttm) cc_final: 0.8327 (mttp)
REVERT: A  110 GLN cc_start: 0.7026 (mt0) cc_final: 0.6760 (tt0)
REVERT: A  160 ARG cc_start: 0.7467 (ptt90) cc_final: 0.7055 (ptp90)
REVERT: A  163 GLU cc_start: 0.7684 (pm20) cc_final: 0.7242 (pm20)
REVERT: A  164 GLN cc_start: 0.8126 (mp10) cc_final: 0.7336 (mp10)
REVERT: A  233 GLU cc_start: 0.8435 (pm20) cc_final: 0.8154 (pm20)
REVERT: A  320 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.6494 (mp0)
REVERT: A  336 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7378 (m-30)
REVERT: B   44 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8150 (mt0)
REVERT: B  115 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8130 (ttp)
REVERT: B  273 ILE cc_start: 0.7989 (tp) cc_final: 0.7515 (mm)
REVERT: B  338 ASP cc_start: 0.7892 (t0) cc_final: 0.7411 (t0)
  outliers start: 33
  outliers final: 17
  residues processed: 97
  average time/residue: 0.0892
  time to fit residues: 10.9108
Evaluate side-chains
  100 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  120 GLU
Chi-restraints excluded: chain A residue  122 ASN
Chi-restraints excluded: chain A residue  214 GLN
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  115 MET
Chi-restraints excluded: chain B residue  122 GLN
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  216 MET
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain B residue  331 GLU
Chi-restraints excluded: chain B residue  355 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 45 optimal weight:    0.6980
   chunk 36 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    1.0384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.167802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.137334 restraints weight = 6044.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3626 rms_B_bonded: 2.45
r_work: 0.3433 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.1120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5427  Z= 0.138
  Angle     :  0.529   5.226   7354  Z= 0.272
  Chirality :  0.042   0.133    809
  Planarity :  0.004   0.033    931
  Dihedral  :  8.615 120.502    782
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 25.48 %
    Favored  : 69.46 %
  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: -0.84 (0.34), residues: 638
  helix:  0.64 (0.35), residues: 239
  sheet: -0.23 (0.66), residues: 72
  loop : -1.59 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  96 
 TYR   0.010   0.001   TYR B  53 
 PHE   0.009   0.001   PHE A 337 
 TRP   0.008   0.001   TRP A 247 
 HIS   0.002   0.001   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 5427)
  covalent geometry    : angle       0.52891 ( 7354)
  hydrogen bonds       : bond        0.03412 (  185)
  hydrogen bonds       : angle       4.52563 (  528)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 81
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 LYS cc_start: 0.8530 (mttm) cc_final: 0.8329 (mttp)
REVERT: A  110 GLN cc_start: 0.6998 (mt0) cc_final: 0.6758 (tt0)
REVERT: A  160 ARG cc_start: 0.7499 (ptt90) cc_final: 0.7072 (ptp90)
REVERT: A  233 GLU cc_start: 0.8417 (pm20) cc_final: 0.8133 (pm20)
REVERT: A  320 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.6450 (mp0)
REVERT: A  336 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7388 (m-30)
REVERT: B   44 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8101 (mt0)
REVERT: B  104 ARG cc_start: 0.8064 (mtp85) cc_final: 0.7861 (mtp85)
REVERT: B  115 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8107 (ttp)
REVERT: B  273 ILE cc_start: 0.7937 (tp) cc_final: 0.7477 (mm)
REVERT: B  338 ASP cc_start: 0.7860 (t0) cc_final: 0.7379 (t0)
  outliers start: 29
  outliers final: 17
  residues processed: 98
  average time/residue: 0.0829
  time to fit residues: 10.3746
Evaluate side-chains
  100 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  120 GLU
Chi-restraints excluded: chain A residue  122 ASN
Chi-restraints excluded: chain A residue  214 GLN
Chi-restraints excluded: chain A residue  217 ASP
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  115 MET
Chi-restraints excluded: chain B residue  122 GLN
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  216 MET
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  272 ILE
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain B residue  355 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 23 optimal weight:    7.9990
   chunk 20 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 18 optimal weight:    0.2980
   chunk 63 optimal weight:    0.0770
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.4744

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.165975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.135480 restraints weight = 6053.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3607 rms_B_bonded: 2.45
r_work: 0.3412 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.1195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5427  Z= 0.180
  Angle     :  0.572   8.070   7354  Z= 0.292
  Chirality :  0.043   0.137    809
  Planarity :  0.004   0.037    931
  Dihedral  :  8.663 121.759    782
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.78 %
    Favored  : 91.22 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 26.00 %
    Favored  : 68.94 %
  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: -0.94 (0.34), residues: 638
  helix:  0.56 (0.35), residues: 238
  sheet: -0.28 (0.65), residues: 72
  loop : -1.64 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 104 
 TYR   0.010   0.001   TYR B  53 
 PHE   0.012   0.001   PHE A 337 
 TRP   0.010   0.001   TRP A 247 
 HIS   0.003   0.001   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 5427)
  covalent geometry    : angle       0.57232 ( 7354)
  hydrogen bonds       : bond        0.03815 (  185)
  hydrogen bonds       : angle       4.59116 (  528)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 80
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 LYS cc_start: 0.8530 (mttm) cc_final: 0.8325 (mttp)
REVERT: A  110 GLN cc_start: 0.7019 (mt0) cc_final: 0.6769 (tt0)
REVERT: A  146 MET cc_start: 0.7814 (mmt) cc_final: 0.7585 (mmt)
REVERT: A  160 ARG cc_start: 0.7591 (ptt90) cc_final: 0.7089 (ptp90)
REVERT: A  164 GLN cc_start: 0.8122 (mp10) cc_final: 0.7531 (mp10)
REVERT: A  320 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.6440 (mp0)
REVERT: A  336 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7354 (m-30)
REVERT: B   44 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.8059 (mt0)
REVERT: B  104 ARG cc_start: 0.8149 (mtp85) cc_final: 0.7907 (mtp85)
REVERT: B  115 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8126 (ttp)
REVERT: B  273 ILE cc_start: 0.7966 (tp) cc_final: 0.7485 (mm)
REVERT: B  338 ASP cc_start: 0.7891 (t0) cc_final: 0.7411 (t0)
  outliers start: 29
  outliers final: 18
  residues processed: 98
  average time/residue: 0.0898
  time to fit residues: 11.0706
Evaluate side-chains
  102 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 80
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  120 GLU
Chi-restraints excluded: chain A residue  214 GLN
Chi-restraints excluded: chain A residue  217 ASP
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue  115 MET
Chi-restraints excluded: chain B residue  122 GLN
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  216 MET
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain B residue  331 GLU
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  355 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 30 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 57 optimal weight:    3.9990
   overall best weight:    1.1586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.166995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.136753 restraints weight = 5961.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3620 rms_B_bonded: 2.43
r_work: 0.3429 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.1219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5427  Z= 0.151
  Angle     :  0.571  11.717   7354  Z= 0.289
  Chirality :  0.042   0.134    809
  Planarity :  0.004   0.037    931
  Dihedral  :  8.523 119.732    782
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 26.00 %
    Favored  : 69.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.88 (0.34), residues: 638
  helix:  0.62 (0.35), residues: 239
  sheet: -0.27 (0.65), residues: 72
  loop : -1.61 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  96 
 TYR   0.013   0.001   TYR B  53 
 PHE   0.010   0.001   PHE A 337 
 TRP   0.008   0.001   TRP A 247 
 HIS   0.002   0.001   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 5427)
  covalent geometry    : angle       0.57120 ( 7354)
  hydrogen bonds       : bond        0.03544 (  185)
  hydrogen bonds       : angle       4.55214 (  528)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 80
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 GLN cc_start: 0.6998 (mt0) cc_final: 0.6763 (tt0)
REVERT: A  160 ARG cc_start: 0.7593 (ptt90) cc_final: 0.7057 (ptp90)
REVERT: A  233 GLU cc_start: 0.8415 (pm20) cc_final: 0.8134 (pm20)
REVERT: A  320 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.6418 (mp0)
REVERT: A  336 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7349 (m-30)
REVERT: B   44 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8057 (mt0)
REVERT: B  104 ARG cc_start: 0.8118 (mtp85) cc_final: 0.7846 (mtp85)
REVERT: B  115 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8122 (ttp)
REVERT: B  273 ILE cc_start: 0.7942 (tp) cc_final: 0.7471 (mm)
REVERT: B  338 ASP cc_start: 0.7861 (t0) cc_final: 0.7386 (t0)
  outliers start: 27
  outliers final: 20
  residues processed: 96
  average time/residue: 0.0868
  time to fit residues: 10.4567
Evaluate side-chains
  104 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 80
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  120 GLU
Chi-restraints excluded: chain A residue  214 GLN
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  217 ASP
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue  115 MET
Chi-restraints excluded: chain B residue  122 GLN
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  216 MET
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain B residue  331 GLU
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain B residue  355 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 57 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 46 optimal weight:    6.9990
   overall best weight:    1.2584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.163950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.134860 restraints weight = 5915.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3624 rms_B_bonded: 2.36
r_work: 0.3433 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.1213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5427  Z= 0.161
  Angle     :  0.567   8.513   7354  Z= 0.289
  Chirality :  0.043   0.136    809
  Planarity :  0.004   0.036    931
  Dihedral  :  8.523 120.036    782
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.31 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 26.00 %
    Favored  : 68.94 %
  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: -0.92 (0.34), residues: 638
  helix:  0.60 (0.35), residues: 239
  sheet: -0.28 (0.65), residues: 72
  loop : -1.65 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  96 
 TYR   0.016   0.001   TYR B  53 
 PHE   0.011   0.001   PHE A 337 
 TRP   0.009   0.001   TRP A 247 
 HIS   0.003   0.001   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 5427)
  covalent geometry    : angle       0.56741 ( 7354)
  hydrogen bonds       : bond        0.03627 (  185)
  hydrogen bonds       : angle       4.57022 (  528)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 79
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 GLN cc_start: 0.7014 (mt0) cc_final: 0.6779 (tt0)
REVERT: A  160 ARG cc_start: 0.7614 (ptt90) cc_final: 0.7052 (ptp90)
REVERT: A  233 GLU cc_start: 0.8408 (pm20) cc_final: 0.8126 (pm20)
REVERT: A  320 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.6384 (mp0)
REVERT: A  336 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7348 (m-30)
REVERT: B   44 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8069 (mt0)
REVERT: B  104 ARG cc_start: 0.8115 (mtp85) cc_final: 0.7857 (mtp85)
REVERT: B  115 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8127 (ttp)
REVERT: B  273 ILE cc_start: 0.7970 (tp) cc_final: 0.7494 (mm)
REVERT: B  338 ASP cc_start: 0.7885 (t0) cc_final: 0.7485 (t0)
  outliers start: 29
  outliers final: 20
  residues processed: 97
  average time/residue: 0.0885
  time to fit residues: 10.8164
Evaluate side-chains
  103 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 79
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  120 GLU
Chi-restraints excluded: chain A residue  214 GLN
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  217 ASP
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue  115 MET
Chi-restraints excluded: chain B residue  122 GLN
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  216 MET
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain B residue  331 GLU
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain B residue  355 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0870
   chunk 58 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 62 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 24 optimal weight:    0.0370
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.5236

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.170570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.140369 restraints weight = 6004.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 2.46
r_work: 0.3468 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.1202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5427  Z= 0.105
  Angle     :  0.544  13.222   7354  Z= 0.274
  Chirality :  0.041   0.130    809
  Planarity :  0.004   0.033    931
  Dihedral  :  8.226 115.846    782
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.46 %
    Favored  : 91.54 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 27.57 %
    Favored  : 69.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.68 (0.34), residues: 638
  helix:  0.82 (0.36), residues: 240
  sheet: -0.34 (0.71), residues: 64
  loop : -1.46 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  96 
 TYR   0.018   0.001   TYR B  53 
 PHE   0.006   0.001   PHE B  76 
 TRP   0.004   0.001   TRP A 247 
 HIS   0.002   0.000   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 5427)
  covalent geometry    : angle       0.54399 ( 7354)
  hydrogen bonds       : bond        0.02971 (  185)
  hydrogen bonds       : angle       4.40510 (  528)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 GLN cc_start: 0.6960 (mt0) cc_final: 0.6733 (tt0)
REVERT: A  160 ARG cc_start: 0.7542 (ptt90) cc_final: 0.7086 (ptp90)
REVERT: A  233 GLU cc_start: 0.8400 (pm20) cc_final: 0.8117 (pm20)
REVERT: A  320 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.6400 (mp0)
REVERT: A  336 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7257 (m-30)
REVERT: B  115 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.8079 (ttp)
REVERT: B  273 ILE cc_start: 0.7811 (tp) cc_final: 0.7373 (mm)
REVERT: B  338 ASP cc_start: 0.7768 (t0) cc_final: 0.7477 (t0)
  outliers start: 18
  outliers final: 14
  residues processed: 96
  average time/residue: 0.0845
  time to fit residues: 10.2591
Evaluate side-chains
  99 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 GLU
Chi-restraints excluded: chain A residue  120 GLU
Chi-restraints excluded: chain A residue  214 GLN
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  115 MET
Chi-restraints excluded: chain B residue  122 GLN
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain B residue  331 GLU
Chi-restraints excluded: chain B residue  355 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 56 optimal weight:    7.9990
   chunk 2 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 26 optimal weight:    0.6980
   chunk 57 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 1 optimal weight:   20.0000
   chunk 29 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    1.0982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.167954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.137578 restraints weight = 6034.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 2.46
r_work: 0.3442 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.1242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5427  Z= 0.146
  Angle     :  0.566  12.127   7354  Z= 0.285
  Chirality :  0.042   0.135    809
  Planarity :  0.004   0.033    931
  Dihedral  :  8.328 117.538    782
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.99 %
    Favored  : 92.01 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 28.10 %
    Favored  : 68.76 %
  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 (0.34), residues: 638
  helix:  0.72 (0.35), residues: 240
  sheet: -0.26 (0.65), residues: 72
  loop : -1.54 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  96 
 TYR   0.017   0.001   TYR B  53 
 PHE   0.010   0.001   PHE A 337 
 TRP   0.008   0.001   TRP A 247 
 HIS   0.002   0.001   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 5427)
  covalent geometry    : angle       0.56604 ( 7354)
  hydrogen bonds       : bond        0.03412 (  185)
  hydrogen bonds       : angle       4.47061 (  528)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1213.30 seconds
wall clock time: 21 minutes 35.50 seconds (1295.50 seconds total)