Starting phenix.real_space_refine
on Tue Mar  3 13:31:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vu8_21388/03_2026/6vu8_21388.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vu8_21388/03_2026/6vu8_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_2026/6vu8_21388.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vu8_21388/03_2026/6vu8_21388.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vu8_21388/03_2026/6vu8_21388.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vu8_21388/03_2026/6vu8_21388.cif"
  }
  resolution = 4.14
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ASP:plan': 1, 'ASN:plan1': 2, 'TPO:plan-1': 1, 'GLU: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, 'ASP:plan': 3, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 20
  Time building chain proxies: 1.36, per 1000 atoms: 0.26
  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: 0.38
  Conformation dependent library (CDL) restraints added in 339.4 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: 0.14
  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: 0.69

  Time building geometry restraints manager: 0.55 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:             0.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.610
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.480
-------------------------------------------------------------------------------
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= 0.266
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.91 (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
 ARG   0.009   0.001   ARG A 255 
 TYR   0.015   0.003   TYR A 445 
 PHE   0.015   0.002   PHE A 232 
 TRP   0.015   0.002   TRP A  66 
 HIS   0.004   0.001   HIS A 477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00573 ( 5340)
  covalent geometry    : angle       1.05312 ( 7228)
  hydrogen bonds       : bond        0.15574 (  230)
  hydrogen bonds       : angle       6.78358 (  678)

*********************** 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  : 0.187 
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: 0.7433 (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: 0.8229 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.0692
  time to fit residues: 15.8608
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  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0070
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0060
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0870
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.4192

-------------------------------------------------------------------------------
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 = 0.3778 r_free = 0.3778 target = 0.127741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.100121 restraints weight = 12696.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.102956 restraints weight = 8312.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.105094 restraints weight = 6190.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.106222 restraints weight = 5012.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.107550 restraints weight = 4371.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.2211

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= 0.120
  Angle     :  0.668   8.132   7228  Z= 0.346
  Chirality :  0.040   0.159    831
  Planarity :  0.005   0.057    939
  Dihedral  :  6.104  25.281    730
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 10.94
  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 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: -3.24 (0.29), residues: 655
  helix: -0.99 (0.27), residues: 341
  sheet: -3.68 (0.87), residues: 21
  loop : -3.54 (0.30), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 458 
 TYR   0.016   0.002   TYR A 151 
 PHE   0.014   0.001   PHE A 163 
 TRP   0.007   0.001   TRP B 258 
 HIS   0.006   0.001   HIS A 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 5340)
  covalent geometry    : angle       0.66780 ( 7228)
  hydrogen bonds       : bond        0.04063 (  230)
  hydrogen bonds       : angle       4.82743 (  678)

*********************** 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  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 ASP cc_start: 0.8520 (p0) cc_final: 0.8231 (p0)
REVERT: A   90 HIS cc_start: 0.8707 (OUTLIER) cc_final: 0.8341 (t-90)
REVERT: A   97 ASP cc_start: 0.9375 (t70) cc_final: 0.8953 (t0)
REVERT: A  151 TYR cc_start: 0.7008 (p90) cc_final: 0.5470 (p90)
REVERT: A  163 PHE cc_start: 0.9135 (m-80) cc_final: 0.8923 (m-80)
REVERT: A  191 LEU cc_start: 0.9006 (pp) cc_final: 0.8544 (pp)
REVERT: A  221 MET cc_start: 0.8550 (tpt) cc_final: 0.8274 (tpt)
REVERT: A  233 ASP cc_start: 0.7796 (p0) cc_final: 0.7468 (p0)
REVERT: A  247 TYR cc_start: 0.8451 (m-80) cc_final: 0.8028 (m-10)
REVERT: A  328 GLU cc_start: 0.8082 (pt0) cc_final: 0.7849 (pt0)
REVERT: A  352 LYS cc_start: 0.8619 (tptp) cc_final: 0.8402 (tptp)
REVERT: A  356 LEU cc_start: 0.8990 (mp) cc_final: 0.7638 (mp)
REVERT: A  396 PHE cc_start: 0.8148 (t80) cc_final: 0.7807 (t80)
REVERT: A  409 TYR cc_start: 0.6527 (t80) cc_final: 0.6237 (t80)
REVERT: B  205 ARG cc_start: 0.7806 (mmm160) cc_final: 0.6589 (mmt180)
REVERT: B  241 ASN cc_start: 0.8522 (p0) cc_final: 0.7500 (p0)
REVERT: B  243 MET cc_start: 0.7932 (ppp) cc_final: 0.7598 (tmm)
REVERT: B  244 HIS cc_start: 0.8700 (m-70) cc_final: 0.8050 (m-70)
REVERT: B  247 MET cc_start: 0.8350 (mtt) cc_final: 0.7953 (mtt)
REVERT: B  311 ASN cc_start: 0.7309 (t0) cc_final: 0.7034 (t0)
REVERT: B  340 THR cc_start: 0.9487 (m) cc_final: 0.9063 (t)
  outliers start: 2
  outliers final: 0
  residues processed: 178
  average time/residue: 0.0547
  time to fit residues: 13.1324
Evaluate side-chains
  138 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 38 optimal weight:    7.9990
   chunk 3 optimal weight:    9.9990
   chunk 40 optimal weight:    3.9990
   chunk 14 optimal weight:    0.6980
   chunk 16 optimal weight:    7.9990
   chunk 23 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0770
   chunk 1 optimal weight:    7.9990
   chunk 46 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.1140

-------------------------------------------------------------------------------
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 = 0.3758 r_free = 0.3758 target = 0.126704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.098781 restraints weight = 12670.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.101578 restraints weight = 8315.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.103386 restraints weight = 6231.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.104879 restraints weight = 5145.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.105796 restraints weight = 4462.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.2878

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= 0.122
  Angle     :  0.657   8.877   7228  Z= 0.335
  Chirality :  0.041   0.184    831
  Planarity :  0.005   0.067    939
  Dihedral  :  5.634  24.004    730
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  4.86 %
    Favored  : 94.77 %
  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: -2.61 (0.31), residues: 655
  helix: -0.33 (0.28), residues: 343
  sheet: -3.51 (0.91), residues: 21
  loop : -3.45 (0.31), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 458 
 TYR   0.022   0.002   TYR A 151 
 PHE   0.013   0.001   PHE A 163 
 TRP   0.011   0.001   TRP A  66 
 HIS   0.008   0.001   HIS A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 5340)
  covalent geometry    : angle       0.65741 ( 7228)
  hydrogen bonds       : bond        0.03660 (  230)
  hydrogen bonds       : angle       4.54990 (  678)

*********************** 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
  176 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 174
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 CYS cc_start: 0.8036 (p) cc_final: 0.7691 (p)
REVERT: A   97 ASP cc_start: 0.9379 (t70) cc_final: 0.9050 (t0)
REVERT: A  118 LEU cc_start: 0.9079 (mm) cc_final: 0.8858 (mm)
REVERT: A  151 TYR cc_start: 0.7073 (p90) cc_final: 0.5758 (p90)
REVERT: A  221 MET cc_start: 0.8608 (tpt) cc_final: 0.7917 (tpt)
REVERT: A  233 ASP cc_start: 0.7822 (p0) cc_final: 0.7508 (p0)
REVERT: A  247 TYR cc_start: 0.8492 (m-80) cc_final: 0.8117 (m-80)
REVERT: A  317 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7381 (mm-30)
REVERT: A  328 GLU cc_start: 0.8089 (pt0) cc_final: 0.7847 (pt0)
REVERT: A  356 LEU cc_start: 0.9092 (mp) cc_final: 0.7852 (mp)
REVERT: A  409 TYR cc_start: 0.6526 (t80) cc_final: 0.6287 (t80)
REVERT: B  205 ARG cc_start: 0.7750 (mmm160) cc_final: 0.6688 (mmt180)
REVERT: B  241 ASN cc_start: 0.8468 (p0) cc_final: 0.6758 (p0)
REVERT: B  244 HIS cc_start: 0.8503 (m-70) cc_final: 0.8193 (m-70)
REVERT: B  271 LYS cc_start: 0.8280 (tmtt) cc_final: 0.7772 (tmtt)
REVERT: B  354 PHE cc_start: 0.6966 (p90) cc_final: 0.6505 (p90)
  outliers start: 2
  outliers final: 0
  residues processed: 174
  average time/residue: 0.0614
  time to fit residues: 14.1077
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  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0970
   chunk 53 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 44 optimal weight:    0.6980
   chunk 1 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0170
   chunk 49 optimal weight:    6.9990
   chunk 56 optimal weight:    4.9990
   chunk 63 optimal weight:   10.0000
   overall best weight:    0.5416

-------------------------------------------------------------------------------
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 = 0.3796 r_free = 0.3796 target = 0.128929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.100565 restraints weight = 12674.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.103404 restraints weight = 8414.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.105488 restraints weight = 6343.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.106940 restraints weight = 5187.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.107881 restraints weight = 4491.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.3458

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= 0.113
  Angle     :  0.660   8.310   7228  Z= 0.329
  Chirality :  0.040   0.177    831
  Planarity :  0.005   0.053    939
  Dihedral  :  5.282  22.930    730
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  4.50 %
    Favored  : 95.14 %
  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: -2.15 (0.32), residues: 655
  helix:  0.09 (0.29), residues: 344
  sheet: -3.22 (0.94), residues: 21
  loop : -3.31 (0.32), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 313 
 TYR   0.021   0.002   TYR A 151 
 PHE   0.019   0.001   PHE A 162 
 TRP   0.009   0.001   TRP A  66 
 HIS   0.007   0.001   HIS A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 5340)
  covalent geometry    : angle       0.66048 ( 7228)
  hydrogen bonds       : bond        0.03317 (  230)
  hydrogen bonds       : angle       4.39856 (  678)

*********************** 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
  183 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 181
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 CYS cc_start: 0.8143 (p) cc_final: 0.7739 (p)
REVERT: A   97 ASP cc_start: 0.9386 (t70) cc_final: 0.9015 (t0)
REVERT: A  118 LEU cc_start: 0.9124 (mm) cc_final: 0.8803 (mm)
REVERT: A  151 TYR cc_start: 0.7064 (p90) cc_final: 0.5748 (p90)
REVERT: A  229 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8082 (t0)
REVERT: A  233 ASP cc_start: 0.7851 (p0) cc_final: 0.7450 (p0)
REVERT: A  317 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7345 (mm-30)
REVERT: A  328 GLU cc_start: 0.7848 (pt0) cc_final: 0.7591 (pt0)
REVERT: A  355 VAL cc_start: 0.9624 (p) cc_final: 0.9423 (p)
REVERT: A  356 LEU cc_start: 0.9072 (mp) cc_final: 0.8395 (tt)
REVERT: B   34 VAL cc_start: 0.8555 (m) cc_final: 0.8250 (m)
REVERT: B  205 ARG cc_start: 0.7621 (mmm160) cc_final: 0.6635 (mmt180)
REVERT: B  241 ASN cc_start: 0.8407 (p0) cc_final: 0.7810 (p0)
REVERT: B  243 MET cc_start: 0.8184 (tmm) cc_final: 0.7795 (tmm)
REVERT: B  247 MET cc_start: 0.8478 (mtt) cc_final: 0.8118 (mtt)
REVERT: B  265 ILE cc_start: 0.8290 (mm) cc_final: 0.8073 (mm)
REVERT: B  346 ASN cc_start: 0.8516 (t0) cc_final: 0.8196 (t0)
REVERT: B  347 ASN cc_start: 0.9009 (m-40) cc_final: 0.8756 (m-40)
  outliers start: 2
  outliers final: 0
  residues processed: 181
  average time/residue: 0.0606
  time to fit residues: 14.6071
Evaluate side-chains
  149 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 148
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0070
   chunk 17 optimal weight:    5.9990
   chunk 45 optimal weight:    0.0050
   chunk 26 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.8018

-------------------------------------------------------------------------------
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 = 0.3797 r_free = 0.3797 target = 0.129054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.100630 restraints weight = 12657.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.103453 restraints weight = 8414.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.105424 restraints weight = 6322.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.106930 restraints weight = 5175.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.107993 restraints weight = 4459.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.3858

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= 0.121
  Angle     :  0.679   8.268   7228  Z= 0.341
  Chirality :  0.041   0.145    831
  Planarity :  0.005   0.049    939
  Dihedral  :  5.171  21.437    730
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.40 %
    Favored  : 91.60 %
  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 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: -1.99 (0.33), residues: 655
  helix:  0.27 (0.29), residues: 343
  sheet: -3.22 (0.84), residues: 21
  loop : -3.28 (0.32), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  27 
 TYR   0.022   0.002   TYR A 151 
 PHE   0.022   0.002   PHE A 163 
 TRP   0.008   0.001   TRP A  66 
 HIS   0.005   0.001   HIS A 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 5340)
  covalent geometry    : angle       0.67934 ( 7228)
  hydrogen bonds       : bond        0.03352 (  230)
  hydrogen bonds       : angle       4.38866 (  678)

*********************** 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: 1
    poor density    : 171
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 ASP cc_start: 0.8464 (p0) cc_final: 0.8206 (p0)
REVERT: A   94 CYS cc_start: 0.8200 (p) cc_final: 0.7782 (p)
REVERT: A   97 ASP cc_start: 0.9396 (t70) cc_final: 0.9010 (t0)
REVERT: A  118 LEU cc_start: 0.9067 (mm) cc_final: 0.8838 (mm)
REVERT: A  151 TYR cc_start: 0.7135 (p90) cc_final: 0.5839 (p90)
REVERT: A  171 LEU cc_start: 0.9078 (mm) cc_final: 0.8663 (mt)
REVERT: A  233 ASP cc_start: 0.7879 (p0) cc_final: 0.7541 (p0)
REVERT: A  317 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7283 (mm-30)
REVERT: A  328 GLU cc_start: 0.7942 (pt0) cc_final: 0.7611 (pt0)
REVERT: B  205 ARG cc_start: 0.7658 (mmm160) cc_final: 0.6558 (mmt180)
REVERT: B  241 ASN cc_start: 0.8063 (p0) cc_final: 0.7493 (p0)
REVERT: B  247 MET cc_start: 0.8394 (mtt) cc_final: 0.8161 (mtt)
REVERT: B  346 ASN cc_start: 0.8535 (t0) cc_final: 0.8155 (t0)
REVERT: B  347 ASN cc_start: 0.9028 (m-40) cc_final: 0.8828 (m-40)
  outliers start: 1
  outliers final: 0
  residues processed: 171
  average time/residue: 0.0583
  time to fit residues: 13.3232
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  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 46 optimal weight:   20.0000
   chunk 33 optimal weight:    5.9990
   chunk 32 optimal weight:    0.0980
   chunk 2 optimal weight:    3.9990
   chunk 9 optimal weight:    7.9990
   chunk 7 optimal weight:    1.9990
   chunk 63 optimal weight:   10.0000
   chunk 48 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 229 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.125293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.096275 restraints weight = 12999.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.098931 restraints weight = 8780.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.100915 restraints weight = 6692.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.102282 restraints weight = 5522.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.103170 restraints weight = 4819.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.3933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5340  Z= 0.151
  Angle     :  0.697   8.096   7228  Z= 0.355
  Chirality :  0.043   0.153    831
  Planarity :  0.005   0.053    939
  Dihedral  :  5.258  22.951    730
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.63 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.60 %
    Favored  : 96.22 %
  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: -1.98 (0.33), residues: 655
  helix:  0.25 (0.29), residues: 343
  sheet: -3.62 (0.78), residues: 21
  loop : -3.21 (0.33), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 458 
 TYR   0.021   0.002   TYR A 151 
 PHE   0.024   0.002   PHE A 163 
 TRP   0.006   0.001   TRP A  66 
 HIS   0.003   0.001   HIS A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 5340)
  covalent geometry    : angle       0.69675 ( 7228)
  hydrogen bonds       : bond        0.03481 (  230)
  hydrogen bonds       : angle       4.52930 (  678)

*********************** 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
  161 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 160
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 ASP cc_start: 0.8381 (p0) cc_final: 0.8148 (p0)
REVERT: A   94 CYS cc_start: 0.8330 (p) cc_final: 0.7907 (p)
REVERT: A   97 ASP cc_start: 0.9390 (t70) cc_final: 0.8974 (t0)
REVERT: A  118 LEU cc_start: 0.9170 (mm) cc_final: 0.8887 (mm)
REVERT: A  125 VAL cc_start: 0.9327 (m) cc_final: 0.9060 (p)
REVERT: A  151 TYR cc_start: 0.7519 (p90) cc_final: 0.6187 (p90)
REVERT: A  233 ASP cc_start: 0.7960 (p0) cc_final: 0.7614 (p0)
REVERT: A  317 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7345 (mm-30)
REVERT: A  328 GLU cc_start: 0.7999 (pt0) cc_final: 0.7708 (pt0)
REVERT: A  356 LEU cc_start: 0.9083 (mp) cc_final: 0.8246 (mp)
REVERT: A  409 TYR cc_start: 0.6559 (t80) cc_final: 0.6015 (t80)
REVERT: B  205 ARG cc_start: 0.7671 (mmm160) cc_final: 0.6596 (mmt180)
REVERT: B  241 ASN cc_start: 0.7997 (p0) cc_final: 0.7740 (p0)
REVERT: B  243 MET cc_start: 0.7995 (tmm) cc_final: 0.7733 (tmm)
REVERT: B  244 HIS cc_start: 0.8548 (m90) cc_final: 0.8021 (m90)
REVERT: B  247 MET cc_start: 0.8453 (mtt) cc_final: 0.7974 (mtt)
REVERT: B  306 GLN cc_start: 0.9206 (mm110) cc_final: 0.8943 (mm110)
REVERT: B  311 ASN cc_start: 0.7193 (t0) cc_final: 0.6833 (m-40)
REVERT: B  340 THR cc_start: 0.9503 (m) cc_final: 0.9088 (t)
REVERT: B  346 ASN cc_start: 0.8492 (t0) cc_final: 0.8159 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 160
  average time/residue: 0.0595
  time to fit residues: 12.9238
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  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 36 optimal weight:    0.0980
   chunk 30 optimal weight:    5.9990
   chunk 37 optimal weight:    0.0970
   chunk 0 optimal weight:   10.0000
   chunk 55 optimal weight:    2.9990
   chunk 49 optimal weight:    7.9990
   chunk 34 optimal weight:    0.3980
   chunk 52 optimal weight:    6.9990
   chunk 53 optimal weight:    0.0970
   overall best weight:    0.2576

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

Flipped N/Q/H residues before XYZ refinement:
A 161 GLN
A 229 ASN
A 344 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.130616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.102198 restraints weight = 12661.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.105179 restraints weight = 8341.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.107202 restraints weight = 6218.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.108816 restraints weight = 5061.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.109881 restraints weight = 4341.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.4376

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= 0.118
  Angle     :  0.691   9.247   7228  Z= 0.343
  Chirality :  0.041   0.207    831
  Planarity :  0.005   0.053    939
  Dihedral  :  5.119  23.529    730
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  2.52 %
    Favored  : 97.30 %
  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: -1.90 (0.33), residues: 655
  helix:  0.28 (0.29), residues: 346
  sheet: -3.37 (0.86), residues: 21
  loop : -3.17 (0.33), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 348 
 TYR   0.023   0.002   TYR A 151 
 PHE   0.017   0.001   PHE A 163 
 TRP   0.009   0.001   TRP A  66 
 HIS   0.008   0.001   HIS A 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 5340)
  covalent geometry    : angle       0.69112 ( 7228)
  hydrogen bonds       : bond        0.03365 (  230)
  hydrogen bonds       : angle       4.32308 (  678)

*********************** 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
  172 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 171
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 CYS cc_start: 0.8319 (p) cc_final: 0.7891 (p)
REVERT: A   97 ASP cc_start: 0.9360 (t70) cc_final: 0.8965 (t0)
REVERT: A  118 LEU cc_start: 0.9120 (mm) cc_final: 0.8801 (mm)
REVERT: A  125 VAL cc_start: 0.9296 (m) cc_final: 0.9008 (p)
REVERT: A  151 TYR cc_start: 0.7447 (p90) cc_final: 0.6102 (p90)
REVERT: A  233 ASP cc_start: 0.7931 (p0) cc_final: 0.7550 (p0)
REVERT: A  328 GLU cc_start: 0.7902 (pt0) cc_final: 0.7686 (pt0)
REVERT: A  434 TYR cc_start: 0.6789 (m-10) cc_final: 0.6101 (m-80)
REVERT: B  241 ASN cc_start: 0.7640 (p0) cc_final: 0.7173 (p0)
REVERT: B  244 HIS cc_start: 0.8390 (m90) cc_final: 0.8118 (m90)
REVERT: B  247 MET cc_start: 0.8595 (mtt) cc_final: 0.8121 (mtm)
REVERT: B  311 ASN cc_start: 0.6998 (t0) cc_final: 0.6664 (m-40)
REVERT: B  340 THR cc_start: 0.9465 (m) cc_final: 0.9044 (t)
REVERT: B  346 ASN cc_start: 0.8462 (t0) cc_final: 0.7958 (t0)
REVERT: B  347 ASN cc_start: 0.9019 (m-40) cc_final: 0.8779 (m-40)
  outliers start: 1
  outliers final: 0
  residues processed: 171
  average time/residue: 0.0550
  time to fit residues: 12.8153
Evaluate side-chains
  137 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 60 optimal weight:    9.9990
   chunk 5 optimal weight:    5.9990
   chunk 27 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 64 optimal weight:    6.9990
   chunk 62 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9990
   chunk 58 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    1.5586

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.126574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.098515 restraints weight = 12769.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.101442 restraints weight = 8479.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.103484 restraints weight = 6336.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.105043 restraints weight = 5161.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.105858 restraints weight = 4438.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.4536

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= 0.137
  Angle     :  0.720   9.157   7228  Z= 0.357
  Chirality :  0.043   0.149    831
  Planarity :  0.005   0.051    939
  Dihedral  :  5.268  25.300    730
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  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: -1.78 (0.33), residues: 655
  helix:  0.44 (0.29), residues: 347
  sheet: -3.37 (0.88), residues: 21
  loop : -3.19 (0.33), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 458 
 TYR   0.024   0.002   TYR A 151 
 PHE   0.019   0.002   PHE A 163 
 TRP   0.006   0.001   TRP A  66 
 HIS   0.006   0.001   HIS A 273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 5340)
  covalent geometry    : angle       0.71983 ( 7228)
  hydrogen bonds       : bond        0.03474 (  230)
  hydrogen bonds       : angle       4.36624 (  678)

*********************** 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
  163 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 CYS cc_start: 0.8360 (p) cc_final: 0.7940 (p)
REVERT: A   97 ASP cc_start: 0.9398 (t70) cc_final: 0.8961 (t0)
REVERT: A  111 MET cc_start: 0.7512 (mmt) cc_final: 0.7304 (mmt)
REVERT: A  118 LEU cc_start: 0.9191 (mm) cc_final: 0.8926 (mm)
REVERT: A  125 VAL cc_start: 0.9343 (m) cc_final: 0.9114 (p)
REVERT: A  151 TYR cc_start: 0.7786 (p90) cc_final: 0.6372 (p90)
REVERT: A  224 LEU cc_start: 0.9534 (mt) cc_final: 0.9218 (mt)
REVERT: A  233 ASP cc_start: 0.7959 (p0) cc_final: 0.7598 (p0)
REVERT: A  247 TYR cc_start: 0.8592 (m-10) cc_final: 0.8302 (m-80)
REVERT: A  328 GLU cc_start: 0.7971 (pt0) cc_final: 0.7639 (pt0)
REVERT: A  434 TYR cc_start: 0.6419 (m-10) cc_final: 0.5667 (m-80)
REVERT: B  241 ASN cc_start: 0.7718 (p0) cc_final: 0.7217 (p0)
REVERT: B  244 HIS cc_start: 0.8387 (m90) cc_final: 0.7983 (m90)
REVERT: B  247 MET cc_start: 0.8338 (mtt) cc_final: 0.8059 (mtt)
REVERT: B  306 GLN cc_start: 0.9184 (mm110) cc_final: 0.8895 (mm110)
REVERT: B  311 ASN cc_start: 0.7102 (t0) cc_final: 0.6694 (m-40)
REVERT: B  340 THR cc_start: 0.9485 (m) cc_final: 0.9089 (t)
REVERT: B  346 ASN cc_start: 0.8532 (t0) cc_final: 0.8175 (t0)
REVERT: B  347 ASN cc_start: 0.9057 (m-40) cc_final: 0.8856 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.0582
  time to fit residues: 12.9127
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  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 47 optimal weight:    8.9990
   chunk 58 optimal weight:    0.0470
   chunk 38 optimal weight:    0.9980
   chunk 36 optimal weight:    7.9990
   chunk 54 optimal weight:    7.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.7278

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.129447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.101815 restraints weight = 12335.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.104832 restraints weight = 8089.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.106957 restraints weight = 5969.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.108425 restraints weight = 4808.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.109428 restraints weight = 4133.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.4719

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= 0.117
  Angle     :  0.697   8.610   7228  Z= 0.342
  Chirality :  0.042   0.162    831
  Planarity :  0.005   0.052    939
  Dihedral  :  5.081  27.026    730
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.55 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  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: -1.64 (0.33), residues: 655
  helix:  0.51 (0.29), residues: 345
  sheet: -3.09 (1.09), residues: 16
  loop : -3.08 (0.33), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 458 
 TYR   0.024   0.001   TYR A 151 
 PHE   0.016   0.001   PHE A 162 
 TRP   0.008   0.001   TRP A  66 
 HIS   0.013   0.001   HIS A 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 5340)
  covalent geometry    : angle       0.69696 ( 7228)
  hydrogen bonds       : bond        0.03344 (  230)
  hydrogen bonds       : angle       4.31153 (  678)

*********************** 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: 0
    poor density    : 169
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 CYS cc_start: 0.8364 (p) cc_final: 0.7932 (p)
REVERT: A   97 ASP cc_start: 0.9369 (t70) cc_final: 0.8914 (t0)
REVERT: A  118 LEU cc_start: 0.9155 (mm) cc_final: 0.8870 (mm)
REVERT: A  125 VAL cc_start: 0.9334 (m) cc_final: 0.9115 (p)
REVERT: A  151 TYR cc_start: 0.7766 (p90) cc_final: 0.6299 (p90)
REVERT: A  233 ASP cc_start: 0.7945 (p0) cc_final: 0.7564 (p0)
REVERT: A  323 THR cc_start: 0.6750 (m) cc_final: 0.6539 (t)
REVERT: A  328 GLU cc_start: 0.7851 (pt0) cc_final: 0.7622 (pt0)
REVERT: A  425 MET cc_start: 0.7858 (pmm) cc_final: 0.7492 (pmm)
REVERT: A  434 TYR cc_start: 0.6499 (m-10) cc_final: 0.5692 (m-80)
REVERT: B  205 ARG cc_start: 0.7834 (mmt180) cc_final: 0.7596 (mmt180)
REVERT: B  241 ASN cc_start: 0.7683 (p0) cc_final: 0.7015 (p0)
REVERT: B  244 HIS cc_start: 0.8427 (m90) cc_final: 0.8081 (m90)
REVERT: B  247 MET cc_start: 0.8398 (mtt) cc_final: 0.8071 (mtt)
REVERT: B  311 ASN cc_start: 0.6984 (t0) cc_final: 0.6568 (m-40)
REVERT: B  340 THR cc_start: 0.9477 (m) cc_final: 0.9082 (t)
REVERT: B  346 ASN cc_start: 0.8534 (t0) cc_final: 0.8053 (t0)
REVERT: B  347 ASN cc_start: 0.9027 (m-40) cc_final: 0.8759 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.0529
  time to fit residues: 12.2903
Evaluate side-chains
  140 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 63 optimal weight:    0.2980
   chunk 15 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 53 optimal weight:    6.9990
   chunk 62 optimal weight:    9.9990
   chunk 46 optimal weight:    0.0170
   chunk 13 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 42 optimal weight:    0.1980
   chunk 38 optimal weight:    4.9990
   overall best weight:    0.4820

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.131987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.103490 restraints weight = 12842.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.106656 restraints weight = 8360.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.108742 restraints weight = 6156.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.110452 restraints weight = 4978.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.111487 restraints weight = 4246.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.4970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   5340  Z= 0.117
  Angle     :  0.705   9.467   7228  Z= 0.345
  Chirality :  0.042   0.154    831
  Planarity :  0.005   0.051    939
  Dihedral  :  5.033  26.024    730
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.18 %
    Favored  : 99.64 %
  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: -1.70 (0.33), residues: 655
  helix:  0.46 (0.29), residues: 347
  sheet: -3.38 (0.90), residues: 21
  loop : -3.09 (0.33), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 458 
 TYR   0.024   0.001   TYR A 151 
 PHE   0.016   0.001   PHE A 162 
 TRP   0.008   0.001   TRP A  66 
 HIS   0.005   0.001   HIS A 273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 5340)
  covalent geometry    : angle       0.70520 ( 7228)
  hydrogen bonds       : bond        0.03400 (  230)
  hydrogen bonds       : angle       4.35084 (  678)

********************** 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
  171 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 170
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 ASP cc_start: 0.9364 (t70) cc_final: 0.8894 (t0)
REVERT: A  111 MET cc_start: 0.7447 (mmt) cc_final: 0.7107 (mmt)
REVERT: A  118 LEU cc_start: 0.9201 (mm) cc_final: 0.8952 (mm)
REVERT: A  125 VAL cc_start: 0.9345 (m) cc_final: 0.9136 (p)
REVERT: A  151 TYR cc_start: 0.7847 (p90) cc_final: 0.6442 (p90)
REVERT: A  224 LEU cc_start: 0.9587 (mt) cc_final: 0.9305 (mt)
REVERT: A  233 ASP cc_start: 0.7976 (p0) cc_final: 0.7601 (p0)
REVERT: A  328 GLU cc_start: 0.7776 (pt0) cc_final: 0.7571 (pt0)
REVERT: A  352 LYS cc_start: 0.8466 (tptp) cc_final: 0.7999 (tptp)
REVERT: A  356 LEU cc_start: 0.8968 (mp) cc_final: 0.7894 (tt)
REVERT: A  380 MET cc_start: 0.8598 (ptp) cc_final: 0.8224 (ptm)
REVERT: A  425 MET cc_start: 0.7886 (pmm) cc_final: 0.7515 (pmm)
REVERT: A  434 TYR cc_start: 0.6386 (m-10) cc_final: 0.5644 (m-80)
REVERT: B  241 ASN cc_start: 0.7694 (p0) cc_final: 0.7129 (p0)
REVERT: B  244 HIS cc_start: 0.8496 (m90) cc_final: 0.8232 (m90)
REVERT: B  247 MET cc_start: 0.8530 (mtt) cc_final: 0.8138 (mtt)
REVERT: B  277 LYS cc_start: 0.8852 (mppt) cc_final: 0.8594 (mmtm)
REVERT: B  340 THR cc_start: 0.9454 (m) cc_final: 0.9027 (t)
REVERT: B  347 ASN cc_start: 0.9014 (m-40) cc_final: 0.8798 (m-40)
  outliers start: 1
  outliers final: 0
  residues processed: 170
  average time/residue: 0.0551
  time to fit residues: 12.8368
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  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 47 optimal weight:    9.9990
   chunk 7 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0770
   chunk 64 optimal weight:    1.9990
   chunk 15 optimal weight:   10.0000
   chunk 41 optimal weight:    0.0970
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 37 optimal weight:    5.9990
   chunk 38 optimal weight:    7.9990
   overall best weight:    0.5738

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.133042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.104468 restraints weight = 12908.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.107669 restraints weight = 8441.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.109962 restraints weight = 6221.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.111622 restraints weight = 4985.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.112642 restraints weight = 4237.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.5154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5340  Z= 0.116
  Angle     :  0.696   7.896   7228  Z= 0.339
  Chirality :  0.042   0.179    831
  Planarity :  0.005   0.052    939
  Dihedral  :  5.035  27.078    730
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  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 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: -1.65 (0.33), residues: 655
  helix:  0.49 (0.29), residues: 351
  sheet: -3.08 (0.97), residues: 21
  loop : -3.13 (0.34), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 458 
 TYR   0.024   0.001   TYR A 151 
 PHE   0.015   0.001   PHE A 162 
 TRP   0.007   0.001   TRP A  66 
 HIS   0.005   0.001   HIS A 273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 5340)
  covalent geometry    : angle       0.69613 ( 7228)
  hydrogen bonds       : bond        0.03405 (  230)
  hydrogen bonds       : angle       4.37026 (  678)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1011.08 seconds
wall clock time: 18 minutes 5.55 seconds (1085.55 seconds total)