Starting phenix.real_space_refine
on Tue Feb 11 21:11:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dv2_27731/02_2025/8dv2_27731.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dv2_27731/02_2025/8dv2_27731.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dv2_27731/02_2025/8dv2_27731.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dv2_27731/02_2025/8dv2_27731.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dv2_27731/02_2025/8dv2_27731.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dv2_27731/02_2025/8dv2_27731.cif"
  }
  resolution = 3.5
  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=   0.001 sd=   0.029
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: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    4186      2.51       5
     N    1075      2.21       5
     O    1247      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: 6545
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1590
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1590
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 11, 'TRANS': 189}
    Chain: "D"
      Number of atoms: 4857
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 595, 4857
          Classifications: {'peptide': 595}
          Link IDs: {'PTRANS': 27, 'TRANS': 567}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 6.10, per 1000 atoms: 0.93
  Number of scatterers: 6545
  At special positions: 0
  Unit cell: (76.608, 88.704, 122.976, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O    1247      8.00
     N    1075      7.00
     C    4186      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 133 " - pdb=" SG  CYS D 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 344 " - pdb=" SG  CYS D 361 " distance=2.06
    Simple disulfide: pdb=" SG  CYS D 530 " - pdb=" SG  CYS D 542 " distance=2.02

  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
  Links applied
    NAG-ASN
      " NAG A1301 " - " ASN A 343 "
      " NAG D1101 " - " ASN D 322 "
      " NAG D1102 " - " ASN D 103 "
      " NAG D1103 " - " ASN D 432 "
      " NAG D1104 " - " ASN D 546 "
      " NAG D1105 " - " ASN D  90 "
      " NAG D1106 " - " ASN D  53 "
  Time building additional restraints: 1.61
  Conformation dependent library (CDL) restraints added in 957.4 milliseconds
  

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1498

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 7 sheets defined
      57.2% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 349 through 353
      removed outlier: 3.623A  pdb=" N   TRP A 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 370
    Processing helix  chain 'A' and resid 386 through 389
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.367A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
      removed outlier: 3.645A  pdb=" N   TYR A 421 " --> pdb=" O   LYS A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'D' and resid 22 through 53
      removed outlier: 4.268A  pdb=" N   ASP D  38 " --> pdb=" O   ILE D  34 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 80
    Processing helix  chain 'D' and resid 81 through 83
      No H-bonds generated for 'chain 'D' and resid 81 through 83'
    Processing helix  chain 'D' and resid 84 through 88
    Processing helix  chain 'D' and resid 90 through 101
    Processing helix  chain 'D' and resid 109 through 129
    Processing helix  chain 'D' and resid 147 through 155
    Processing helix  chain 'D' and resid 157 through 170
      removed outlier: 3.605A  pdb=" N   TRP D 168 " --> pdb=" O   ALA D 164 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ARG D 169 " --> pdb=" O   TRP D 165 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 171 through 194
      Proline residue:  D 178  - end of helix
      removed outlier: 3.790A  pdb=" N   GLU D 182 " --> pdb=" O   PRO D 178 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 198 through 205
    Processing helix  chain 'D' and resid 206 through 208
      No H-bonds generated for 'chain 'D' and resid 206 through 208'
    Processing helix  chain 'D' and resid 219 through 249
      removed outlier: 4.248A  pdb=" N   ILE D 223 " --> pdb=" O   ARG D 219 " (cutoff:3.500A)
      Proline residue:  D 235  - end of helix
    Processing helix  chain 'D' and resid 265 through 267
      No H-bonds generated for 'chain 'D' and resid 265 through 267'
    Processing helix  chain 'D' and resid 275 through 277
      No H-bonds generated for 'chain 'D' and resid 275 through 277'
    Processing helix  chain 'D' and resid 278 through 283
    Processing helix  chain 'D' and resid 293 through 300
    Processing helix  chain 'D' and resid 303 through 318
    Processing helix  chain 'D' and resid 324 through 331
    Processing helix  chain 'D' and resid 365 through 385
    Processing helix  chain 'D' and resid 386 through 388
      No H-bonds generated for 'chain 'D' and resid 386 through 388'
    Processing helix  chain 'D' and resid 389 through 393
    Processing helix  chain 'D' and resid 399 through 414
      removed outlier: 3.685A  pdb=" N   THR D 414 " --> pdb=" O   LEU D 410 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 414 through 421
    Processing helix  chain 'D' and resid 431 through 447
    Processing helix  chain 'D' and resid 449 through 465
    Processing helix  chain 'D' and resid 472 through 484
    Processing helix  chain 'D' and resid 498 through 502
    Processing helix  chain 'D' and resid 503 through 508
    Processing helix  chain 'D' and resid 513 through 533
    Processing helix  chain 'D' and resid 538 through 542
    Processing helix  chain 'D' and resid 547 through 559
      removed outlier: 4.107A  pdb=" N   MET D 557 " --> pdb=" O   LYS D 553 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 565 through 575
    Processing helix  chain 'D' and resid 581 through 599
      Proline residue:  D 590  - end of helix
      removed outlier: 3.617A  pdb=" N   ASP D 597 " --> pdb=" O   THR D 593 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 600 through 602
      No H-bonds generated for 'chain 'D' and resid 600 through 602'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
    Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362
      removed outlier: 6.709A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'D' and resid 131 through 133
    Processing sheet with id=AA6, first strand: chain 'D' and resid 262 through 263
      removed outlier: 6.082A  pdb=" N   LEU D 262 " --> pdb=" O   VAL D 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'D' and resid 347 through 350

    322 hydrogen bonds defined for protein.
    909 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: 1.93

  Time building geometry restraints manager: 1.88 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1305
        1.32 -     1.45: 2125
        1.45 -     1.58: 3229
        1.58 -     1.71: 10
        1.71 -     1.84: 58
  Bond restraints: 6727
  Sorted by residual:
  bond pdb=" CB  HIS D 265 "
       pdb=" CG  HIS D 265 "
    ideal  model  delta    sigma   weight residual
    1.497  1.425  0.072 1.40e-02 5.10e+03 2.68e+01
  bond pdb=" CB  HIS D 535 "
       pdb=" CG  HIS D 535 "
    ideal  model  delta    sigma   weight residual
    1.497  1.425  0.072 1.40e-02 5.10e+03 2.64e+01
  bond pdb=" CB  ASN A 422 "
       pdb=" CG  ASN A 422 "
    ideal  model  delta    sigma   weight residual
    1.516  1.391  0.125 2.50e-02 1.60e+03 2.50e+01
  bond pdb=" CZ  ARG D 460 "
       pdb=" NH2 ARG D 460 "
    ideal  model  delta    sigma   weight residual
    1.330  1.274  0.056 1.30e-02 5.92e+03 1.83e+01
  bond pdb=" CZ  ARG D 161 "
       pdb=" NH2 ARG D 161 "
    ideal  model  delta    sigma   weight residual
    1.330  1.278  0.052 1.30e-02 5.92e+03 1.60e+01
  ... (remaining 6722 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.33: 7882
        2.33 -     4.67: 1070
        4.67 -     7.00: 171
        7.00 -     9.33: 15
        9.33 -    11.67: 5
  Bond angle restraints: 9143
  Sorted by residual:
  angle pdb=" N   SER D 170 "
        pdb=" CA  SER D 170 "
        pdb=" C   SER D 170 "
      ideal   model   delta    sigma   weight residual
     110.35   98.98   11.37 1.38e+00 5.25e-01 6.79e+01
  angle pdb=" C   GLU D 489 "
        pdb=" N   PRO D 490 "
        pdb=" CA  PRO D 490 "
      ideal   model   delta    sigma   weight residual
     119.87  128.34   -8.47 1.04e+00 9.25e-01 6.63e+01
  angle pdb=" C   GLY A 526 "
        pdb=" N   PRO A 527 "
        pdb=" CA  PRO A 527 "
      ideal   model   delta    sigma   weight residual
     119.85  127.88   -8.03 1.01e+00 9.80e-01 6.33e+01
  angle pdb=" CB  ASN D  90 "
        pdb=" CG  ASN D  90 "
        pdb=" ND2 ASN D  90 "
      ideal   model   delta    sigma   weight residual
     116.40  128.07  -11.67 1.50e+00 4.44e-01 6.05e+01
  angle pdb=" N   TYR A 380 "
        pdb=" CA  TYR A 380 "
        pdb=" C   TYR A 380 "
      ideal   model   delta    sigma   weight residual
     114.31  104.49    9.82 1.29e+00 6.01e-01 5.80e+01
  ... (remaining 9138 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.29: 3878
       17.29 -    34.58: 140
       34.58 -    51.88: 25
       51.88 -    69.17: 15
       69.17 -    86.46: 5
  Dihedral angle restraints: 4063
    sinusoidal: 1728
      harmonic: 2335
  Sorted by residual:
  dihedral pdb=" C   TYR A 421 "
           pdb=" N   TYR A 421 "
           pdb=" CA  TYR A 421 "
           pdb=" CB  TYR A 421 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.06   11.46     0      2.50e+00 1.60e-01 2.10e+01
  dihedral pdb=" N   TYR A 421 "
           pdb=" C   TYR A 421 "
           pdb=" CA  TYR A 421 "
           pdb=" CB  TYR A 421 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  133.46  -10.66     0      2.50e+00 1.60e-01 1.82e+01
  dihedral pdb=" CA  PRO D 389 "
           pdb=" C   PRO D 389 "
           pdb=" N   PHE D 390 "
           pdb=" CA  PHE D 390 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.18  -18.82     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 4060 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.114: 739
       0.114 -    0.229: 209
       0.229 -    0.343: 21
       0.343 -    0.457: 7
       0.457 -    0.572: 1
  Chirality restraints: 977
  Sorted by residual:
  chirality pdb=" CA  TYR A 421 "
            pdb=" N   TYR A 421 "
            pdb=" C   TYR A 421 "
            pdb=" CB  TYR A 421 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.94    0.57 2.00e-01 2.50e+01 8.17e+00
  chirality pdb=" C1  NAG D1102 "
            pdb=" ND2 ASN D 103 "
            pdb=" C2  NAG D1102 "
            pdb=" O5  NAG D1102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.84    0.44 2.00e-01 2.50e+01 4.84e+00
  chirality pdb=" C1  NAG D1104 "
            pdb=" ND2 ASN D 546 "
            pdb=" C2  NAG D1104 "
            pdb=" O5  NAG D1104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.79    0.39 2.00e-01 2.50e+01 3.83e+00
  ... (remaining 974 not shown)

  Planarity restraints: 1184
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN D  53 "    0.015 2.00e-02 2.50e+03   7.67e-02 7.35e+01
        pdb=" CG  ASN D  53 "    0.023 2.00e-02 2.50e+03
        pdb=" OD1 ASN D  53 "   -0.076 2.00e-02 2.50e+03
        pdb=" ND2 ASN D  53 "    0.125 2.00e-02 2.50e+03
        pdb=" C1  NAG D1106 "   -0.086 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN D 103 "   -0.013 2.00e-02 2.50e+03   4.66e-02 2.71e+01
        pdb=" CG  ASN D 103 "   -0.011 2.00e-02 2.50e+03
        pdb=" OD1 ASN D 103 "    0.046 2.00e-02 2.50e+03
        pdb=" ND2 ASN D 103 "   -0.075 2.00e-02 2.50e+03
        pdb=" C1  NAG D1102 "    0.053 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN D 432 "   -0.008 2.00e-02 2.50e+03   4.30e-02 2.31e+01
        pdb=" CG  ASN D 432 "   -0.014 2.00e-02 2.50e+03
        pdb=" OD1 ASN D 432 "    0.043 2.00e-02 2.50e+03
        pdb=" ND2 ASN D 432 "   -0.069 2.00e-02 2.50e+03
        pdb=" C1  NAG D1103 "    0.048 2.00e-02 2.50e+03
  ... (remaining 1181 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1264
        2.76 -     3.29: 6404
        3.29 -     3.83: 11299
        3.83 -     4.36: 14413
        4.36 -     4.90: 22737
  Nonbonded interactions: 56117
  Sorted by model distance:
  nonbonded pdb=" O4  NAG D1102 "
            pdb=" O6  NAG D1102 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O4  NAG D1101 "
            pdb=" O6  NAG D1101 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" N   SER D 170 "
            pdb=" O   SER D 170 "
     model   vdw
     2.348 2.496
  nonbonded pdb=" O4  NAG D1104 "
            pdb=" O6  NAG D1104 "
     model   vdw
     2.372 3.040
  nonbonded pdb=" N   TYR A 380 "
            pdb=" N   GLY A 381 "
     model   vdw
     2.385 2.560
  ... (remaining 56112 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:             7.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     20.390
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
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      :  0.018   0.125   6727  Z= 1.143
  Angle     :  1.678  11.668   9143  Z= 1.145
  Chirality :  0.104   0.572    977
  Planarity :  0.009   0.067   1177
  Dihedral  : 10.740  86.458   2544
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 1.33
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.89 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  1.00 %
    Favored  : 98.86 %
  Cbeta Deviations :  0.13 %
  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: -0.17 (0.28), residues: 792
  helix: -0.42 (0.23), residues: 391
  sheet:  0.78 (0.73), residues: 61
  loop :  0.38 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.009   TRP D 349 
 HIS   0.014   0.003   HIS D 535 
 PHE   0.028   0.006   PHE D 390 
 TYR   0.059   0.008   TYR D 199 
 ARG   0.010   0.001   ARG D 161 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 206
  time to evaluate  : 0.710 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 ASN cc_start: 0.7073 (t0) cc_final: 0.6510 (m110)
REVERT: A  418 ILE cc_start: 0.9251 (mm) cc_final: 0.8602 (mm)
REVERT: D  119 ILE cc_start: 0.8518 (mt) cc_final: 0.8257 (mt)
REVERT: D  155 SER cc_start: 0.8440 (t) cc_final: 0.8027 (p)
REVERT: D  291 ILE cc_start: 0.8495 (pt) cc_final: 0.7995 (mp)
REVERT: D  362 THR cc_start: 0.7357 (m) cc_final: 0.6892 (m)
REVERT: D  441 LYS cc_start: 0.8693 (tttt) cc_final: 0.8471 (tptp)
REVERT: D  474 MET cc_start: 0.8360 (mmp) cc_final: 0.8030 (mmm)
REVERT: D  480 MET cc_start: 0.8661 (mtp) cc_final: 0.8432 (mtt)
  outliers start: 1
  outliers final: 1
  residues processed: 207
  average time/residue: 0.2255
  time to fit residues: 58.8915
Evaluate side-chains
  117 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 116
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   90 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    0.0170
   chunk 59 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 40 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   chunk 37 optimal weight:    0.5980
   chunk 46 optimal weight:    0.1980
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.4018

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

Flipped N/Q/H residues before XYZ refinement:
A 414 GLN
A 493 GLN
A 498 GLN
A 506 GLN
D 154 ASN
** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.096540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.085570 restraints weight = 18102.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.088208 restraints weight = 8221.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.089903 restraints weight = 4721.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.3382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6727  Z= 0.207
  Angle     :  0.702  13.940   9143  Z= 0.360
  Chirality :  0.056   0.767    977
  Planarity :  0.005   0.055   1177
  Dihedral  :  8.090  88.017   1013
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.89 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  :  9.01 %
    Favored  : 88.98 %
  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:  0.96 (0.30), residues: 792
  helix:  1.11 (0.26), residues: 390
  sheet:  0.06 (0.72), residues: 61
  loop :  0.36 (0.34), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP D 478 
 HIS   0.003   0.001   HIS D 374 
 PHE   0.017   0.001   PHE D 369 
 TYR   0.017   0.001   TYR D 385 
 ARG   0.003   0.000   ARG D 219 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 149
  time to evaluate  : 0.874 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  206 ASP cc_start: 0.8607 (t0) cc_final: 0.8281 (t0)
REVERT: D  441 LYS cc_start: 0.8814 (tttt) cc_final: 0.8355 (tptp)
REVERT: D  483 GLU cc_start: 0.8437 (tp30) cc_final: 0.8005 (tp30)
  outliers start: 14
  outliers final: 8
  residues processed: 158
  average time/residue: 0.2082
  time to fit residues: 43.6774
Evaluate side-chains
  108 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   90 ASN
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  154 ASN
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  379 ILE
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain D residue  503 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 47 optimal weight:    0.7980
   chunk 65 optimal weight:    0.4980
   chunk 25 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0970
   chunk 28 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 373 HIS
D 401 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.094226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.083487 restraints weight = 18168.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.085893 restraints weight = 8591.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.087467 restraints weight = 5067.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.4110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6727  Z= 0.217
  Angle     :  0.665  10.001   9143  Z= 0.340
  Chirality :  0.053   0.594    977
  Planarity :  0.004   0.050   1177
  Dihedral  :  7.724  85.826   1013
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  2.02 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 11.87 %
    Favored  : 85.84 %
  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:  1.11 (0.30), residues: 792
  helix:  1.31 (0.26), residues: 393
  sheet: -0.03 (0.69), residues: 60
  loop :  0.36 (0.35), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP D 478 
 HIS   0.004   0.001   HIS D 535 
 PHE   0.025   0.002   PHE D 327 
 TYR   0.022   0.001   TYR A 380 
 ARG   0.004   0.001   ARG A 466 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  394 ASN cc_start: 0.7476 (t0) cc_final: 0.7253 (t0)
REVERT: A  462 LYS cc_start: 0.7739 (mppt) cc_final: 0.7388 (mppt)
REVERT: D   74 LYS cc_start: 0.9198 (mtmm) cc_final: 0.8850 (mtmm)
REVERT: D  206 ASP cc_start: 0.8572 (t0) cc_final: 0.7918 (t0)
REVERT: D  285 PHE cc_start: 0.6833 (m-80) cc_final: 0.6097 (m-80)
REVERT: D  287 GLN cc_start: 0.5964 (pm20) cc_final: 0.5392 (mm-40)
REVERT: D  360 MET cc_start: 0.7975 (tmm) cc_final: 0.7513 (ttt)
REVERT: D  406 GLU cc_start: 0.8394 (tp30) cc_final: 0.7728 (tp30)
REVERT: D  441 LYS cc_start: 0.8847 (tttt) cc_final: 0.8407 (tptp)
REVERT: D  470 LYS cc_start: 0.7656 (mmmm) cc_final: 0.7094 (mmmm)
REVERT: D  474 MET cc_start: 0.8408 (mmp) cc_final: 0.7883 (mmt)
REVERT: D  483 GLU cc_start: 0.8402 (tp30) cc_final: 0.8105 (tp30)
REVERT: D  601 ASN cc_start: 0.8070 (t0) cc_final: 0.7824 (t0)
  outliers start: 16
  outliers final: 12
  residues processed: 129
  average time/residue: 0.1815
  time to fit residues: 31.5495
Evaluate side-chains
  116 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   90 ASN
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  154 ASN
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  478 TRP
Chi-restraints excluded: chain D residue  498 CYS
Chi-restraints excluded: chain D residue  522 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 74 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 47 optimal weight:    0.5980
   chunk 55 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 3 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 154 ASN
D 210 ASN
D 401 HIS
D 417 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.092085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.081246 restraints weight = 18616.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.083595 restraints weight = 8844.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.085120 restraints weight = 5236.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.4776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   6727  Z= 0.256
  Angle     :  0.654  11.326   9143  Z= 0.334
  Chirality :  0.052   0.492    977
  Planarity :  0.004   0.051   1177
  Dihedral  :  6.785  56.793   1013
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.15 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 13.02 %
    Favored  : 83.98 %
  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:  0.99 (0.30), residues: 792
  helix:  1.35 (0.26), residues: 401
  sheet: -0.25 (0.70), residues: 60
  loop :  0.10 (0.34), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP D 478 
 HIS   0.003   0.001   HIS A 519 
 PHE   0.026   0.002   PHE D 327 
 TYR   0.024   0.002   TYR D 497 
 ARG   0.002   0.001   ARG A 454 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 113
  time to evaluate  : 0.790 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  394 ASN cc_start: 0.7321 (t0) cc_final: 0.7068 (t0)
REVERT: A  417 LYS cc_start: 0.9238 (tppt) cc_final: 0.9007 (tppt)
REVERT: A  421 TYR cc_start: 0.7898 (OUTLIER) cc_final: 0.6290 (p90)
REVERT: D  238 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8424 (mt-10)
REVERT: D  270 MET cc_start: 0.7711 (tpp) cc_final: 0.7323 (tpp)
REVERT: D  360 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7752 (ttt)
REVERT: D  406 GLU cc_start: 0.8356 (tp30) cc_final: 0.7692 (tp30)
REVERT: D  441 LYS cc_start: 0.8846 (tttt) cc_final: 0.8434 (tptp)
REVERT: D  470 LYS cc_start: 0.8126 (mmmm) cc_final: 0.7703 (mmtt)
REVERT: D  483 GLU cc_start: 0.8501 (tp30) cc_final: 0.8250 (tp30)
REVERT: D  488 VAL cc_start: 0.8033 (OUTLIER) cc_final: 0.7732 (m)
REVERT: D  601 ASN cc_start: 0.8115 (t0) cc_final: 0.7915 (t0)
  outliers start: 21
  outliers final: 14
  residues processed: 127
  average time/residue: 0.1932
  time to fit residues: 32.4485
Evaluate side-chains
  114 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  421 TYR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain D residue   90 ASN
Chi-restraints excluded: chain D residue  132 VAL
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  291 ILE
Chi-restraints excluded: chain D residue  360 MET
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  478 TRP
Chi-restraints excluded: chain D residue  487 VAL
Chi-restraints excluded: chain D residue  488 VAL
Chi-restraints excluded: chain D residue  498 CYS
Chi-restraints excluded: chain D residue  522 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 73 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 46 optimal weight:    0.1980
   chunk 65 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 265 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 = 0.3507 r_free = 0.3507 target = 0.092105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.081408 restraints weight = 18492.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.083735 restraints weight = 8841.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.085243 restraints weight = 5281.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.5209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6727  Z= 0.214
  Angle     :  0.609   7.234   9143  Z= 0.314
  Chirality :  0.051   0.440    977
  Planarity :  0.004   0.048   1177
  Dihedral  :  5.920  52.690   1013
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.40 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 13.73 %
    Favored  : 82.83 %
  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:  1.12 (0.30), residues: 792
  helix:  1.51 (0.26), residues: 397
  sheet: -0.24 (0.70), residues: 60
  loop :  0.13 (0.34), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP D 478 
 HIS   0.003   0.001   HIS A 519 
 PHE   0.026   0.002   PHE D 327 
 TYR   0.017   0.001   TYR A 380 
 ARG   0.003   0.000   ARG A 357 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.727 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  394 ASN cc_start: 0.7245 (t0) cc_final: 0.7039 (t0)
REVERT: A  462 LYS cc_start: 0.7950 (mppt) cc_final: 0.7604 (mppt)
REVERT: D  152 MET cc_start: 0.6292 (mmm) cc_final: 0.6063 (mmm)
REVERT: D  270 MET cc_start: 0.7761 (tpp) cc_final: 0.7525 (tpp)
REVERT: D  323 MET cc_start: 0.9423 (tpp) cc_final: 0.9089 (mmm)
REVERT: D  360 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7143 (tmm)
REVERT: D  375 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8060 (mm-30)
REVERT: D  406 GLU cc_start: 0.8345 (tp30) cc_final: 0.7714 (tp30)
REVERT: D  441 LYS cc_start: 0.8825 (tttt) cc_final: 0.8403 (tptp)
  outliers start: 24
  outliers final: 16
  residues processed: 123
  average time/residue: 0.1927
  time to fit residues: 31.4715
Evaluate side-chains
  119 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   90 ASN
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  360 MET
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  366 MET
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  478 TRP
Chi-restraints excluded: chain D residue  487 VAL
Chi-restraints excluded: chain D residue  498 CYS
Chi-restraints excluded: chain D residue  522 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 46 optimal weight:    0.0000
   overall best weight:    0.6788

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** D  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 535 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 = 0.3498 r_free = 0.3498 target = 0.091674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.081073 restraints weight = 18522.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.083362 restraints weight = 8911.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.084874 restraints weight = 5348.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.5513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6727  Z= 0.219
  Angle     :  0.605   6.223   9143  Z= 0.313
  Chirality :  0.050   0.422    977
  Planarity :  0.004   0.047   1177
  Dihedral  :  5.792  52.951   1013
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.78 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 15.31 %
    Favored  : 81.26 %
  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:  1.20 (0.30), residues: 792
  helix:  1.59 (0.26), residues: 396
  sheet: -0.26 (0.70), residues: 60
  loop :  0.15 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP D 478 
 HIS   0.003   0.001   HIS A 519 
 PHE   0.018   0.001   PHE D  31 
 TYR   0.016   0.001   TYR A 380 
 ARG   0.002   0.000   ARG D 482 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.726 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  406 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8342 (mt-10)
REVERT: A  462 LYS cc_start: 0.7967 (mppt) cc_final: 0.7606 (mppt)
REVERT: D  152 MET cc_start: 0.6614 (mmm) cc_final: 0.6200 (mmm)
REVERT: D  182 GLU cc_start: 0.8255 (tt0) cc_final: 0.8018 (tt0)
REVERT: D  270 MET cc_start: 0.7829 (tpp) cc_final: 0.7534 (tpp)
REVERT: D  375 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8012 (mm-30)
REVERT: D  441 LYS cc_start: 0.8807 (tttt) cc_final: 0.8420 (tptp)
REVERT: D  470 LYS cc_start: 0.8402 (mmmm) cc_final: 0.8176 (tptt)
REVERT: D  589 GLU cc_start: 0.7765 (tp30) cc_final: 0.7564 (tp30)
  outliers start: 24
  outliers final: 20
  residues processed: 120
  average time/residue: 0.2333
  time to fit residues: 36.8604
Evaluate side-chains
  124 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  421 TYR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   90 ASN
Chi-restraints excluded: chain D residue  123 MET
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  261 CYS
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  366 MET
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  478 TRP
Chi-restraints excluded: chain D residue  487 VAL
Chi-restraints excluded: chain D residue  498 CYS
Chi-restraints excluded: chain D residue  522 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 47 optimal weight:    0.4980
   chunk 25 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 64 optimal weight:    0.5980
   chunk 51 optimal weight:    0.0670
   chunk 31 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0770
   chunk 75 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.3676

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** D  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 265 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 = 0.3538 r_free = 0.3538 target = 0.093794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.082988 restraints weight = 18683.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.085317 restraints weight = 9055.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.086853 restraints weight = 5454.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.5685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   6727  Z= 0.176
  Angle     :  0.574   7.637   9143  Z= 0.295
  Chirality :  0.048   0.401    977
  Planarity :  0.004   0.045   1177
  Dihedral  :  5.523  52.080   1013
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.27 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 17.02 %
    Favored  : 79.97 %
  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:  1.40 (0.30), residues: 792
  helix:  1.68 (0.26), residues: 394
  sheet:  0.34 (0.78), residues: 50
  loop :  0.26 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP D 478 
 HIS   0.003   0.001   HIS D 374 
 PHE   0.029   0.001   PHE D 327 
 TYR   0.016   0.001   TYR D 385 
 ARG   0.003   0.000   ARG D 115 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  462 LYS cc_start: 0.7906 (mppt) cc_final: 0.7511 (mppt)
REVERT: D  115 ARG cc_start: 0.8515 (tpp-160) cc_final: 0.8129 (tpm170)
REVERT: D  152 MET cc_start: 0.6529 (mmm) cc_final: 0.6159 (mmm)
REVERT: D  182 GLU cc_start: 0.8270 (tt0) cc_final: 0.8043 (tt0)
REVERT: D  237 TYR cc_start: 0.9086 (t80) cc_final: 0.8883 (t80)
REVERT: D  270 MET cc_start: 0.7826 (tpp) cc_final: 0.7518 (tpp)
REVERT: D  323 MET cc_start: 0.9414 (tpp) cc_final: 0.9107 (mmm)
REVERT: D  441 LYS cc_start: 0.8780 (tttt) cc_final: 0.8297 (tptp)
REVERT: D  470 LYS cc_start: 0.8439 (mmmm) cc_final: 0.8006 (tptt)
REVERT: D  516 TYR cc_start: 0.8816 (t80) cc_final: 0.8540 (t80)
  outliers start: 21
  outliers final: 17
  residues processed: 125
  average time/residue: 0.1949
  time to fit residues: 32.6309
Evaluate side-chains
  119 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain A residue  516 GLU
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   90 ASN
Chi-restraints excluded: chain D residue  123 MET
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  366 MET
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  478 TRP
Chi-restraints excluded: chain D residue  498 CYS
Chi-restraints excluded: chain D residue  522 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 75 optimal weight:    0.2980
   chunk 33 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 63 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 55 optimal weight:    0.7980
   chunk 17 optimal weight:    0.2980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** D  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 535 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 = 0.3518 r_free = 0.3518 target = 0.092703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.081795 restraints weight = 18914.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.084137 restraints weight = 9237.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.085665 restraints weight = 5566.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.5853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6727  Z= 0.209
  Angle     :  0.634   7.949   9143  Z= 0.325
  Chirality :  0.051   0.464    977
  Planarity :  0.004   0.043   1177
  Dihedral  :  5.649  48.944   1013
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.03 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 17.02 %
    Favored  : 79.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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:  1.38 (0.30), residues: 792
  helix:  1.68 (0.26), residues: 397
  sheet:  0.36 (0.79), residues: 50
  loop :  0.21 (0.35), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP D 478 
 HIS   0.004   0.001   HIS D 493 
 PHE   0.029   0.002   PHE D 327 
 TYR   0.023   0.001   TYR D 497 
 ARG   0.002   0.000   ARG A 454 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 110
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  152 MET cc_start: 0.6462 (mmm) cc_final: 0.6109 (mmm)
REVERT: D  182 GLU cc_start: 0.8305 (tt0) cc_final: 0.8065 (tt0)
REVERT: D  237 TYR cc_start: 0.9104 (t80) cc_final: 0.8898 (t80)
REVERT: D  270 MET cc_start: 0.7848 (tpp) cc_final: 0.7599 (tpp)
REVERT: D  332 MET cc_start: 0.8120 (mmm) cc_final: 0.7843 (tpp)
REVERT: D  375 GLU cc_start: 0.8631 (mm-30) cc_final: 0.7942 (mm-30)
REVERT: D  406 GLU cc_start: 0.8227 (tp30) cc_final: 0.7649 (tp30)
REVERT: D  441 LYS cc_start: 0.8798 (tttt) cc_final: 0.8324 (tptp)
REVERT: D  470 LYS cc_start: 0.8435 (mmmm) cc_final: 0.8058 (tptt)
REVERT: D  493 HIS cc_start: 0.6276 (m-70) cc_final: 0.5315 (m90)
REVERT: D  497 TYR cc_start: 0.7218 (m-80) cc_final: 0.6476 (m-10)
REVERT: D  589 GLU cc_start: 0.7786 (tp30) cc_final: 0.7580 (tp30)
  outliers start: 24
  outliers final: 21
  residues processed: 122
  average time/residue: 0.1970
  time to fit residues: 31.9427
Evaluate side-chains
  126 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain A residue  516 GLU
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   90 ASN
Chi-restraints excluded: chain D residue  123 MET
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  261 CYS
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  366 MET
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  447 VAL
Chi-restraints excluded: chain D residue  456 LEU
Chi-restraints excluded: chain D residue  478 TRP
Chi-restraints excluded: chain D residue  498 CYS
Chi-restraints excluded: chain D residue  522 GLN
Chi-restraints excluded: chain D residue  604 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 75 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 73 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** D  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 535 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 = 0.3488 r_free = 0.3488 target = 0.091046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.080173 restraints weight = 18941.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.082472 restraints weight = 9211.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.083975 restraints weight = 5560.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.5989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6727  Z= 0.249
  Angle     :  0.641   8.363   9143  Z= 0.331
  Chirality :  0.049   0.418    977
  Planarity :  0.004   0.043   1177
  Dihedral  :  5.890  51.654   1013
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.90 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 17.31 %
    Favored  : 79.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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:  1.20 (0.31), residues: 792
  helix:  1.64 (0.26), residues: 397
  sheet: -0.31 (0.72), residues: 60
  loop :  0.07 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP D 478 
 HIS   0.003   0.001   HIS A 519 
 PHE   0.030   0.002   PHE D 327 
 TYR   0.020   0.002   TYR D 497 
 ARG   0.002   0.000   ARG A 454 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  421 TYR cc_start: 0.7708 (OUTLIER) cc_final: 0.7264 (p90)
REVERT: D  115 ARG cc_start: 0.8566 (tpp-160) cc_final: 0.8301 (tpm170)
REVERT: D  152 MET cc_start: 0.6470 (mmm) cc_final: 0.6076 (mmm)
REVERT: D  270 MET cc_start: 0.7841 (tpp) cc_final: 0.7565 (tpp)
REVERT: D  332 MET cc_start: 0.8181 (mmm) cc_final: 0.7965 (tpp)
REVERT: D  375 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8044 (mm-30)
REVERT: D  406 GLU cc_start: 0.8230 (tp30) cc_final: 0.7693 (tp30)
REVERT: D  441 LYS cc_start: 0.8832 (tttt) cc_final: 0.8436 (tptp)
REVERT: D  470 LYS cc_start: 0.8497 (mmmm) cc_final: 0.8101 (tptt)
REVERT: D  489 GLU cc_start: 0.6303 (mp0) cc_final: 0.5988 (mt-10)
REVERT: D  493 HIS cc_start: 0.6392 (m-70) cc_final: 0.5231 (m90)
  outliers start: 22
  outliers final: 19
  residues processed: 115
  average time/residue: 0.2112
  time to fit residues: 32.0280
Evaluate side-chains
  119 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  421 TYR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   90 ASN
Chi-restraints excluded: chain D residue  123 MET
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  261 CYS
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  366 MET
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  447 VAL
Chi-restraints excluded: chain D residue  456 LEU
Chi-restraints excluded: chain D residue  498 CYS
Chi-restraints excluded: chain D residue  522 GLN
Chi-restraints excluded: chain D residue  604 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 56 optimal weight:    0.0060
   chunk 26 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0670
   chunk 4 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.4334

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** D  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 535 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 = 0.3537 r_free = 0.3537 target = 0.093686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.082731 restraints weight = 18940.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.085075 restraints weight = 9185.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.086589 restraints weight = 5536.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.6139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6727  Z= 0.196
  Angle     :  0.624   8.289   9143  Z= 0.322
  Chirality :  0.047   0.402    977
  Planarity :  0.004   0.044   1177
  Dihedral  :  5.306  40.308   1013
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.53 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 17.88 %
    Favored  : 79.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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:  1.33 (0.30), residues: 792
  helix:  1.71 (0.26), residues: 395
  sheet:  0.42 (0.81), residues: 50
  loop :  0.08 (0.35), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D 473 
 HIS   0.002   0.001   HIS D 535 
 PHE   0.028   0.001   PHE D 327 
 TYR   0.019   0.001   TYR D 497 
 ARG   0.004   0.000   ARG D 518 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  421 TYR cc_start: 0.7644 (OUTLIER) cc_final: 0.6925 (p90)
REVERT: D  115 ARG cc_start: 0.8546 (tpp-160) cc_final: 0.8330 (tpm170)
REVERT: D  152 MET cc_start: 0.6459 (mmm) cc_final: 0.6123 (mmm)
REVERT: D  237 TYR cc_start: 0.9092 (t80) cc_final: 0.8872 (t80)
REVERT: D  270 MET cc_start: 0.7846 (tpp) cc_final: 0.7583 (tpp)
REVERT: D  323 MET cc_start: 0.9443 (tpp) cc_final: 0.9183 (mmm)
REVERT: D  375 GLU cc_start: 0.8691 (mm-30) cc_final: 0.7930 (mm-30)
REVERT: D  406 GLU cc_start: 0.8206 (tp30) cc_final: 0.7624 (tp30)
REVERT: D  441 LYS cc_start: 0.8797 (tttt) cc_final: 0.8295 (tptp)
REVERT: D  470 LYS cc_start: 0.8476 (mmmm) cc_final: 0.8185 (tptt)
REVERT: D  479 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8171 (tm-30)
  outliers start: 21
  outliers final: 18
  residues processed: 123
  average time/residue: 0.1958
  time to fit residues: 31.8606
Evaluate side-chains
  119 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  421 TYR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   90 ASN
Chi-restraints excluded: chain D residue  123 MET
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  261 CYS
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  366 MET
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  456 LEU
Chi-restraints excluded: chain D residue  498 CYS
Chi-restraints excluded: chain D residue  522 GLN
Chi-restraints excluded: chain D residue  604 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 31 optimal weight:    0.3980
   chunk 47 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 62 optimal weight:    0.7980
   chunk 68 optimal weight:    0.4980
   chunk 40 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 76 optimal weight:    0.7980
   chunk 74 optimal weight:    0.0060
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** D  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 535 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 = 0.3543 r_free = 0.3543 target = 0.094075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.082990 restraints weight = 18875.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.085345 restraints weight = 9201.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.086881 restraints weight = 5550.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.6237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6727  Z= 0.199
  Angle     :  0.625   8.122   9143  Z= 0.326
  Chirality :  0.047   0.393    977
  Planarity :  0.005   0.050   1177
  Dihedral  :  5.188  40.551   1013
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.03 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 17.74 %
    Favored  : 79.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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:  1.31 (0.31), residues: 792
  helix:  1.70 (0.26), residues: 398
  sheet:  0.46 (0.81), residues: 50
  loop :  0.04 (0.35), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP D 478 
 HIS   0.006   0.001   HIS D 493 
 PHE   0.029   0.001   PHE D 327 
 TYR   0.016   0.001   TYR D 385 
 ARG   0.006   0.000   ARG D 482 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2598.62 seconds
wall clock time: 47 minutes 52.87 seconds (2872.87 seconds total)