Starting phenix.real_space_refine
on Tue Feb 11 10:15:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vu8_21388/02_2025/6vu8_21388.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vu8_21388/02_2025/6vu8_21388.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vu8_21388/02_2025/6vu8_21388.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vu8_21388/02_2025/6vu8_21388.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vu8_21388/02_2025/6vu8_21388.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vu8_21388/02_2025/6vu8_21388.cif"
  }
  resolution = 4.14
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      30      5.16       5
     C    3313      2.51       5
     N     913      2.21       5
     O     991      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5249
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 485, 3815
          Classifications: {'peptide': 485}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 23, 'TRANS': 461}
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 31
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'TPO:plan-1': 1, 'ASN:plan1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "B"
      Number of atoms: 1434
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 1434
          Classifications: {'peptide': 184}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 2, 'TRANS': 181}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 58
          Unresolved non-hydrogen angles: 68
          Unresolved non-hydrogen dihedrals: 48
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 20
  Time building chain proxies: 3.57, per 1000 atoms: 0.68
  Number of scatterers: 5249
  At special positions: 0
  Unit cell: (118.72, 64.66, 87.98, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     P       2     15.00
     O     991      8.00
     N     913      7.00
     C    3313      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.32
  Conformation dependent library (CDL) restraints added in 640.7 milliseconds
  

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

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

    230 hydrogen bonds defined for protein.
    678 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.22

  Time building geometry restraints manager: 1.54 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:             0.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     15.690
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.104   5340  Z= 0.386
  Angle     :  1.053  13.846   7228  Z= 0.553
  Chirality :  0.054   0.336    831
  Planarity :  0.007   0.065    939
  Dihedral  : 16.207  89.443   1986
  Min Nonbonded Distance : 2.262

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

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

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

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

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.670 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 ASP cc_start: 0.8585 (p0) cc_final: 0.8345 (p0)
REVERT: A   27 ARG cc_start: 0.9105 (ptm160) cc_final: 0.8624 (ttp-110)
REVERT: A   66 TRP cc_start: 0.8568 (m-90) cc_final: 0.8303 (m-90)
REVERT: A   97 ASP cc_start: 0.9469 (t70) cc_final: 0.9202 (t0)
REVERT: A  151 TYR cc_start: 0.8069 (p90) cc_final: 0.7860 (p90)
REVERT: A  162 PHE cc_start: 0.9119 (t80) cc_final: 0.8542 (t80)
REVERT: A  169 PHE cc_start: 0.8987 (t80) cc_final: 0.8728 (t80)
REVERT: A  194 ASP cc_start: 0.9081 (m-30) cc_final: 0.8442 (m-30)
REVERT: A  197 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8405 (mp0)
REVERT: A  222 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8270 (mt-10)
REVERT: A  233 ASP cc_start: 0.8003 (p0) cc_final: 0.7739 (p0)
REVERT: A  247 TYR cc_start: 0.8494 (m-80) cc_final: 0.8160 (m-80)
REVERT: A  259 MET cc_start: 0.8229 (mmt) cc_final: 0.7968 (mmp)
REVERT: A  328 GLU cc_start: 0.8336 (pt0) cc_final: 0.7983 (pt0)
REVERT: A  352 LYS cc_start: 0.8627 (tptp) cc_final: 0.8418 (tptp)
REVERT: A  356 LEU cc_start: 0.8773 (mp) cc_final: 0.7719 (mp)
REVERT: B  205 ARG cc_start: 0.7434 (mmm160) cc_final: 0.6504 (mmt180)
REVERT: B  241 ASN cc_start: 0.8572 (p0) cc_final: 0.7384 (p0)
REVERT: B  242 ARG cc_start: 0.8631 (mtt180) cc_final: 0.8375 (mtp180)
REVERT: B  243 MET cc_start: 0.8217 (ppp) cc_final: 0.7900 (tmm)
REVERT: B  244 HIS cc_start: 0.8743 (m-70) cc_final: 0.8320 (m-70)
REVERT: B  247 MET cc_start: 0.8695 (mtt) cc_final: 0.8228 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.1699
  time to fit residues: 38.4913
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  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 55 optimal weight:   10.0000
   chunk 50 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 59 optimal weight:    0.0980
   overall best weight:    0.7180

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

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

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.126386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.098980 restraints weight = 12528.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.101834 restraints weight = 8223.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.103847 restraints weight = 6122.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.2095

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

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

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

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

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

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 177
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.7345 (mp0) cc_final: 0.7145 (pm20)
REVERT: A   16 ASP cc_start: 0.8549 (p0) cc_final: 0.8273 (p0)
REVERT: A   66 TRP cc_start: 0.8530 (m-90) cc_final: 0.8311 (m-90)
REVERT: A   90 HIS cc_start: 0.8720 (OUTLIER) cc_final: 0.8353 (t-90)
REVERT: A   97 ASP cc_start: 0.9394 (t70) cc_final: 0.8997 (t0)
REVERT: A  151 TYR cc_start: 0.7065 (p90) cc_final: 0.5493 (p90)
REVERT: A  163 PHE cc_start: 0.9178 (m-80) cc_final: 0.8921 (m-80)
REVERT: A  191 LEU cc_start: 0.9016 (pp) cc_final: 0.8553 (pp)
REVERT: A  194 ASP cc_start: 0.8817 (m-30) cc_final: 0.8505 (m-30)
REVERT: A  197 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8187 (mt-10)
REVERT: A  221 MET cc_start: 0.8563 (tpt) cc_final: 0.7871 (tpt)
REVERT: A  233 ASP cc_start: 0.7800 (p0) cc_final: 0.7478 (p0)
REVERT: A  247 TYR cc_start: 0.8387 (m-80) cc_final: 0.8031 (m-10)
REVERT: A  328 GLU cc_start: 0.8080 (pt0) cc_final: 0.7856 (pt0)
REVERT: A  356 LEU cc_start: 0.9031 (mp) cc_final: 0.8128 (mp)
REVERT: A  396 PHE cc_start: 0.8160 (t80) cc_final: 0.7815 (t80)
REVERT: B  205 ARG cc_start: 0.7765 (mmm160) cc_final: 0.6545 (mmt180)
REVERT: B  241 ASN cc_start: 0.8564 (p0) cc_final: 0.6902 (p0)
REVERT: B  244 HIS cc_start: 0.8740 (m-70) cc_final: 0.8220 (m-70)
REVERT: B  247 MET cc_start: 0.8395 (mtt) cc_final: 0.8043 (mtt)
REVERT: B  311 ASN cc_start: 0.7332 (t0) cc_final: 0.7046 (t0)
REVERT: B  340 THR cc_start: 0.9508 (m) cc_final: 0.9083 (t)
  outliers start: 2
  outliers final: 0
  residues processed: 178
  average time/residue: 0.1526
  time to fit residues: 36.0845
Evaluate side-chains
  143 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 142
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 51 optimal weight:   20.0000
   chunk 57 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 54 optimal weight:    7.9990
   chunk 46 optimal weight:    0.0030
   chunk 5 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9980
   chunk 33 optimal weight:    0.4980
   chunk 14 optimal weight:    0.0060
   overall best weight:    0.7008

-------------------------------------------------------------------------------
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 = 0.3775 r_free = 0.3775 target = 0.127939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.100237 restraints weight = 12708.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.103100 restraints weight = 8277.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.105202 restraints weight = 6180.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.2841

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= 0.173
  Angle     :  0.656   8.419   7228  Z= 0.332
  Chirality :  0.040   0.192    831
  Planarity :  0.005   0.067    939
  Dihedral  :  5.618  23.506    730
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.24 %
    Favored  : 91.76 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.61 (0.31), residues: 655
  helix: -0.32 (0.28), residues: 343
  sheet: -3.48 (0.92), residues: 21
  loop : -3.45 (0.31), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 258 
 HIS   0.010   0.001   HIS A  90 
 PHE   0.013   0.001   PHE A 163 
 TYR   0.024   0.002   TYR A 434 
 ARG   0.006   0.000   ARG A 458 

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

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 182
  time to evaluate  : 0.639 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 CYS cc_start: 0.8014 (p) cc_final: 0.7686 (p)
REVERT: A   97 ASP cc_start: 0.9387 (t70) cc_final: 0.9071 (t0)
REVERT: A  118 LEU cc_start: 0.9090 (mm) cc_final: 0.8865 (mm)
REVERT: A  151 TYR cc_start: 0.7064 (p90) cc_final: 0.5689 (p90)
REVERT: A  221 MET cc_start: 0.8581 (tpt) cc_final: 0.7916 (tpt)
REVERT: A  233 ASP cc_start: 0.7843 (p0) cc_final: 0.7498 (p0)
REVERT: A  247 TYR cc_start: 0.8484 (m-80) cc_final: 0.8056 (m-80)
REVERT: A  317 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7381 (mm-30)
REVERT: A  328 GLU cc_start: 0.8063 (pt0) cc_final: 0.7816 (pt0)
REVERT: B  205 ARG cc_start: 0.7780 (mmm160) cc_final: 0.6681 (mmt180)
REVERT: B  241 ASN cc_start: 0.8598 (p0) cc_final: 0.7994 (p0)
REVERT: B  243 MET cc_start: 0.8123 (tmm) cc_final: 0.7630 (tmm)
REVERT: B  244 HIS cc_start: 0.8700 (m-70) cc_final: 0.8194 (m-70)
REVERT: B  247 MET cc_start: 0.8521 (mtt) cc_final: 0.8248 (mtt)
REVERT: B  354 PHE cc_start: 0.6955 (p90) cc_final: 0.6539 (p90)
  outliers start: 2
  outliers final: 0
  residues processed: 182
  average time/residue: 0.1589
  time to fit residues: 38.5030
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  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 47 optimal weight:    8.9990
   chunk 13 optimal weight:   10.0000
   chunk 8 optimal weight:    0.5980
   chunk 38 optimal weight:    6.9990
   chunk 45 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 17 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9990
   chunk 29 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.8184

-------------------------------------------------------------------------------
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
B 294 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.128522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.099894 restraints weight = 12746.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.102804 restraints weight = 8353.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.104891 restraints weight = 6249.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.3313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5340  Z= 0.180
  Angle     :  0.655   8.289   7228  Z= 0.328
  Chirality :  0.040   0.189    831
  Planarity :  0.005   0.053    939
  Dihedral  :  5.319  22.843    730
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.63 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  4.50 %
    Favored  : 94.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.23 (0.32), residues: 655
  helix:  0.08 (0.29), residues: 343
  sheet: -3.48 (0.91), residues: 21
  loop : -3.39 (0.31), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  66 
 HIS   0.007   0.001   HIS A  90 
 PHE   0.018   0.002   PHE A 162 
 TYR   0.021   0.002   TYR A 151 
 ARG   0.006   0.000   ARG B 313 

*********************** 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
  181 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 178
  time to evaluate  : 0.597 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 CYS cc_start: 0.8145 (p) cc_final: 0.7756 (p)
REVERT: A   97 ASP cc_start: 0.9397 (t70) cc_final: 0.9022 (t0)
REVERT: A  118 LEU cc_start: 0.9095 (mm) cc_final: 0.8780 (mm)
REVERT: A  151 TYR cc_start: 0.7136 (p90) cc_final: 0.5824 (p90)
REVERT: A  229 ASN cc_start: 0.8627 (OUTLIER) cc_final: 0.8205 (t0)
REVERT: A  233 ASP cc_start: 0.7888 (p0) cc_final: 0.7575 (p0)
REVERT: A  247 TYR cc_start: 0.8532 (m-80) cc_final: 0.8184 (m-80)
REVERT: A  317 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7391 (mm-30)
REVERT: A  328 GLU cc_start: 0.8056 (pt0) cc_final: 0.7736 (pt0)
REVERT: B  205 ARG cc_start: 0.7583 (mmm160) cc_final: 0.6517 (mmt180)
REVERT: B  241 ASN cc_start: 0.8534 (p0) cc_final: 0.7858 (p0)
REVERT: B  243 MET cc_start: 0.8139 (tmm) cc_final: 0.7635 (tmm)
REVERT: B  244 HIS cc_start: 0.8659 (m-70) cc_final: 0.8323 (m-70)
REVERT: B  247 MET cc_start: 0.8433 (mtt) cc_final: 0.7968 (mtt)
REVERT: B  346 ASN cc_start: 0.8454 (t0) cc_final: 0.8006 (t0)
REVERT: B  347 ASN cc_start: 0.9025 (m-40) cc_final: 0.8777 (m-40)
  outliers start: 3
  outliers final: 0
  residues processed: 179
  average time/residue: 0.1521
  time to fit residues: 35.5201
Evaluate side-chains
  146 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 49 optimal weight:    8.9990
   chunk 10 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 50 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0170
   chunk 21 optimal weight:    6.9990
   chunk 53 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.9622

-------------------------------------------------------------------------------
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 = 0.3788 r_free = 0.3788 target = 0.128216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.099402 restraints weight = 12815.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.102251 restraints weight = 8555.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.104310 restraints weight = 6447.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.3630

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= 0.183
  Angle     :  0.673   8.252   7228  Z= 0.338
  Chirality :  0.041   0.157    831
  Planarity :  0.005   0.050    939
  Dihedral  :  5.190  22.006    730
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.05 (0.32), residues: 655
  helix:  0.28 (0.29), residues: 342
  sheet: -3.21 (0.92), residues: 21
  loop : -3.40 (0.31), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  66 
 HIS   0.005   0.001   HIS A  90 
 PHE   0.021   0.002   PHE A 163 
 TYR   0.031   0.002   TYR A 434 
 ARG   0.008   0.001   ARG A  27 

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

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.590 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 ASP cc_start: 0.8478 (p0) cc_final: 0.8235 (p0)
REVERT: A   94 CYS cc_start: 0.8265 (p) cc_final: 0.7842 (p)
REVERT: A   97 ASP cc_start: 0.9399 (t70) cc_final: 0.9028 (t0)
REVERT: A  111 MET cc_start: 0.7696 (mmt) cc_final: 0.7448 (mmt)
REVERT: A  118 LEU cc_start: 0.9126 (mm) cc_final: 0.8859 (mm)
REVERT: A  151 TYR cc_start: 0.7270 (p90) cc_final: 0.5886 (p90)
REVERT: A  171 LEU cc_start: 0.9001 (mm) cc_final: 0.8648 (mt)
REVERT: A  233 ASP cc_start: 0.7905 (p0) cc_final: 0.7578 (p0)
REVERT: A  247 TYR cc_start: 0.8594 (m-80) cc_final: 0.8255 (m-80)
REVERT: A  317 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7276 (mm-30)
REVERT: A  328 GLU cc_start: 0.7907 (pt0) cc_final: 0.7636 (pt0)
REVERT: B  205 ARG cc_start: 0.7613 (mmm160) cc_final: 0.6459 (mmt180)
REVERT: B  243 MET cc_start: 0.8029 (tmm) cc_final: 0.7579 (tmm)
REVERT: B  244 HIS cc_start: 0.8789 (m-70) cc_final: 0.8450 (m-70)
REVERT: B  311 ASN cc_start: 0.7253 (t0) cc_final: 0.6895 (m-40)
REVERT: B  346 ASN cc_start: 0.8497 (t0) cc_final: 0.8203 (t0)
REVERT: B  347 ASN cc_start: 0.9026 (m-40) cc_final: 0.8806 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.1492
  time to fit residues: 34.7182
Evaluate side-chains
  134 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 47 optimal weight:    8.9990
   chunk 1 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   chunk 40 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.1184

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.127903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.098877 restraints weight = 12812.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.101616 restraints weight = 8577.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.103655 restraints weight = 6547.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.3831

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= 0.193
  Angle     :  0.675   8.093   7228  Z= 0.338
  Chirality :  0.042   0.195    831
  Planarity :  0.005   0.054    939
  Dihedral  :  5.170  25.567    730
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 12.67
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.88 (0.32), residues: 655
  helix:  0.41 (0.29), residues: 342
  sheet: -3.15 (0.92), residues: 21
  loop : -3.29 (0.32), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  66 
 HIS   0.004   0.001   HIS A 273 
 PHE   0.023   0.002   PHE A 163 
 TYR   0.028   0.002   TYR A 434 
 ARG   0.008   0.000   ARG B  32 

*********************** 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
  173 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 172
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 ASP cc_start: 0.8369 (p0) cc_final: 0.8135 (p0)
REVERT: A   94 CYS cc_start: 0.8294 (p) cc_final: 0.7836 (p)
REVERT: A   97 ASP cc_start: 0.9416 (t70) cc_final: 0.9032 (t0)
REVERT: A  118 LEU cc_start: 0.9157 (mm) cc_final: 0.8840 (mm)
REVERT: A  151 TYR cc_start: 0.7425 (p90) cc_final: 0.6098 (p90)
REVERT: A  233 ASP cc_start: 0.7940 (p0) cc_final: 0.7624 (p0)
REVERT: A  247 TYR cc_start: 0.8612 (m-80) cc_final: 0.8347 (m-80)
REVERT: A  317 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7227 (mm-30)
REVERT: A  328 GLU cc_start: 0.7952 (pt0) cc_final: 0.7618 (pt0)
REVERT: B  205 ARG cc_start: 0.7566 (mmm160) cc_final: 0.6490 (mmt180)
REVERT: B  241 ASN cc_start: 0.8440 (p0) cc_final: 0.7896 (p0)
REVERT: B  243 MET cc_start: 0.7990 (tmm) cc_final: 0.7446 (tmm)
REVERT: B  244 HIS cc_start: 0.8753 (m-70) cc_final: 0.8445 (m-70)
REVERT: B  311 ASN cc_start: 0.7206 (t0) cc_final: 0.6819 (m-40)
REVERT: B  346 ASN cc_start: 0.8500 (t0) cc_final: 0.8120 (t0)
REVERT: B  347 ASN cc_start: 0.9040 (m-40) cc_final: 0.8787 (m-40)
  outliers start: 1
  outliers final: 0
  residues processed: 172
  average time/residue: 0.1504
  time to fit residues: 34.6036
Evaluate side-chains
  130 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 32 optimal weight:    9.9990
   chunk 40 optimal weight:    0.0030
   chunk 19 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    5.9990
   chunk 8 optimal weight:    0.0050
   overall best weight:    0.5004

-------------------------------------------------------------------------------
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 306 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.130381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.101498 restraints weight = 12622.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.104476 restraints weight = 8345.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.106623 restraints weight = 6229.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.4223

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= 0.178
  Angle     :  0.700   9.113   7228  Z= 0.342
  Chirality :  0.042   0.198    831
  Planarity :  0.005   0.052    939
  Dihedral  :  5.116  27.161    730
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.40 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  2.16 %
    Favored  : 97.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.32), residues: 655
  helix:  0.52 (0.29), residues: 342
  sheet: -3.14 (0.92), residues: 21
  loop : -3.27 (0.31), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  66 
 HIS   0.008   0.001   HIS A 344 
 PHE   0.018   0.001   PHE A 163 
 TYR   0.023   0.002   TYR A 151 
 ARG   0.008   0.000   ARG A 458 

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

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 172
  time to evaluate  : 0.634 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 CYS cc_start: 0.8300 (p) cc_final: 0.7847 (p)
REVERT: A   97 ASP cc_start: 0.9391 (t70) cc_final: 0.8966 (t0)
REVERT: A  118 LEU cc_start: 0.9119 (mm) cc_final: 0.8831 (mm)
REVERT: A  151 TYR cc_start: 0.7469 (p90) cc_final: 0.6124 (p90)
REVERT: A  233 ASP cc_start: 0.7961 (p0) cc_final: 0.7569 (p0)
REVERT: A  317 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7190 (mm-30)
REVERT: A  328 GLU cc_start: 0.7887 (pt0) cc_final: 0.7556 (pt0)
REVERT: B  205 ARG cc_start: 0.7613 (mmm160) cc_final: 0.6539 (mmt180)
REVERT: B  243 MET cc_start: 0.7779 (tmm) cc_final: 0.7286 (tmm)
REVERT: B  244 HIS cc_start: 0.8668 (m-70) cc_final: 0.8404 (m-70)
REVERT: B  265 ILE cc_start: 0.8096 (mm) cc_final: 0.7841 (mm)
REVERT: B  311 ASN cc_start: 0.6998 (t0) cc_final: 0.6638 (m-40)
REVERT: B  340 THR cc_start: 0.9469 (m) cc_final: 0.9035 (t)
REVERT: B  346 ASN cc_start: 0.8476 (t0) cc_final: 0.8149 (t0)
REVERT: B  347 ASN cc_start: 0.8992 (m-40) cc_final: 0.8763 (m-40)
  outliers start: 2
  outliers final: 0
  residues processed: 172
  average time/residue: 0.1455
  time to fit residues: 33.4152
Evaluate side-chains
  132 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 46 optimal weight:   10.0000
   chunk 39 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 42 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.3810 r_free = 0.3810 target = 0.129515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.101085 restraints weight = 12502.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.104025 restraints weight = 8293.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.106103 restraints weight = 6233.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.4491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5340  Z= 0.193
  Angle     :  0.700   8.160   7228  Z= 0.346
  Chirality :  0.042   0.148    831
  Planarity :  0.004   0.050    939
  Dihedral  :  5.179  27.760    730
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 13.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.26 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.33), residues: 655
  helix:  0.54 (0.29), residues: 346
  sheet: -3.32 (0.85), residues: 21
  loop : -3.24 (0.31), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  66 
 HIS   0.005   0.001   HIS A  90 
 PHE   0.015   0.001   PHE A 163 
 TYR   0.024   0.002   TYR A 151 
 ARG   0.005   0.000   ARG A 348 

*********************** 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
  169 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 168
  time to evaluate  : 0.616 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 CYS cc_start: 0.8354 (p) cc_final: 0.7914 (p)
REVERT: A   97 ASP cc_start: 0.9382 (t70) cc_final: 0.8962 (t0)
REVERT: A  118 LEU cc_start: 0.9122 (mm) cc_final: 0.8839 (mm)
REVERT: A  151 TYR cc_start: 0.7776 (p90) cc_final: 0.6364 (p90)
REVERT: A  233 ASP cc_start: 0.7945 (p0) cc_final: 0.7549 (p0)
REVERT: A  328 GLU cc_start: 0.7858 (pt0) cc_final: 0.7526 (pt0)
REVERT: A  356 LEU cc_start: 0.8686 (mp) cc_final: 0.8264 (tt)
REVERT: B  265 ILE cc_start: 0.8199 (mm) cc_final: 0.7953 (mm)
REVERT: B  311 ASN cc_start: 0.6932 (t0) cc_final: 0.6606 (m-40)
REVERT: B  340 THR cc_start: 0.9479 (m) cc_final: 0.9054 (t)
REVERT: B  346 ASN cc_start: 0.8502 (t0) cc_final: 0.8131 (t0)
REVERT: B  347 ASN cc_start: 0.9019 (m-40) cc_final: 0.8788 (m-40)
  outliers start: 1
  outliers final: 0
  residues processed: 168
  average time/residue: 0.1475
  time to fit residues: 32.8795
Evaluate side-chains
  134 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 32 optimal weight:    0.5980
   chunk 43 optimal weight:    9.9990
   chunk 18 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 46 optimal weight:    9.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 229 ASN
** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.130146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.101733 restraints weight = 12890.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.104731 restraints weight = 8466.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.106898 restraints weight = 6322.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.4665

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= 0.188
  Angle     :  0.705   8.892   7228  Z= 0.348
  Chirality :  0.043   0.152    831
  Planarity :  0.005   0.051    939
  Dihedral  :  5.162  29.589    730
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 13.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.08 %
    Favored  : 98.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.33), residues: 655
  helix:  0.52 (0.29), residues: 343
  sheet: -3.13 (0.88), residues: 21
  loop : -3.12 (0.32), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  66 
 HIS   0.014   0.001   HIS A 344 
 PHE   0.014   0.001   PHE A 163 
 TYR   0.024   0.002   TYR A 151 
 ARG   0.005   0.000   ARG A 348 

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

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 166
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 CYS cc_start: 0.8407 (p) cc_final: 0.7956 (p)
REVERT: A   97 ASP cc_start: 0.9451 (t70) cc_final: 0.9055 (t0)
REVERT: A  118 LEU cc_start: 0.9152 (mm) cc_final: 0.8578 (mm)
REVERT: A  125 VAL cc_start: 0.9354 (m) cc_final: 0.9151 (p)
REVERT: A  151 TYR cc_start: 0.7833 (p90) cc_final: 0.6380 (p90)
REVERT: A  224 LEU cc_start: 0.9586 (mt) cc_final: 0.9309 (mt)
REVERT: A  233 ASP cc_start: 0.8013 (p0) cc_final: 0.7635 (p0)
REVERT: A  328 GLU cc_start: 0.7829 (pt0) cc_final: 0.7620 (pt0)
REVERT: A  356 LEU cc_start: 0.8870 (mp) cc_final: 0.8447 (tt)
REVERT: B  241 ASN cc_start: 0.7948 (p0) cc_final: 0.7686 (p0)
REVERT: B  244 HIS cc_start: 0.8254 (m-70) cc_final: 0.7787 (m-70)
REVERT: B  247 MET cc_start: 0.8316 (mtt) cc_final: 0.8022 (mtt)
REVERT: B  272 ASP cc_start: 0.8453 (p0) cc_final: 0.8173 (p0)
REVERT: B  275 GLU cc_start: 0.8320 (mp0) cc_final: 0.8016 (mp0)
REVERT: B  277 LYS cc_start: 0.8894 (mppt) cc_final: 0.8646 (mmtm)
REVERT: B  311 ASN cc_start: 0.7156 (t0) cc_final: 0.6631 (m-40)
REVERT: B  340 THR cc_start: 0.9488 (m) cc_final: 0.9039 (t)
REVERT: B  346 ASN cc_start: 0.8506 (t0) cc_final: 0.8046 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 166
  average time/residue: 0.1473
  time to fit residues: 33.1915
Evaluate side-chains
  134 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 24 optimal weight:    6.9990
   chunk 55 optimal weight:    1.9990
   chunk 59 optimal weight:    7.9990
   chunk 61 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    5.9990
   chunk 15 optimal weight:   10.0000
   chunk 32 optimal weight:    0.1980
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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 = 0.3810 r_free = 0.3810 target = 0.129298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.101421 restraints weight = 12456.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.104361 restraints weight = 8229.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.106338 restraints weight = 6169.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.4769

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= 0.196
  Angle     :  0.725   9.021   7228  Z= 0.357
  Chirality :  0.043   0.152    831
  Planarity :  0.005   0.053    939
  Dihedral  :  5.220  27.171    730
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.54 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (0.32), residues: 655
  helix:  0.55 (0.29), residues: 342
  sheet: -2.70 (1.10), residues: 16
  loop : -3.07 (0.32), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  66 
 HIS   0.009   0.001   HIS B 244 
 PHE   0.013   0.001   PHE A 163 
 TYR   0.024   0.002   TYR A 151 
 ARG   0.005   0.000   ARG A 348 

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

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 170
  time to evaluate  : 0.608 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 CYS cc_start: 0.8429 (p) cc_final: 0.7970 (p)
REVERT: A   97 ASP cc_start: 0.9456 (t70) cc_final: 0.9038 (t0)
REVERT: A  118 LEU cc_start: 0.9118 (mm) cc_final: 0.8541 (mm)
REVERT: A  151 TYR cc_start: 0.7832 (p90) cc_final: 0.6400 (p90)
REVERT: A  224 LEU cc_start: 0.9599 (mt) cc_final: 0.9329 (mt)
REVERT: A  233 ASP cc_start: 0.7954 (p0) cc_final: 0.7586 (p0)
REVERT: A  328 GLU cc_start: 0.7922 (pt0) cc_final: 0.7701 (pt0)
REVERT: A  356 LEU cc_start: 0.8965 (mp) cc_final: 0.8493 (tt)
REVERT: A  377 VAL cc_start: 0.8775 (m) cc_final: 0.8541 (m)
REVERT: A  380 MET cc_start: 0.8687 (ptp) cc_final: 0.8270 (ptm)
REVERT: A  425 MET cc_start: 0.7870 (pmm) cc_final: 0.7480 (pmm)
REVERT: B  205 ARG cc_start: 0.7810 (mmt180) cc_final: 0.7556 (mmt180)
REVERT: B  241 ASN cc_start: 0.7935 (p0) cc_final: 0.7497 (p0)
REVERT: B  244 HIS cc_start: 0.8309 (m-70) cc_final: 0.8101 (m90)
REVERT: B  247 MET cc_start: 0.8300 (mtt) cc_final: 0.8009 (mtt)
REVERT: B  265 ILE cc_start: 0.8208 (mm) cc_final: 0.7969 (mm)
REVERT: B  277 LYS cc_start: 0.8884 (mppt) cc_final: 0.8641 (mmtm)
REVERT: B  311 ASN cc_start: 0.7008 (t0) cc_final: 0.6552 (m-40)
REVERT: B  340 THR cc_start: 0.9498 (m) cc_final: 0.9065 (t)
REVERT: B  346 ASN cc_start: 0.8515 (t0) cc_final: 0.8085 (t0)
REVERT: B  347 ASN cc_start: 0.9024 (m-40) cc_final: 0.8795 (m-40)
  outliers start: 1
  outliers final: 0
  residues processed: 170
  average time/residue: 0.1318
  time to fit residues: 30.1684
Evaluate side-chains
  139 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 1 optimal weight:    0.8980
   chunk 62 optimal weight:    0.0000
   chunk 2 optimal weight:    0.9990
   chunk 3 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9990
   chunk 26 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 41 optimal weight:    0.7980
   chunk 5 optimal weight:    5.9990
   chunk 50 optimal weight:    4.9990
   overall best weight:    0.7388

-------------------------------------------------------------------------------
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**
A 344 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.131290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.103837 restraints weight = 12055.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.106820 restraints weight = 7894.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.109066 restraints weight = 5850.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.4930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5340  Z= 0.185
  Angle     :  0.723   8.931   7228  Z= 0.354
  Chirality :  0.042   0.136    831
  Planarity :  0.005   0.057    939
  Dihedral  :  5.092  28.069    730
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.24 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  0.18 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.32), residues: 655
  helix:  0.48 (0.29), residues: 346
  sheet: -3.18 (0.88), residues: 21
  loop : -3.07 (0.32), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  66 
 HIS   0.009   0.001   HIS B 244 
 PHE   0.013   0.001   PHE A 301 
 TYR   0.024   0.002   TYR A 151 
 ARG   0.005   0.000   ARG A 348 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1942.17 seconds
wall clock time: 35 minutes 27.30 seconds (2127.30 seconds total)