Starting phenix.real_space_refine
on Tue Mar 11 20:39:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dv2_27731/03_2025/8dv2_27731.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dv2_27731/03_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_27731/03_2025/8dv2_27731.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dv2_27731/03_2025/8dv2_27731.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dv2_27731/03_2025/8dv2_27731.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dv2_27731/03_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-5624/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: 5.89, per 1000 atoms: 0.90
  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: 1.67
  Conformation dependent library (CDL) restraints added in 944.1 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: 0.72
  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: 1.87

  Time building geometry restraints manager: 2.01 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:             4.460
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.880
  Find NCS groups from input model:        0.070
  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:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.550
-------------------------------------------------------------------------------
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  : 0.813 
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: 0.2269
  time to fit residues: 59.3593
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  : 0.784 
-------------------------------------------------------------------------------
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 = 0.3582 r_free = 0.3582 target = 0.096670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.085626 restraints weight = 18050.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.088263 restraints weight = 8189.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.089974 restraints weight = 4711.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
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  : 0.794 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  206 ASP cc_start: 0.8612 (t0) cc_final: 0.8285 (t0)
REVERT: D  441 LYS cc_start: 0.8817 (tttt) cc_final: 0.8354 (tptp)
REVERT: D  483 GLU cc_start: 0.8445 (tp30) cc_final: 0.8013 (tp30)
  outliers start: 14
  outliers final: 8
  residues processed: 158
  average time/residue: 0.2002
  time to fit residues: 41.6874
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  : 0.756 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 47 optimal weight:    0.3980
   chunk 65 optimal weight:    0.4980
   chunk 25 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   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**
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 = 0.3526 r_free = 0.3526 target = 0.093873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.083101 restraints weight = 18227.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.085507 restraints weight = 8569.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.087087 restraints weight = 5045.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.4141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   6727  Z= 0.231
  Angle     :  0.669  10.093   9143  Z= 0.342
  Chirality :  0.053   0.588    977
  Planarity :  0.004   0.051   1177
  Dihedral  :  7.709  84.814   1013
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  2.02 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 12.02 %
    Favored  : 85.69 %
  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:  1.09 (0.30), residues: 792
  helix:  1.31 (0.26), residues: 393
  sheet: -0.10 (0.69), residues: 60
  loop :  0.34 (0.35), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP D 478 
 HIS   0.004   0.001   HIS D 535 
 PHE   0.024   0.002   PHE D 327 
 TYR   0.023   0.001   TYR A 380 
 ARG   0.004   0.001   ARG D 482 

*********************** 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  : 0.966 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  394 ASN cc_start: 0.7480 (t0) cc_final: 0.7257 (t0)
REVERT: A  462 LYS cc_start: 0.7783 (mppt) cc_final: 0.7422 (mppt)
REVERT: D   74 LYS cc_start: 0.9201 (mtmm) cc_final: 0.8851 (mtmm)
REVERT: D  206 ASP cc_start: 0.8573 (t0) cc_final: 0.7931 (t0)
REVERT: D  285 PHE cc_start: 0.6829 (m-80) cc_final: 0.6077 (m-80)
REVERT: D  287 GLN cc_start: 0.5971 (pm20) cc_final: 0.5404 (mm-40)
REVERT: D  360 MET cc_start: 0.7946 (tmm) cc_final: 0.7536 (ttt)
REVERT: D  406 GLU cc_start: 0.8401 (tp30) cc_final: 0.7730 (tp30)
REVERT: D  441 LYS cc_start: 0.8857 (tttt) cc_final: 0.8413 (tptp)
REVERT: D  470 LYS cc_start: 0.7712 (mmmm) cc_final: 0.7186 (mmmm)
REVERT: D  474 MET cc_start: 0.8421 (mmp) cc_final: 0.7887 (mmt)
REVERT: D  483 GLU cc_start: 0.8423 (tp30) cc_final: 0.8131 (tp30)
REVERT: D  601 ASN cc_start: 0.8082 (t0) cc_final: 0.7840 (t0)
  outliers start: 16
  outliers final: 12
  residues processed: 129
  average time/residue: 0.1760
  time to fit residues: 31.1318
Evaluate side-chains
  114 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 8 optimal weight:    0.0070
   chunk 31 optimal weight:    3.9990
   chunk 47 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0980
   overall best weight:    0.5800

-------------------------------------------------------------------------------
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 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3518 r_free = 0.3518 target = 0.093548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.082635 restraints weight = 18615.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.085023 restraints weight = 8823.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.086562 restraints weight = 5214.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.4771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6727  Z= 0.209
  Angle     :  0.625  11.099   9143  Z= 0.316
  Chirality :  0.051   0.478    977
  Planarity :  0.004   0.051   1177
  Dihedral  :  6.723  60.545   1013
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.02 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 13.45 %
    Favored  : 83.83 %
  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:  1.11 (0.30), residues: 792
  helix:  1.42 (0.26), residues: 401
  sheet: -0.17 (0.69), residues: 60
  loop :  0.20 (0.35), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP D 478 
 HIS   0.004   0.001   HIS D 493 
 PHE   0.023   0.001   PHE D 327 
 TYR   0.021   0.002   TYR D 497 
 ARG   0.002   0.000   ARG D 115 

*********************** 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
  137 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  394 ASN cc_start: 0.7276 (t0) cc_final: 0.7036 (t0)
REVERT: D  270 MET cc_start: 0.7697 (tpp) cc_final: 0.7299 (tpp)
REVERT: D  360 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7669 (ttt)
REVERT: D  375 GLU cc_start: 0.8622 (mm-30) cc_final: 0.7992 (mm-30)
REVERT: D  406 GLU cc_start: 0.8352 (tp30) cc_final: 0.7624 (tp30)
REVERT: D  441 LYS cc_start: 0.8836 (tttt) cc_final: 0.8402 (tptp)
REVERT: D  483 GLU cc_start: 0.8487 (tp30) cc_final: 0.8219 (tp30)
REVERT: D  488 VAL cc_start: 0.8004 (OUTLIER) cc_final: 0.7673 (m)
REVERT: D  601 ASN cc_start: 0.8108 (t0) cc_final: 0.7898 (t0)
  outliers start: 19
  outliers final: 15
  residues processed: 129
  average time/residue: 0.1929
  time to fit residues: 33.0051
Evaluate side-chains
  116 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
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  405 ASP
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  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  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:    2.9990
   chunk 73 optimal weight:    0.0870
   chunk 36 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 46 optimal weight:    0.4980
   chunk 65 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.6358

-------------------------------------------------------------------------------
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 = 0.3519 r_free = 0.3519 target = 0.092709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.081986 restraints weight = 18515.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.084323 restraints weight = 8763.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.085839 restraints weight = 5218.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.5141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6727  Z= 0.216
  Angle     :  0.617   9.059   9143  Z= 0.316
  Chirality :  0.051   0.443    977
  Planarity :  0.004   0.049   1177
  Dihedral  :  5.963  52.490   1013
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.40 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 13.73 %
    Favored  : 83.26 %
  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:  1.24 (0.30), residues: 792
  helix:  1.58 (0.26), residues: 397
  sheet: -0.15 (0.70), residues: 60
  loop :  0.21 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP D 478 
 HIS   0.004   0.001   HIS D 493 
 PHE   0.026   0.002   PHE D 308 
 TYR   0.024   0.001   TYR D 497 
 ARG   0.003   0.000   ARG A 454 

*********************** 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
  127 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 106
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  394 ASN cc_start: 0.7251 (t0) cc_final: 0.7035 (t0)
REVERT: A  421 TYR cc_start: 0.7688 (OUTLIER) cc_final: 0.6398 (p90)
REVERT: A  462 LYS cc_start: 0.7893 (mppt) cc_final: 0.7515 (mppt)
REVERT: A  486 PHE cc_start: 0.6915 (t80) cc_final: 0.6711 (t80)
REVERT: D  123 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7700 (mpp)
REVERT: D  249 MET cc_start: 0.6992 (mmm) cc_final: 0.6732 (mmm)
REVERT: D  270 MET cc_start: 0.7742 (tpp) cc_final: 0.7524 (tpp)
REVERT: D  332 MET cc_start: 0.8309 (mmm) cc_final: 0.8009 (ttm)
REVERT: D  360 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.6936 (tmm)
REVERT: D  375 GLU cc_start: 0.8662 (mm-30) cc_final: 0.7946 (mm-30)
REVERT: D  406 GLU cc_start: 0.8353 (tp30) cc_final: 0.7676 (tp30)
REVERT: D  441 LYS cc_start: 0.8829 (tttt) cc_final: 0.8427 (tptp)
REVERT: D  483 GLU cc_start: 0.8543 (tp30) cc_final: 0.8299 (tp30)
REVERT: D  488 VAL cc_start: 0.8136 (OUTLIER) cc_final: 0.7860 (m)
  outliers start: 21
  outliers final: 15
  residues processed: 119
  average time/residue: 0.2052
  time to fit residues: 32.7912
Evaluate side-chains
  115 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
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  488 CYS
Chi-restraints excluded: chain D residue   73 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  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  488 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:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 76 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3482 r_free = 0.3482 target = 0.090733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.080203 restraints weight = 18541.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.082478 restraints weight = 8906.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.083953 restraints weight = 5333.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.5479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   6727  Z= 0.259
  Angle     :  0.619   6.577   9143  Z= 0.323
  Chirality :  0.051   0.432    977
  Planarity :  0.004   0.046   1177
  Dihedral  :  5.908  53.496   1013
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.03 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 15.02 %
    Favored  : 81.40 %
  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:  1.18 (0.30), residues: 792
  helix:  1.55 (0.26), residues: 397
  sheet: -0.27 (0.70), residues: 60
  loop :  0.18 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP D 478 
 HIS   0.004   0.001   HIS D 493 
 PHE   0.023   0.002   PHE D 308 
 TYR   0.025   0.002   TYR D 497 
 ARG   0.003   0.001   ARG A 454 

*********************** 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
  128 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 103
  time to evaluate  : 0.823 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  182 GLU cc_start: 0.8351 (tt0) cc_final: 0.8100 (tt0)
REVERT: D  249 MET cc_start: 0.7057 (mmm) cc_final: 0.6789 (mmm)
REVERT: D  270 MET cc_start: 0.7823 (tpp) cc_final: 0.7515 (tpp)
REVERT: D  366 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.7996 (ttp)
REVERT: D  375 GLU cc_start: 0.8709 (mm-30) cc_final: 0.7969 (mm-30)
REVERT: D  406 GLU cc_start: 0.8329 (tp30) cc_final: 0.7766 (tp30)
REVERT: D  441 LYS cc_start: 0.8822 (tttt) cc_final: 0.8437 (tptp)
REVERT: D  482 ARG cc_start: 0.8116 (mpp80) cc_final: 0.7903 (mpp80)
REVERT: D  488 VAL cc_start: 0.8282 (OUTLIER) cc_final: 0.8042 (m)
  outliers start: 25
  outliers final: 17
  residues processed: 117
  average time/residue: 0.1906
  time to fit residues: 29.4638
Evaluate side-chains
  118 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
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  405 ASP
Chi-restraints excluded: chain A residue  421 TYR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  488 CYS
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  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  488 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:    0.9990
   chunk 32 optimal weight:    0.6980
   chunk 64 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 75 optimal weight:    0.0770
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.6138

-------------------------------------------------------------------------------
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 = 0.3498 r_free = 0.3498 target = 0.091734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.081123 restraints weight = 18683.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.083417 restraints weight = 8965.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.084931 restraints weight = 5364.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.5613

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= 0.209
  Angle     :  0.605   7.825   9143  Z= 0.312
  Chirality :  0.049   0.415    977
  Planarity :  0.004   0.046   1177
  Dihedral  :  5.718  52.947   1013
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.65 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 16.31 %
    Favored  : 80.26 %
  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:  1.33 (0.30), residues: 792
  helix:  1.68 (0.26), residues: 394
  sheet:  0.28 (0.78), residues: 50
  loop :  0.15 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP D 478 
 HIS   0.004   0.001   HIS D 493 
 PHE   0.031   0.002   PHE D 327 
 TYR   0.017   0.001   TYR D 497 
 ARG   0.002   0.000   ARG A 454 

*********************** 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
  130 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 106
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  343 ASN cc_start: 0.8084 (m-40) cc_final: 0.7867 (t0)
REVERT: A  406 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8436 (mt-10)
REVERT: D  115 ARG cc_start: 0.8546 (tpp-160) cc_final: 0.8277 (tpm170)
REVERT: D  123 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7782 (mpp)
REVERT: D  182 GLU cc_start: 0.8318 (tt0) cc_final: 0.8084 (tt0)
REVERT: D  249 MET cc_start: 0.7067 (mmm) cc_final: 0.6848 (mmm)
REVERT: D  270 MET cc_start: 0.7827 (tpp) cc_final: 0.7486 (tpp)
REVERT: D  323 MET cc_start: 0.9423 (tpp) cc_final: 0.9118 (mmm)
REVERT: D  375 GLU cc_start: 0.8634 (mm-30) cc_final: 0.7887 (mm-30)
REVERT: D  441 LYS cc_start: 0.8796 (tttt) cc_final: 0.8407 (tptp)
REVERT: D  482 ARG cc_start: 0.8054 (mpp80) cc_final: 0.7779 (mpp80)
REVERT: D  488 VAL cc_start: 0.8360 (OUTLIER) cc_final: 0.8129 (m)
  outliers start: 24
  outliers final: 20
  residues processed: 119
  average time/residue: 0.1984
  time to fit residues: 31.4228
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  : 0.763 
-------------------------------------------------------------------------------
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  405 ASP
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   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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 50 optimal weight:    0.4980
   chunk 43 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 42 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 378 HIS
** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.089776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.079218 restraints weight = 18789.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.081484 restraints weight = 9098.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.082898 restraints weight = 5464.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.5780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   6727  Z= 0.294
  Angle     :  0.646   8.142   9143  Z= 0.336
  Chirality :  0.051   0.436    977
  Planarity :  0.004   0.043   1177
  Dihedral  :  5.957  54.117   1013
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.66 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 16.31 %
    Favored  : 80.11 %
  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:  1.10 (0.31), residues: 792
  helix:  1.56 (0.26), residues: 397
  sheet: -0.47 (0.72), residues: 60
  loop :  0.06 (0.36), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP D 478 
 HIS   0.007   0.001   HIS D 493 
 PHE   0.030   0.002   PHE D 327 
 TYR   0.017   0.002   TYR D 497 
 ARG   0.002   0.000   ARG D 245 

*********************** 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
  131 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 106
  time to evaluate  : 0.711 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  115 ARG cc_start: 0.8573 (tpp-160) cc_final: 0.8372 (tpm170)
REVERT: D  182 GLU cc_start: 0.8393 (tt0) cc_final: 0.8179 (tt0)
REVERT: D  249 MET cc_start: 0.7150 (mmm) cc_final: 0.6918 (mmm)
REVERT: D  270 MET cc_start: 0.7864 (tpp) cc_final: 0.7602 (tpp)
REVERT: D  323 MET cc_start: 0.9427 (tpp) cc_final: 0.9147 (mmm)
REVERT: D  375 GLU cc_start: 0.8668 (mm-30) cc_final: 0.7865 (mm-30)
REVERT: D  441 LYS cc_start: 0.8821 (tttt) cc_final: 0.8451 (tptp)
REVERT: D  493 HIS cc_start: 0.6407 (m-70) cc_final: 0.6014 (m90)
REVERT: D  497 TYR cc_start: 0.7217 (m-10) cc_final: 0.6555 (m-10)
  outliers start: 25
  outliers final: 19
  residues processed: 119
  average time/residue: 0.2040
  time to fit residues: 32.1255
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  : 0.693 
-------------------------------------------------------------------------------
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  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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 59 optimal weight:    0.1980
   chunk 52 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 75 optimal weight:    0.4980
   chunk 40 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 73 optimal weight:    0.7980
   chunk 58 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3518 r_free = 0.3518 target = 0.092629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.082176 restraints weight = 18599.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.084409 restraints weight = 9124.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.085862 restraints weight = 5524.548|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.5911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6727  Z= 0.205
  Angle     :  0.617   8.631   9143  Z= 0.319
  Chirality :  0.049   0.419    977
  Planarity :  0.004   0.045   1177
  Dihedral  :  5.665  52.786   1013
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.65 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 17.31 %
    Favored  : 79.83 %
  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:  1.18 (0.31), residues: 792
  helix:  1.65 (0.26), residues: 395
  sheet: -0.50 (0.73), residues: 60
  loop :  0.09 (0.35), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP D 478 
 HIS   0.004   0.001   HIS D 493 
 PHE   0.029   0.002   PHE D 327 
 TYR   0.026   0.001   TYR D 158 
 ARG   0.004   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
  136 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   35 GLN cc_start: 0.8782 (mp10) cc_final: 0.8573 (mp10)
REVERT: D  237 TYR cc_start: 0.9099 (t80) cc_final: 0.8893 (t80)
REVERT: D  270 MET cc_start: 0.7859 (tpp) cc_final: 0.7635 (tpp)
REVERT: D  323 MET cc_start: 0.9419 (tpp) cc_final: 0.9111 (mmm)
REVERT: D  441 LYS cc_start: 0.8755 (tttt) cc_final: 0.8321 (tptp)
REVERT: D  493 HIS cc_start: 0.6311 (m-70) cc_final: 0.5592 (m-70)
REVERT: D  497 TYR cc_start: 0.7064 (m-10) cc_final: 0.6428 (m-10)
  outliers start: 20
  outliers final: 18
  residues processed: 127
  average time/residue: 0.1875
  time to fit residues: 32.1925
Evaluate side-chains
  122 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 LYS
Chi-restraints excluded: chain A residue  385 THR
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   73 LEU
Chi-restraints excluded: chain D residue   79 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  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  498 CYS
Chi-restraints excluded: chain D residue  522 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 56 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 36 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.3484 r_free = 0.3484 target = 0.090925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.080342 restraints weight = 19153.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.082624 restraints weight = 9154.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.084126 restraints weight = 5491.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.6025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   6727  Z= 0.248
  Angle     :  0.658   8.815   9143  Z= 0.341
  Chirality :  0.050   0.416    977
  Planarity :  0.005   0.050   1177
  Dihedral  :  5.731  53.337   1013
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.66 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 18.03 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.00 (0.31), residues: 792
  helix:  1.53 (0.26), residues: 397
  sheet: -0.54 (0.73), residues: 60
  loop : -0.05 (0.36), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP D 478 
 HIS   0.003   0.001   HIS A 519 
 PHE   0.033   0.002   PHE A 486 
 TYR   0.025   0.002   TYR D 158 
 ARG   0.003   0.000   ARG A 454 

********************** 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
  128 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.703 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  343 ASN cc_start: 0.8128 (m-40) cc_final: 0.7906 (t0)
REVERT: A  421 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.7210 (p90)
REVERT: D  270 MET cc_start: 0.7862 (tpp) cc_final: 0.7587 (tpp)
REVERT: D  323 MET cc_start: 0.9447 (tpp) cc_final: 0.9158 (mmm)
REVERT: D  375 GLU cc_start: 0.8608 (mm-30) cc_final: 0.7844 (mm-30)
REVERT: D  406 GLU cc_start: 0.8199 (tp30) cc_final: 0.7590 (tp30)
REVERT: D  441 LYS cc_start: 0.8830 (tttt) cc_final: 0.8335 (tptp)
REVERT: D  474 MET cc_start: 0.8431 (mmp) cc_final: 0.8205 (mmm)
REVERT: D  493 HIS cc_start: 0.6527 (m-70) cc_final: 0.5054 (m170)
  outliers start: 23
  outliers final: 19
  residues processed: 118
  average time/residue: 0.1783
  time to fit residues: 28.6540
Evaluate side-chains
  123 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 LYS
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   73 LEU
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   90 ASN
Chi-restraints excluded: chain D residue  111 ASP
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  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:    0.9990
   chunk 31 optimal weight:    0.0060
   chunk 47 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 62 optimal weight:    0.0980
   chunk 68 optimal weight:    0.0970
   chunk 40 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 76 optimal weight:    0.5980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.2994

-------------------------------------------------------------------------------
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 = 0.3537 r_free = 0.3537 target = 0.093839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.083027 restraints weight = 19146.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.085393 restraints weight = 9212.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.086938 restraints weight = 5510.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.6182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6727  Z= 0.186
  Angle     :  0.615   8.027   9143  Z= 0.318
  Chirality :  0.048   0.388    977
  Planarity :  0.005   0.047   1177
  Dihedral  :  5.451  51.968   1013
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 18.74 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.21 (0.31), residues: 792
  helix:  1.66 (0.26), residues: 394
  sheet:  0.15 (0.81), residues: 50
  loop : -0.01 (0.35), residues: 348

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   0.024   0.001   TYR D 158 
 ARG   0.004   0.000   ARG D 482 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2588.04 seconds
wall clock time: 45 minutes 45.32 seconds (2745.32 seconds total)