Starting phenix.real_space_refine
on Thu Mar  6 06:49:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vu8_21388/03_2025/6vu8_21388.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vu8_21388/03_2025/6vu8_21388.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vu8_21388/03_2025/6vu8_21388.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vu8_21388/03_2025/6vu8_21388.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vu8_21388/03_2025/6vu8_21388.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vu8_21388/03_2025/6vu8_21388.cif"
  }
  resolution = 4.14
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      30      5.16       5
     C    3313      2.51       5
     N     913      2.21       5
     O     991      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5249
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 485, 3815
          Classifications: {'peptide': 485}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 23, 'TRANS': 461}
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 31
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'TPO:plan-1': 1, 'ASN:plan1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "B"
      Number of atoms: 1434
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 1434
          Classifications: {'peptide': 184}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 2, 'TRANS': 181}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 58
          Unresolved non-hydrogen angles: 68
          Unresolved non-hydrogen dihedrals: 48
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 20
  Time building chain proxies: 3.74, per 1000 atoms: 0.71
  Number of scatterers: 5249
  At special positions: 0
  Unit cell: (118.72, 64.66, 87.98, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     P       2     15.00
     O     991      8.00
     N     913      7.00
     C    3313      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: 1.30
  Conformation dependent library (CDL) restraints added in 639.4 milliseconds
  

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1278

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 1 sheets defined
      56.2% alpha, 2.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 11
      removed outlier: 3.592A  pdb=" N   VAL A   6 " --> pdb=" O   GLU A   2 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   GLU A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 14 through 29
      removed outlier: 4.233A  pdb=" N   ARG A  27 " --> pdb=" O   ARG A  23 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   GLU A  28 " --> pdb=" O   SER A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 39 through 57
    Processing helix  chain 'A' and resid 62 through 75
      removed outlier: 4.125A  pdb=" N   TRP A  66 " --> pdb=" O   HIS A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 97
    Processing helix  chain 'A' and resid 110 through 127
      removed outlier: 3.700A  pdb=" N   LEU A 114 " --> pdb=" O   ASP A 110 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   SER A 127 " --> pdb=" O   ASN A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 138
    Processing helix  chain 'A' and resid 140 through 151
      removed outlier: 3.806A  pdb=" N   LEU A 144 " --> pdb=" O   LEU A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 173
      removed outlier: 3.517A  pdb=" N   GLN A 161 " --> pdb=" O   PRO A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 184
      removed outlier: 3.706A  pdb=" N   GLN A 184 " --> pdb=" O   GLN A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 201
      removed outlier: 4.282A  pdb=" N   LEU A 191 " --> pdb=" O   HIS A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 231
      removed outlier: 3.782A  pdb=" N   THR A 231 " --> pdb=" O   LEU A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 260
      removed outlier: 4.609A  pdb=" N   LEU A 246 " --> pdb=" O   GLU A 242 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   TYR A 247 " --> pdb=" O   ASP A 243 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   HIS A 256 " --> pdb=" O   THR A 252 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   CYS A 257 " --> pdb=" O   LEU A 253 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   VAL A 258 " --> pdb=" O   LEU A 254 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   MET A 259 " --> pdb=" O   ARG A 255 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ALA A 260 " --> pdb=" O   HIS A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 280
      removed outlier: 3.884A  pdb=" N   HIS A 271 " --> pdb=" O   THR A 267 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   ASN A 276 " --> pdb=" O   GLY A 272 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   ASN A 280 " --> pdb=" O   ASN A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 288 through 292
      removed outlier: 4.161A  pdb=" N   LEU A 292 " --> pdb=" O   LEU A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 321
      removed outlier: 4.539A  pdb=" N   HIS A 321 " --> pdb=" O   GLU A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 342
    Processing helix  chain 'A' and resid 344 through 356
      removed outlier: 4.481A  pdb=" N   ARG A 348 " --> pdb=" O   HIS A 344 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   LYS A 349 " --> pdb=" O   ARG A 345 " (cutoff:3.500A)
      removed outlier: 4.753A  pdb=" N   PHE A 350 " --> pdb=" O   PRO A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 380
      removed outlier: 3.886A  pdb=" N   ARG A 378 " --> pdb=" O   ASN A 374 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 398
      removed outlier: 3.839A  pdb=" N   GLU A 393 " --> pdb=" O   ARG A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 423
      removed outlier: 6.388A  pdb=" N   GLY A 417 " --> pdb=" O   GLY A 413 " (cutoff:3.500A)
      removed outlier: 6.000A  pdb=" N   LEU A 418 " --> pdb=" O   ASN A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 482
      removed outlier: 4.288A  pdb=" N   LEU A 482 " --> pdb=" O   GLU A 478 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 53
      removed outlier: 3.543A  pdb=" N   ILE B  49 " --> pdb=" O   GLY B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 255
      removed outlier: 3.584A  pdb=" N   ASN B 255 " --> pdb=" O   ASP B 251 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 260
      removed outlier: 3.605A  pdb=" N   THR B 260 " --> pdb=" O   LYS B 257 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 279
      removed outlier: 4.026A  pdb=" N   PHE B 274 " --> pdb=" O   LYS B 270 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   LYS B 279 " --> pdb=" O   GLU B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 310
      removed outlier: 3.554A  pdb=" N   ALA B 299 " --> pdb=" O   THR B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 336 through 351
      removed outlier: 4.332A  pdb=" N   THR B 340 " --> pdb=" O   PHE B 336 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 220 through 225
      removed outlier: 3.588A  pdb=" N   ALA B 220 " --> pdb=" O   SER B 263 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ILE B 265 " --> pdb=" O   ALA B 220 " (cutoff:3.500A)
      removed outlier: 5.089A  pdb=" N   PHE B 267 " --> pdb=" O   ILE B 222 " (cutoff:3.500A)
      removed outlier: 4.924A  pdb=" N   CYS B 224 " --> pdb=" O   PHE B 267 " (cutoff:3.500A)

    230 hydrogen bonds defined for protein.
    678 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: 1.27

  Time building geometry restraints manager: 1.56 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1770
        1.34 -     1.46: 1040
        1.46 -     1.58: 2479
        1.58 -     1.70: 7
        1.70 -     1.81: 44
  Bond restraints: 5340
  Sorted by residual:
  bond pdb=" OG1 TPO A 440 "
       pdb=" P   TPO A 440 "
    ideal  model  delta    sigma   weight residual
    1.717  1.613  0.104 2.00e-02 2.50e+03 2.68e+01
  bond pdb=" O1P TPO A 440 "
       pdb=" P   TPO A 440 "
    ideal  model  delta    sigma   weight residual
    1.525  1.608 -0.083 2.00e-02 2.50e+03 1.73e+01
  bond pdb=" O3P TPO A 440 "
       pdb=" P   TPO A 440 "
    ideal  model  delta    sigma   weight residual
    1.528  1.609 -0.081 2.00e-02 2.50e+03 1.63e+01
  bond pdb=" C   ALA A 331 "
       pdb=" N   PRO A 332 "
    ideal  model  delta    sigma   weight residual
    1.337  1.374 -0.036 1.24e-02 6.50e+03 8.64e+00
  bond pdb=" O2P TPO A 440 "
       pdb=" P   TPO A 440 "
    ideal  model  delta    sigma   weight residual
    1.528  1.481  0.047 2.00e-02 2.50e+03 5.51e+00
  ... (remaining 5335 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.77: 7033
        2.77 -     5.54: 161
        5.54 -     8.31: 23
        8.31 -    11.08: 8
       11.08 -    13.85: 3
  Bond angle restraints: 7228
  Sorted by residual:
  angle pdb=" C   GLN A 322 "
        pdb=" N   THR A 323 "
        pdb=" CA  THR A 323 "
      ideal   model   delta    sigma   weight residual
     121.54  130.54   -9.00 1.91e+00 2.74e-01 2.22e+01
  angle pdb=" N   SER A  30 "
        pdb=" CA  SER A  30 "
        pdb=" C   SER A  30 "
      ideal   model   delta    sigma   weight residual
     110.97  115.96   -4.99 1.09e+00 8.42e-01 2.09e+01
  angle pdb=" C   ARG B 313 "
        pdb=" N   LYS B 314 "
        pdb=" CA  LYS B 314 "
      ideal   model   delta    sigma   weight residual
     122.61  129.06   -6.45 1.56e+00 4.11e-01 1.71e+01
  angle pdb=" C   VAL B 218 "
        pdb=" N   THR B 219 "
        pdb=" CA  THR B 219 "
      ideal   model   delta    sigma   weight residual
     120.82  126.64   -5.82 1.41e+00 5.03e-01 1.70e+01
  angle pdb=" CA  LEU A 424 "
        pdb=" CB  LEU A 424 "
        pdb=" CG  LEU A 424 "
      ideal   model   delta    sigma   weight residual
     116.30  130.15  -13.85 3.50e+00 8.16e-02 1.56e+01
  ... (remaining 7223 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 2835
       17.89 -    35.78: 355
       35.78 -    53.67: 54
       53.67 -    71.55: 11
       71.55 -    89.44: 9
  Dihedral angle restraints: 3264
    sinusoidal: 1306
      harmonic: 1958
  Sorted by residual:
  dihedral pdb=" CA  ASN A 207 "
           pdb=" C   ASN A 207 "
           pdb=" N   PRO A 208 "
           pdb=" CA  PRO A 208 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.70   27.30     0      5.00e+00 4.00e-02 2.98e+01
  dihedral pdb=" CA  ARG A 365 "
           pdb=" C   ARG A 365 "
           pdb=" N   PRO A 366 "
           pdb=" CA  PRO A 366 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.75   25.25     0      5.00e+00 4.00e-02 2.55e+01
  dihedral pdb=" CA  ALA B  41 "
           pdb=" C   ALA B  41 "
           pdb=" N   GLY B  42 "
           pdb=" CA  GLY B  42 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.54  -23.46     0      5.00e+00 4.00e-02 2.20e+01
  ... (remaining 3261 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 675
       0.067 -    0.134: 137
       0.134 -    0.202: 16
       0.202 -    0.269: 2
       0.269 -    0.336: 1
  Chirality restraints: 831
  Sorted by residual:
  chirality pdb=" CB  ILE B 221 "
            pdb=" CA  ILE B 221 "
            pdb=" CG1 ILE B 221 "
            pdb=" CG2 ILE B 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.31    0.34 2.00e-01 2.50e+01 2.82e+00
  chirality pdb=" CG  LEU A 418 "
            pdb=" CB  LEU A 418 "
            pdb=" CD1 LEU A 418 "
            pdb=" CD2 LEU A 418 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.38   -0.20 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CB  VAL A 377 "
            pdb=" CA  VAL A 377 "
            pdb=" CG1 VAL A 377 "
            pdb=" CG2 VAL A 377 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.02e+00
  ... (remaining 828 not shown)

  Planarity restraints: 939
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 365 "    0.043 5.00e-02 4.00e+02   6.51e-02 6.79e+00
        pdb=" N   PRO A 366 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A 366 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 366 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 287 "    0.042 5.00e-02 4.00e+02   6.36e-02 6.48e+00
        pdb=" N   PRO B 288 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO B 288 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 288 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 203 "   -0.041 5.00e-02 4.00e+02   6.25e-02 6.26e+00
        pdb=" N   PRO A 204 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO A 204 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 204 "   -0.035 5.00e-02 4.00e+02
  ... (remaining 936 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1322
        2.79 -     3.32: 5039
        3.32 -     3.84: 8432
        3.84 -     4.37: 9418
        4.37 -     4.90: 15249
  Nonbonded interactions: 39460
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 270 "
            pdb=" OG1 THR A 274 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" OE2 GLU A 197 "
            pdb=" OH  TYR A 249 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" O   LYS B 257 "
            pdb=" OG1 THR B 260 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   PHE A 406 "
            pdb=" OG1 THR A 410 "
     model   vdw
     2.326 3.040
  nonbonded pdb=" NH2 ARG A 255 "
            pdb=" O   LEU A 286 "
     model   vdw
     2.334 3.120
  ... (remaining 39455 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.260
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     16.370
  Find NCS groups from input model:        0.050
  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:             0.010
  Load rotamer database and sin/cos tables:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
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      :  0.006   0.104   5340  Z= 0.386
  Angle     :  1.053  13.846   7228  Z= 0.553
  Chirality :  0.054   0.336    831
  Planarity :  0.007   0.065    939
  Dihedral  : 16.207  89.443   1986
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.92 %
    Favored  : 90.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 11.17 %
    Favored  : 88.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.91 (0.24), residues: 655
  helix: -2.78 (0.20), residues: 332
  sheet: -3.68 (0.93), residues: 21
  loop : -3.80 (0.29), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A  66 
 HIS   0.004   0.001   HIS A 477 
 PHE   0.015   0.002   PHE A 232 
 TYR   0.015   0.003   TYR A 445 
 ARG   0.009   0.001   ARG A 255 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.586 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 ASP cc_start: 0.8585 (p0) cc_final: 0.8345 (p0)
REVERT: A   27 ARG cc_start: 0.9105 (ptm160) cc_final: 0.8624 (ttp-110)
REVERT: A   66 TRP cc_start: 0.8568 (m-90) cc_final: 0.8303 (m-90)
REVERT: A   97 ASP cc_start: 0.9469 (t70) cc_final: 0.9202 (t0)
REVERT: A  151 TYR cc_start: 0.8069 (p90) cc_final: 0.7860 (p90)
REVERT: A  162 PHE cc_start: 0.9119 (t80) cc_final: 0.8542 (t80)
REVERT: A  169 PHE cc_start: 0.8987 (t80) cc_final: 0.8728 (t80)
REVERT: A  194 ASP cc_start: 0.9081 (m-30) cc_final: 0.8442 (m-30)
REVERT: A  197 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8405 (mp0)
REVERT: A  222 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8270 (mt-10)
REVERT: A  233 ASP cc_start: 0.8003 (p0) cc_final: 0.7739 (p0)
REVERT: A  247 TYR cc_start: 0.8494 (m-80) cc_final: 0.8160 (m-80)
REVERT: A  259 MET cc_start: 0.8229 (mmt) cc_final: 0.7968 (mmp)
REVERT: A  328 GLU cc_start: 0.8336 (pt0) cc_final: 0.7983 (pt0)
REVERT: A  352 LYS cc_start: 0.8627 (tptp) cc_final: 0.8418 (tptp)
REVERT: A  356 LEU cc_start: 0.8773 (mp) cc_final: 0.7719 (mp)
REVERT: B  205 ARG cc_start: 0.7434 (mmm160) cc_final: 0.6504 (mmt180)
REVERT: B  241 ASN cc_start: 0.8572 (p0) cc_final: 0.7384 (p0)
REVERT: B  242 ARG cc_start: 0.8631 (mtt180) cc_final: 0.8375 (mtp180)
REVERT: B  243 MET cc_start: 0.8217 (ppp) cc_final: 0.7900 (tmm)
REVERT: B  244 HIS cc_start: 0.8743 (m-70) cc_final: 0.8320 (m-70)
REVERT: B  247 MET cc_start: 0.8695 (mtt) cc_final: 0.8228 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.1626
  time to fit residues: 36.9956
Evaluate side-chains
  136 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 55 optimal weight:   10.0000
   chunk 50 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 59 optimal weight:    0.0980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  29 HIS
A  40 GLN
A  87 GLN
A  90 HIS
A 229 ASN
A 276 ASN
A 344 HIS
B 322 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.126421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.098894 restraints weight = 12549.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.101692 restraints weight = 8233.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.103760 restraints weight = 6185.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.2095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5340  Z= 0.192
  Angle     :  0.675   8.333   7228  Z= 0.350
  Chirality :  0.041   0.155    831
  Planarity :  0.005   0.057    939
  Dihedral  :  6.192  25.342    730
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.70 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  6.49 %
    Favored  : 93.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.30 (0.29), residues: 655
  helix: -1.04 (0.26), residues: 341
  sheet: -3.67 (0.86), residues: 21
  loop : -3.56 (0.30), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 258 
 HIS   0.006   0.001   HIS A 344 
 PHE   0.014   0.002   PHE A 163 
 TYR   0.015   0.002   TYR A 151 
 ARG   0.006   0.001   ARG A 458 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 177
  time to evaluate  : 0.586 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.7341 (mp0) cc_final: 0.7141 (pm20)
REVERT: A   16 ASP cc_start: 0.8550 (p0) cc_final: 0.8274 (p0)
REVERT: A   66 TRP cc_start: 0.8532 (m-90) cc_final: 0.8313 (m-90)
REVERT: A   90 HIS cc_start: 0.8721 (OUTLIER) cc_final: 0.8356 (t-90)
REVERT: A   97 ASP cc_start: 0.9391 (t70) cc_final: 0.8992 (t0)
REVERT: A  151 TYR cc_start: 0.7071 (p90) cc_final: 0.5494 (p90)
REVERT: A  163 PHE cc_start: 0.9177 (m-80) cc_final: 0.8921 (m-80)
REVERT: A  191 LEU cc_start: 0.9017 (pp) cc_final: 0.8555 (pp)
REVERT: A  194 ASP cc_start: 0.8814 (m-30) cc_final: 0.8502 (m-30)
REVERT: A  197 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8184 (mt-10)
REVERT: A  221 MET cc_start: 0.8558 (tpt) cc_final: 0.7867 (tpt)
REVERT: A  233 ASP cc_start: 0.7806 (p0) cc_final: 0.7484 (p0)
REVERT: A  247 TYR cc_start: 0.8390 (m-80) cc_final: 0.8034 (m-10)
REVERT: A  328 GLU cc_start: 0.8085 (pt0) cc_final: 0.7858 (pt0)
REVERT: A  356 LEU cc_start: 0.9033 (mp) cc_final: 0.8128 (mp)
REVERT: A  396 PHE cc_start: 0.8158 (t80) cc_final: 0.7812 (t80)
REVERT: B  205 ARG cc_start: 0.7765 (mmm160) cc_final: 0.6544 (mmt180)
REVERT: B  241 ASN cc_start: 0.8566 (p0) cc_final: 0.6902 (p0)
REVERT: B  244 HIS cc_start: 0.8738 (m-70) cc_final: 0.8218 (m-70)
REVERT: B  247 MET cc_start: 0.8396 (mtt) cc_final: 0.8042 (mtt)
REVERT: B  311 ASN cc_start: 0.7345 (t0) cc_final: 0.7058 (t0)
REVERT: B  340 THR cc_start: 0.9509 (m) cc_final: 0.9084 (t)
  outliers start: 2
  outliers final: 0
  residues processed: 178
  average time/residue: 0.1403
  time to fit residues: 33.4634
Evaluate side-chains
  143 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 142
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 51 optimal weight:   20.0000
   chunk 57 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   chunk 46 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0980
   chunk 14 optimal weight:    0.6980
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 229 ASN
A 344 HIS
B 256 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.125930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.098355 restraints weight = 12677.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.101140 restraints weight = 8342.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.103140 restraints weight = 6247.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5340  Z= 0.197
  Angle     :  0.667   8.358   7228  Z= 0.340
  Chirality :  0.041   0.188    831
  Planarity :  0.005   0.069    939
  Dihedral  :  5.746  23.822    730
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.40 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  4.68 %
    Favored  : 94.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.65 (0.31), residues: 655
  helix: -0.36 (0.28), residues: 342
  sheet: -3.54 (0.90), residues: 21
  loop : -3.45 (0.31), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 258 
 HIS   0.010   0.001   HIS A  90 
 PHE   0.012   0.001   PHE A 163 
 TYR   0.025   0.002   TYR A 434 
 ARG   0.007   0.001   ARG A 458 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 180
  time to evaluate  : 0.663 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.7240 (mp0) cc_final: 0.6982 (pm20)
REVERT: A   66 TRP cc_start: 0.8584 (m-90) cc_final: 0.8378 (m-90)
REVERT: A   94 CYS cc_start: 0.8047 (p) cc_final: 0.7699 (p)
REVERT: A   97 ASP cc_start: 0.9378 (t70) cc_final: 0.9048 (t0)
REVERT: A  111 MET cc_start: 0.8081 (mmt) cc_final: 0.7872 (mpp)
REVERT: A  118 LEU cc_start: 0.9113 (mm) cc_final: 0.8895 (mm)
REVERT: A  151 TYR cc_start: 0.7232 (p90) cc_final: 0.5838 (p90)
REVERT: A  194 ASP cc_start: 0.8801 (m-30) cc_final: 0.8487 (m-30)
REVERT: A  221 MET cc_start: 0.8595 (tpt) cc_final: 0.7869 (tpt)
REVERT: A  233 ASP cc_start: 0.7835 (p0) cc_final: 0.7526 (p0)
REVERT: A  247 TYR cc_start: 0.8439 (m-80) cc_final: 0.8097 (m-80)
REVERT: A  317 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7445 (mm-30)
REVERT: A  328 GLU cc_start: 0.8097 (pt0) cc_final: 0.7855 (pt0)
REVERT: A  356 LEU cc_start: 0.9138 (mp) cc_final: 0.8352 (mp)
REVERT: B  205 ARG cc_start: 0.7773 (mmm160) cc_final: 0.6623 (mmt180)
REVERT: B  241 ASN cc_start: 0.8618 (p0) cc_final: 0.7725 (p0)
REVERT: B  244 HIS cc_start: 0.8694 (m-70) cc_final: 0.8078 (m-70)
REVERT: B  247 MET cc_start: 0.8506 (mtt) cc_final: 0.8155 (mtt)
REVERT: B  347 ASN cc_start: 0.8984 (m-40) cc_final: 0.8773 (m-40)
REVERT: B  354 PHE cc_start: 0.7023 (p90) cc_final: 0.6581 (p90)
  outliers start: 2
  outliers final: 0
  residues processed: 180
  average time/residue: 0.1734
  time to fit residues: 41.0594
Evaluate side-chains
  138 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 47 optimal weight:   10.0000
   chunk 13 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 38 optimal weight:    9.9990
   chunk 45 optimal weight:    0.0770
   chunk 14 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0470
   chunk 29 optimal weight:    6.9990
   chunk 20 optimal weight:    6.9990
   overall best weight:    1.0240

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

Flipped N/Q/H residues before XYZ refinement:
A 229 ASN
A 324 HIS
A 344 HIS
B 213 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.127305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.098922 restraints weight = 12963.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.101736 restraints weight = 8534.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.103812 restraints weight = 6424.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.3142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5340  Z= 0.180
  Angle     :  0.663   8.388   7228  Z= 0.334
  Chirality :  0.041   0.189    831
  Planarity :  0.005   0.056    939
  Dihedral  :  5.455  23.591    730
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  4.14 %
    Favored  : 95.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.28 (0.32), residues: 655
  helix:  0.01 (0.29), residues: 343
  sheet: -3.38 (0.94), residues: 21
  loop : -3.37 (0.31), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 258 
 HIS   0.007   0.001   HIS A  90 
 PHE   0.018   0.002   PHE A 162 
 TYR   0.021   0.002   TYR A 151 
 ARG   0.008   0.000   ARG A  27 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 176
  time to evaluate  : 0.950 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 THR cc_start: 0.8741 (p) cc_final: 0.8473 (t)
REVERT: A   94 CYS cc_start: 0.8148 (p) cc_final: 0.7805 (p)
REVERT: A   97 ASP cc_start: 0.9391 (t70) cc_final: 0.9013 (t0)
REVERT: A  118 LEU cc_start: 0.9099 (mm) cc_final: 0.8782 (mm)
REVERT: A  151 TYR cc_start: 0.7392 (p90) cc_final: 0.5938 (p90)
REVERT: A  194 ASP cc_start: 0.8952 (m-30) cc_final: 0.8321 (m-30)
REVERT: A  197 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8118 (mt-10)
REVERT: A  229 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8206 (t0)
REVERT: A  233 ASP cc_start: 0.7898 (p0) cc_final: 0.7592 (p0)
REVERT: A  247 TYR cc_start: 0.8506 (m-80) cc_final: 0.8194 (m-80)
REVERT: A  317 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7435 (mm-30)
REVERT: A  328 GLU cc_start: 0.8239 (pt0) cc_final: 0.7804 (pt0)
REVERT: A  356 LEU cc_start: 0.9077 (mp) cc_final: 0.8332 (mp)
REVERT: B  205 ARG cc_start: 0.7715 (mmm160) cc_final: 0.6612 (mmt180)
REVERT: B  241 ASN cc_start: 0.8577 (p0) cc_final: 0.7904 (p0)
REVERT: B  244 HIS cc_start: 0.8703 (m-70) cc_final: 0.8009 (m-70)
REVERT: B  247 MET cc_start: 0.8451 (mtt) cc_final: 0.8019 (mtt)
REVERT: B  265 ILE cc_start: 0.8236 (mm) cc_final: 0.8031 (mm)
REVERT: B  347 ASN cc_start: 0.9017 (m-40) cc_final: 0.8801 (m-40)
  outliers start: 2
  outliers final: 0
  residues processed: 176
  average time/residue: 0.1936
  time to fit residues: 46.2890
Evaluate side-chains
  141 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 140
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 50 optimal weight:    7.9990
   chunk 41 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 3 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 229 ASN
B 213 HIS
B 346 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.126625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.098438 restraints weight = 12836.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.101255 restraints weight = 8496.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.103265 restraints weight = 6385.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.3482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5340  Z= 0.193
  Angle     :  0.682   8.407   7228  Z= 0.344
  Chirality :  0.042   0.161    831
  Planarity :  0.005   0.052    939
  Dihedral  :  5.338  21.769    730
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.10 (0.32), residues: 655
  helix:  0.15 (0.29), residues: 343
  sheet: -3.30 (0.94), residues: 21
  loop : -3.29 (0.32), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  66 
 HIS   0.006   0.001   HIS A  90 
 PHE   0.022   0.002   PHE A 163 
 TYR   0.032   0.002   TYR A 434 
 ARG   0.006   0.001   ARG A  27 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.726 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 CYS cc_start: 0.8301 (p) cc_final: 0.7906 (p)
REVERT: A   97 ASP cc_start: 0.9387 (t70) cc_final: 0.9030 (t0)
REVERT: A  111 MET cc_start: 0.7804 (mmt) cc_final: 0.7541 (mmt)
REVERT: A  118 LEU cc_start: 0.9105 (mm) cc_final: 0.8823 (mm)
REVERT: A  151 TYR cc_start: 0.7486 (p90) cc_final: 0.5919 (p90)
REVERT: A  171 LEU cc_start: 0.9103 (mm) cc_final: 0.8858 (mt)
REVERT: A  194 ASP cc_start: 0.8938 (m-30) cc_final: 0.8323 (m-30)
REVERT: A  197 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8067 (mt-10)
REVERT: A  233 ASP cc_start: 0.7920 (p0) cc_final: 0.7601 (p0)
REVERT: A  247 TYR cc_start: 0.8576 (m-80) cc_final: 0.8287 (m-80)
REVERT: A  317 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7332 (mm-30)
REVERT: A  328 GLU cc_start: 0.7927 (pt0) cc_final: 0.7429 (pt0)
REVERT: A  356 LEU cc_start: 0.9163 (mp) cc_final: 0.8528 (mp)
REVERT: B  205 ARG cc_start: 0.7625 (mmm160) cc_final: 0.6542 (mmt180)
REVERT: B  241 ASN cc_start: 0.8515 (p0) cc_final: 0.7798 (p0)
REVERT: B  244 HIS cc_start: 0.8604 (m-70) cc_final: 0.8263 (m-70)
REVERT: B  247 MET cc_start: 0.8338 (mtt) cc_final: 0.8032 (mtt)
REVERT: B  277 LYS cc_start: 0.8993 (mppt) cc_final: 0.8772 (mmtt)
REVERT: B  311 ASN cc_start: 0.7275 (t0) cc_final: 0.6874 (m-40)
REVERT: B  346 ASN cc_start: 0.8421 (t160) cc_final: 0.7881 (t160)
  outliers start: 0
  outliers final: 0
  residues processed: 172
  average time/residue: 0.1746
  time to fit residues: 39.2818
Evaluate side-chains
  143 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0060
   chunk 45 optimal weight:    0.0670
   chunk 33 optimal weight:    0.8980
   chunk 38 optimal weight:    6.9990
   chunk 40 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.1938

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

Flipped N/Q/H residues before XYZ refinement:
A 229 ASN
B 213 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.126149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.097987 restraints weight = 12676.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.100804 restraints weight = 8534.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.102833 restraints weight = 6423.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.3702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5340  Z= 0.192
  Angle     :  0.675   9.868   7228  Z= 0.338
  Chirality :  0.041   0.198    831
  Planarity :  0.005   0.048    939
  Dihedral  :  5.283  25.708    730
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  2.70 %
    Favored  : 97.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.93 (0.33), residues: 655
  helix:  0.27 (0.29), residues: 343
  sheet: -3.26 (0.92), residues: 21
  loop : -3.18 (0.33), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  66 
 HIS   0.004   0.001   HIS A  90 
 PHE   0.018   0.002   PHE A 163 
 TYR   0.019   0.002   TYR A 151 
 ARG   0.006   0.000   ARG A  27 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 163
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 CYS cc_start: 0.8329 (p) cc_final: 0.7870 (p)
REVERT: A   97 ASP cc_start: 0.9397 (t70) cc_final: 0.9002 (t0)
REVERT: A  111 MET cc_start: 0.7688 (mmt) cc_final: 0.7457 (mmt)
REVERT: A  118 LEU cc_start: 0.9133 (mm) cc_final: 0.8830 (mm)
REVERT: A  125 VAL cc_start: 0.9247 (m) cc_final: 0.8982 (p)
REVERT: A  151 TYR cc_start: 0.7411 (p90) cc_final: 0.5885 (p90)
REVERT: A  194 ASP cc_start: 0.8915 (m-30) cc_final: 0.8345 (m-30)
REVERT: A  197 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8029 (mt-10)
REVERT: A  233 ASP cc_start: 0.7942 (p0) cc_final: 0.7582 (p0)
REVERT: A  247 TYR cc_start: 0.8613 (m-80) cc_final: 0.8348 (m-80)
REVERT: A  317 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7271 (mm-30)
REVERT: A  328 GLU cc_start: 0.7912 (pt0) cc_final: 0.7543 (pt0)
REVERT: A  356 LEU cc_start: 0.9090 (mp) cc_final: 0.8513 (mp)
REVERT: B  205 ARG cc_start: 0.7620 (mmm160) cc_final: 0.6545 (mmt180)
REVERT: B  244 HIS cc_start: 0.8873 (m-70) cc_final: 0.8386 (m-70)
REVERT: B  247 MET cc_start: 0.8449 (mtt) cc_final: 0.8112 (mtt)
REVERT: B  265 ILE cc_start: 0.8302 (mm) cc_final: 0.8060 (mm)
REVERT: B  311 ASN cc_start: 0.7240 (t0) cc_final: 0.6863 (m-40)
REVERT: B  340 THR cc_start: 0.9492 (m) cc_final: 0.9100 (t)
REVERT: B  346 ASN cc_start: 0.8517 (t0) cc_final: 0.7996 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 163
  average time/residue: 0.1352
  time to fit residues: 29.9832
Evaluate side-chains
  132 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0000
   chunk 23 optimal weight:    0.9990
   chunk 62 optimal weight:    4.9990
   chunk 22 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 51 optimal weight:    9.9990
   chunk 38 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0040
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
A 229 ASN
A 344 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.128457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.100856 restraints weight = 12389.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.103803 restraints weight = 8200.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.105795 restraints weight = 6104.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.4016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5340  Z= 0.175
  Angle     :  0.675   8.321   7228  Z= 0.337
  Chirality :  0.042   0.152    831
  Planarity :  0.005   0.051    939
  Dihedral  :  5.179  22.190    730
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  2.88 %
    Favored  : 96.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.83 (0.33), residues: 655
  helix:  0.37 (0.29), residues: 344
  sheet: -3.23 (0.90), residues: 21
  loop : -3.16 (0.32), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  66 
 HIS   0.008   0.001   HIS A 344 
 PHE   0.015   0.001   PHE A 163 
 TYR   0.019   0.002   TYR A 151 
 ARG   0.005   0.000   ARG A 458 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 174
  time to evaluate  : 0.629 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 CYS cc_start: 0.8322 (p) cc_final: 0.7871 (p)
REVERT: A   97 ASP cc_start: 0.9377 (t70) cc_final: 0.8989 (t0)
REVERT: A  118 LEU cc_start: 0.9116 (mm) cc_final: 0.8824 (mm)
REVERT: A  125 VAL cc_start: 0.9295 (m) cc_final: 0.9065 (p)
REVERT: A  151 TYR cc_start: 0.7547 (p90) cc_final: 0.6043 (p90)
REVERT: A  194 ASP cc_start: 0.8826 (m-30) cc_final: 0.8429 (m-30)
REVERT: A  197 GLU cc_start: 0.8499 (mt-10) cc_final: 0.7963 (mt-10)
REVERT: A  233 ASP cc_start: 0.7954 (p0) cc_final: 0.7582 (p0)
REVERT: A  247 TYR cc_start: 0.8575 (m-80) cc_final: 0.8202 (m-80)
REVERT: A  317 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7198 (mm-30)
REVERT: A  328 GLU cc_start: 0.7770 (pt0) cc_final: 0.7359 (pt0)
REVERT: A  356 LEU cc_start: 0.8954 (mp) cc_final: 0.8398 (mp)
REVERT: B  205 ARG cc_start: 0.7623 (mmm160) cc_final: 0.6509 (mmt180)
REVERT: B  241 ASN cc_start: 0.8340 (p0) cc_final: 0.7665 (p0)
REVERT: B  265 ILE cc_start: 0.8290 (mm) cc_final: 0.8089 (mm)
REVERT: B  311 ASN cc_start: 0.7141 (t0) cc_final: 0.6697 (m-40)
REVERT: B  340 THR cc_start: 0.9484 (m) cc_final: 0.9085 (t)
REVERT: B  346 ASN cc_start: 0.8517 (t0) cc_final: 0.7978 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 174
  average time/residue: 0.1450
  time to fit residues: 33.9080
Evaluate side-chains
  136 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 46 optimal weight:    0.1980
   chunk 39 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 42 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   chunk 14 optimal weight:    0.6980
   chunk 37 optimal weight:    3.9990
   chunk 34 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 43 optimal weight:    5.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 123 ASN
** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 161 GLN
A 229 ASN
** A 280 ASN ** 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 = 0.3797 r_free = 0.3797 target = 0.128707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.100178 restraints weight = 13045.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.103229 restraints weight = 8650.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.105302 restraints weight = 6444.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.4178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5340  Z= 0.200
  Angle     :  0.706  11.070   7228  Z= 0.350
  Chirality :  0.043   0.158    831
  Planarity :  0.005   0.049    939
  Dihedral  :  5.315  25.564    730
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 13.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.08 %
    Favored  : 98.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.82 (0.32), residues: 655
  helix:  0.34 (0.29), residues: 347
  sheet: -3.20 (0.91), residues: 21
  loop : -3.15 (0.33), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  66 
 HIS   0.011   0.001   HIS B 244 
 PHE   0.018   0.002   PHE A 163 
 TYR   0.018   0.002   TYR A 151 
 ARG   0.005   0.000   ARG A 458 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 161
  time to evaluate  : 0.554 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 CYS cc_start: 0.8367 (p) cc_final: 0.7939 (p)
REVERT: A   97 ASP cc_start: 0.9388 (t70) cc_final: 0.8995 (t0)
REVERT: A  118 LEU cc_start: 0.9186 (mm) cc_final: 0.8954 (mm)
REVERT: A  125 VAL cc_start: 0.9321 (m) cc_final: 0.9100 (p)
REVERT: A  194 ASP cc_start: 0.8816 (m-30) cc_final: 0.8276 (m-30)
REVERT: A  197 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8033 (mt-10)
REVERT: A  233 ASP cc_start: 0.7985 (p0) cc_final: 0.7591 (p0)
REVERT: A  268 GLU cc_start: 0.8113 (pm20) cc_final: 0.7909 (tp30)
REVERT: A  317 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7276 (mm-30)
REVERT: A  356 LEU cc_start: 0.9120 (mp) cc_final: 0.8539 (mp)
REVERT: A  377 VAL cc_start: 0.8820 (m) cc_final: 0.8542 (m)
REVERT: A  380 MET cc_start: 0.8660 (ptp) cc_final: 0.8246 (ptm)
REVERT: B  205 ARG cc_start: 0.7637 (mmm160) cc_final: 0.6583 (mmt180)
REVERT: B  241 ASN cc_start: 0.8545 (p0) cc_final: 0.7162 (p0)
REVERT: B  265 ILE cc_start: 0.8198 (mm) cc_final: 0.7983 (mm)
REVERT: B  311 ASN cc_start: 0.7098 (t0) cc_final: 0.6708 (m-40)
REVERT: B  340 THR cc_start: 0.9496 (m) cc_final: 0.9121 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 161
  average time/residue: 0.1354
  time to fit residues: 29.5633
Evaluate side-chains
  127 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 43 optimal weight:    0.0040
   chunk 18 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0770
   chunk 16 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 17 optimal weight:    7.9990
   chunk 54 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0010
   overall best weight:    0.6160

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

Flipped N/Q/H residues before XYZ refinement:
A 229 ASN
** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 344 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 = 0.3826 r_free = 0.3826 target = 0.131140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.102537 restraints weight = 12959.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.105615 restraints weight = 8606.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.107866 restraints weight = 6449.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.4471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5340  Z= 0.171
  Angle     :  0.705   9.612   7228  Z= 0.345
  Chirality :  0.042   0.151    831
  Planarity :  0.005   0.050    939
  Dihedral  :  5.169  24.084    730
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.72 %
    Favored  : 99.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.33), residues: 655
  helix:  0.51 (0.29), residues: 345
  sheet: -3.08 (0.95), residues: 21
  loop : -3.04 (0.33), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  66 
 HIS   0.017   0.001   HIS A 344 
 PHE   0.012   0.001   PHE A 163 
 TYR   0.019   0.002   TYR A 151 
 ARG   0.006   0.000   ARG A 348 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 168
  time to evaluate  : 0.588 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 CYS cc_start: 0.8362 (p) cc_final: 0.7908 (p)
REVERT: A   97 ASP cc_start: 0.9364 (t70) cc_final: 0.8990 (t0)
REVERT: A  111 MET cc_start: 0.7491 (mmt) cc_final: 0.7219 (mmt)
REVERT: A  118 LEU cc_start: 0.9184 (mm) cc_final: 0.8907 (mm)
REVERT: A  125 VAL cc_start: 0.9336 (m) cc_final: 0.9126 (p)
REVERT: A  194 ASP cc_start: 0.8752 (m-30) cc_final: 0.8236 (m-30)
REVERT: A  197 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8018 (mt-10)
REVERT: A  233 ASP cc_start: 0.8016 (p0) cc_final: 0.7636 (p0)
REVERT: A  247 TYR cc_start: 0.8526 (m-10) cc_final: 0.8281 (m-80)
REVERT: A  268 GLU cc_start: 0.8012 (pm20) cc_final: 0.7615 (tm-30)
REVERT: A  327 LYS cc_start: 0.8801 (ttpt) cc_final: 0.8516 (tttt)
REVERT: A  328 GLU cc_start: 0.7650 (pt0) cc_final: 0.7432 (pp20)
REVERT: A  356 LEU cc_start: 0.9025 (mp) cc_final: 0.8451 (mp)
REVERT: A  425 MET cc_start: 0.7769 (pmm) cc_final: 0.7399 (pmm)
REVERT: B  244 HIS cc_start: 0.8720 (m90) cc_final: 0.8476 (m90)
REVERT: B  245 GLU cc_start: 0.9154 (tp30) cc_final: 0.8920 (tp30)
REVERT: B  247 MET cc_start: 0.8686 (mtt) cc_final: 0.8374 (mtt)
REVERT: B  250 PHE cc_start: 0.9055 (t80) cc_final: 0.8827 (t80)
REVERT: B  275 GLU cc_start: 0.8348 (mp0) cc_final: 0.8136 (mp0)
REVERT: B  306 GLN cc_start: 0.8914 (mm110) cc_final: 0.8646 (mp10)
REVERT: B  311 ASN cc_start: 0.7101 (t0) cc_final: 0.6725 (m-40)
REVERT: B  340 THR cc_start: 0.9482 (m) cc_final: 0.9082 (t)
REVERT: B  347 ASN cc_start: 0.9034 (m-40) cc_final: 0.8795 (m-40)
  outliers start: 1
  outliers final: 0
  residues processed: 168
  average time/residue: 0.1441
  time to fit residues: 32.8380
Evaluate side-chains
  135 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 24 optimal weight:    6.9990
   chunk 55 optimal weight:    2.9990
   chunk 59 optimal weight:    5.9990
   chunk 61 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 64 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    5.9990
   chunk 15 optimal weight:    7.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 123 ASN
A 229 ASN
** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.125236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.096704 restraints weight = 13015.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.099547 restraints weight = 8707.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.101588 restraints weight = 6539.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.4360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5340  Z= 0.254
  Angle     :  0.785  10.625   7228  Z= 0.386
  Chirality :  0.045   0.130    831
  Planarity :  0.005   0.059    939
  Dihedral  :  5.461  28.546    730
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 14.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.63 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  0.36 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.80 (0.33), residues: 655
  helix:  0.34 (0.28), residues: 344
  sheet: -3.05 (0.96), residues: 21
  loop : -3.08 (0.34), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 258 
 HIS   0.006   0.001   HIS A 273 
 PHE   0.015   0.002   PHE A 163 
 TYR   0.023   0.002   TYR A 434 
 ARG   0.012   0.001   ARG A 348 

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 164
  time to evaluate  : 0.625 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 CYS cc_start: 0.8455 (p) cc_final: 0.8021 (p)
REVERT: A   97 ASP cc_start: 0.9404 (t70) cc_final: 0.8981 (t0)
REVERT: A  118 LEU cc_start: 0.9275 (mm) cc_final: 0.9074 (mm)
REVERT: A  125 VAL cc_start: 0.9364 (m) cc_final: 0.9142 (p)
REVERT: A  194 ASP cc_start: 0.8887 (m-30) cc_final: 0.8337 (m-30)
REVERT: A  197 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8157 (mt-10)
REVERT: A  224 LEU cc_start: 0.9534 (mt) cc_final: 0.9164 (mt)
REVERT: A  233 ASP cc_start: 0.7958 (p0) cc_final: 0.7616 (p0)
REVERT: A  268 GLU cc_start: 0.8086 (pm20) cc_final: 0.7699 (tp30)
REVERT: A  328 GLU cc_start: 0.7652 (pt0) cc_final: 0.7263 (pp20)
REVERT: A  329 CYS cc_start: 0.8111 (m) cc_final: 0.7063 (m)
REVERT: A  380 MET cc_start: 0.8544 (ptm) cc_final: 0.8343 (ptm)
REVERT: A  425 MET cc_start: 0.7743 (pmm) cc_final: 0.7329 (pmm)
REVERT: B  247 MET cc_start: 0.8715 (mtt) cc_final: 0.8338 (mtt)
REVERT: B  260 THR cc_start: 0.7624 (p) cc_final: 0.7377 (t)
REVERT: B  265 ILE cc_start: 0.8250 (mm) cc_final: 0.7986 (mm)
REVERT: B  311 ASN cc_start: 0.7053 (t0) cc_final: 0.6693 (m-40)
REVERT: B  340 THR cc_start: 0.9521 (m) cc_final: 0.9113 (t)
REVERT: B  347 ASN cc_start: 0.9079 (m-40) cc_final: 0.8783 (m-40)
  outliers start: 2
  outliers final: 1
  residues processed: 164
  average time/residue: 0.1278
  time to fit residues: 28.8842
Evaluate side-chains
  136 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 135
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 1 optimal weight:    0.7980
   chunk 62 optimal weight:    0.0060
   chunk 2 optimal weight:    0.9990
   chunk 3 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0060
   chunk 0 optimal weight:    9.9990
   chunk 41 optimal weight:    0.5980
   chunk 5 optimal weight:    5.9990
   chunk 50 optimal weight:    0.3980
   overall best weight:    0.3612

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

Flipped N/Q/H residues before XYZ refinement:
A 229 ASN
** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 344 HIS
** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 294 ASN
** B 346 ASN ** 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 = 0.3827 r_free = 0.3827 target = 0.131084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.102666 restraints weight = 12806.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.105781 restraints weight = 8474.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.108067 restraints weight = 6301.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.4689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5340  Z= 0.174
  Angle     :  0.732   9.089   7228  Z= 0.359
  Chirality :  0.042   0.200    831
  Planarity :  0.005   0.058    939
  Dihedral  :  5.246  25.182    730
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.54 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.33), residues: 655
  helix:  0.33 (0.29), residues: 350
  sheet: -2.32 (1.23), residues: 16
  loop : -3.00 (0.33), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  66 
 HIS   0.009   0.001   HIS B 244 
 PHE   0.013   0.001   PHE A 163 
 TYR   0.015   0.002   TYR A 151 
 ARG   0.004   0.000   ARG A 348 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2071.17 seconds
wall clock time: 37 minutes 41.46 seconds (2261.46 seconds total)