Starting phenix.real_space_refine
on Tue Feb 11 08:51:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wcr_32428/02_2025/7wcr_32428.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wcr_32428/02_2025/7wcr_32428.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/7wcr_32428/02_2025/7wcr_32428.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wcr_32428/02_2025/7wcr_32428.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wcr_32428/02_2025/7wcr_32428.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wcr_32428/02_2025/7wcr_32428.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=   0.053
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      21      5.16       5
     C    3094      2.51       5
     N     800      2.21       5
     O     965      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4880
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1563
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 197, 1563
          Classifications: {'peptide': 197}
          Link IDs: {'PTRANS': 11, 'TRANS': 185}
    Chain: "a"
      Number of atoms: 1627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1627
          Classifications: {'peptide': 214}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 200}
    Chain: "b"
      Number of atoms: 1690
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1690
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 7, 'TRANS': 205}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
  Time building chain proxies: 4.28, per 1000 atoms: 0.88
  Number of scatterers: 4880
  At special positions: 0
  Unit cell: (68.859, 87.44, 138.811, 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      21     16.00
     O     965      8.00
     N     800      7.00
     C    3094      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.00
    Simple disulfide: pdb=" SG  CYS a  22 " - pdb=" SG  CYS a  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS a 144 " - pdb=" SG  CYS a 199 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b  23 " - pdb=" SG  CYS b  94 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b 139 " - pdb=" SG  CYS b 199 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.09
  Conformation dependent library (CDL) restraints added in 626.2 milliseconds
  

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1176

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 12 sheets defined
      7.3% alpha, 38.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.69
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 341
      removed outlier: 4.042A  pdb=" N   VAL A 341 " --> pdb=" O   PHE A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 370
      removed outlier: 3.530A  pdb=" N   TYR A 369 " --> pdb=" O   TYR A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 387
      removed outlier: 3.963A  pdb=" N   LEU A 387 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.966A  pdb=" N   VAL A 407 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 87 through 91
      removed outlier: 3.648A  pdb=" N   SER a  91 " --> pdb=" O   PHE a  88 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 85 through 89
      removed outlier: 3.826A  pdb=" N   LEU b  89 " --> pdb=" O   ALA b  86 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 126 through 132
    Processing helix  chain 'b' and resid 188 through 193
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.921A  pdb=" N   ASN A 354 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   SER A 399 " --> pdb=" O   ASN A 354 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ILE A 358 " --> pdb=" O   VAL A 395 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLU A 516 " --> pdb=" O   ASN A 394 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'a' and resid 3 through 6
    Processing sheet with id=AA3, first strand: chain 'a' and resid 10 through 12
      removed outlier: 6.268A  pdb=" N   GLU a  10 " --> pdb=" O   THR a 114 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   THR a  33 " --> pdb=" O   ASP a  99 " (cutoff:3.500A)
      removed outlier: 6.993A  pdb=" N   MET a  34 " --> pdb=" O   GLY a  50 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   GLY a  50 " --> pdb=" O   MET a  34 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   TRP a  36 " --> pdb=" O   ILE a  48 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'a' and resid 10 through 12
      removed outlier: 6.268A  pdb=" N   GLU a  10 " --> pdb=" O   THR a 114 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'a' and resid 124 through 128
      removed outlier: 3.735A  pdb=" N   GLY a 143 " --> pdb=" O   LEU a 128 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLY a 148 " --> pdb=" O   TYR a 179 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   TYR a 179 " --> pdb=" O   GLY a 148 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'a' and resid 124 through 128
      removed outlier: 3.735A  pdb=" N   GLY a 143 " --> pdb=" O   LEU a 128 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLY a 148 " --> pdb=" O   TYR a 179 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   TYR a 179 " --> pdb=" O   GLY a 148 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'a' and resid 155 through 158
      removed outlier: 3.763A  pdb=" N   VAL a 197 " --> pdb=" O   ILE a 214 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   VAL a 210 " --> pdb=" O   VAL a 201 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   THR a 208 " --> pdb=" O   HIS a 203 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'b' and resid 4 through 7
      removed outlier: 3.770A  pdb=" N   THR b  22 " --> pdb=" O   SER b   7 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   ASP b  76 " --> pdb=" O   SER b  73 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'b' and resid 10 through 12
      removed outlier: 7.079A  pdb=" N   LEU b  11 " --> pdb=" O   GLU b 111 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   LEU b  39 " --> pdb=" O   TYR b  55 " (cutoff:3.500A)
      removed outlier: 5.018A  pdb=" N   TYR b  55 " --> pdb=" O   LEU b  39 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   TRP b  41 " --> pdb=" O   LEU b  53 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'b' and resid 30 through 31
      removed outlier: 3.732A  pdb=" N   LYS b  36 " --> pdb=" O   TYR b  31 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'b' and resid 121 through 123
      removed outlier: 3.562A  pdb=" N   SER b 121 " --> pdb=" O   PHE b 140 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   VAL b 138 " --> pdb=" O   PHE b 123 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LEU b 184 " --> pdb=" O   VAL b 137 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   CYS b 139 " --> pdb=" O   SER b 182 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   SER b 182 " --> pdb=" O   CYS b 139 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   TYR b 178 " --> pdb=" O   ASN b 143 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'b' and resid 158 through 159
      removed outlier: 3.525A  pdb=" N   ASN b 150 " --> pdb=" O   THR b 202 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   TYR b 197 " --> pdb=" O   PHE b 214 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   PHE b 214 " --> pdb=" O   TYR b 197 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   CYS b 199 " --> pdb=" O   LYS b 212 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   LYS b 212 " --> pdb=" O   CYS b 199 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ALA b 201 " --> pdb=" O   ILE b 210 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ILE b 210 " --> pdb=" O   ALA b 201 " (cutoff:3.500A)

    160 hydrogen bonds defined for protein.
    393 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: 1.39

  Time building geometry restraints manager: 1.31 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1398
        1.33 -     1.46: 1043
        1.46 -     1.58: 2540
        1.58 -     1.70: 0
        1.70 -     1.82: 26
  Bond restraints: 5007
  Sorted by residual:
  bond pdb=" CA  PHE A 490 "
       pdb=" C   PHE A 490 "
    ideal  model  delta    sigma   weight residual
    1.528  1.503  0.025 1.18e-02 7.18e+03 4.62e+00
  bond pdb=" C   ASN a  52 "
       pdb=" O   ASN a  52 "
    ideal  model  delta    sigma   weight residual
    1.241  1.213  0.027 1.33e-02 5.65e+03 4.22e+00
  bond pdb=" CA  GLN A 493 "
       pdb=" C   GLN A 493 "
    ideal  model  delta    sigma   weight residual
    1.528  1.497  0.031 1.51e-02 4.39e+03 4.11e+00
  bond pdb=" CA  ILE a  55 "
       pdb=" C   ILE a  55 "
    ideal  model  delta    sigma   weight residual
    1.530  1.508  0.022 1.12e-02 7.97e+03 3.99e+00
  bond pdb=" C   LEU A 492 "
       pdb=" O   LEU A 492 "
    ideal  model  delta    sigma   weight residual
    1.235  1.214  0.021 1.18e-02 7.18e+03 3.18e+00
  ... (remaining 5002 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.50: 6530
        1.50 -     3.00: 240
        3.00 -     4.51: 37
        4.51 -     6.01: 8
        6.01 -     7.51: 10
  Bond angle restraints: 6825
  Sorted by residual:
  angle pdb=" C   LYS a  65 "
        pdb=" N   ASP a  66 "
        pdb=" CA  ASP a  66 "
      ideal   model   delta    sigma   weight residual
     122.08  129.13   -7.05 1.47e+00 4.63e-01 2.30e+01
  angle pdb=" N   TYR A 489 "
        pdb=" CA  TYR A 489 "
        pdb=" C   TYR A 489 "
      ideal   model   delta    sigma   weight residual
     109.65  116.18   -6.53 1.56e+00 4.11e-01 1.75e+01
  angle pdb=" C   ARG b 113 "
        pdb=" N   ALA b 114 "
        pdb=" CA  ALA b 114 "
      ideal   model   delta    sigma   weight residual
     121.70  129.21   -7.51 1.80e+00 3.09e-01 1.74e+01
  angle pdb=" N   ASP a  56 "
        pdb=" CA  ASP a  56 "
        pdb=" C   ASP a  56 "
      ideal   model   delta    sigma   weight residual
     111.39  117.09   -5.70 1.38e+00 5.25e-01 1.71e+01
  angle pdb=" C   ILE a  51 "
        pdb=" CA  ILE a  51 "
        pdb=" CB  ILE a  51 "
      ideal   model   delta    sigma   weight residual
     111.29  105.20    6.09 1.64e+00 3.72e-01 1.38e+01
  ... (remaining 6820 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.46: 2652
       15.46 -    30.93: 244
       30.93 -    46.39: 59
       46.39 -    61.85: 14
       61.85 -    77.31: 7
  Dihedral angle restraints: 2976
    sinusoidal: 1136
      harmonic: 1840
  Sorted by residual:
  dihedral pdb=" CB  CYS b 139 "
           pdb=" SG  CYS b 139 "
           pdb=" SG  CYS b 199 "
           pdb=" CB  CYS b 199 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  169.59  -76.59     1      1.00e+01 1.00e-02 7.37e+01
  dihedral pdb=" CB  CYS A 336 "
           pdb=" SG  CYS A 336 "
           pdb=" SG  CYS A 361 "
           pdb=" CB  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   16.61   76.39     1      1.00e+01 1.00e-02 7.34e+01
  dihedral pdb=" CA  GLY A 502 "
           pdb=" C   GLY A 502 "
           pdb=" N   VAL A 503 "
           pdb=" CA  VAL A 503 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -138.94  -41.06     0      5.00e+00 4.00e-02 6.74e+01
  ... (remaining 2973 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 596
       0.050 -    0.099: 118
       0.099 -    0.149: 35
       0.149 -    0.199: 5
       0.199 -    0.248: 1
  Chirality restraints: 755
  Sorted by residual:
  chirality pdb=" CA  ASP a  56 "
            pdb=" N   ASP a  56 "
            pdb=" C   ASP a  56 "
            pdb=" CB  ASP a  56 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.54e+00
  chirality pdb=" CB  ILE b 155 "
            pdb=" CA  ILE b 155 "
            pdb=" CG1 ILE b 155 "
            pdb=" CG2 ILE b 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.31e-01
  chirality pdb=" CA  TYR A 489 "
            pdb=" N   TYR A 489 "
            pdb=" C   TYR A 489 "
            pdb=" CB  TYR A 489 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.20e-01
  ... (remaining 752 not shown)

  Planarity restraints: 875
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 502 "   -0.010 2.00e-02 2.50e+03   1.96e-02 3.85e+00
        pdb=" C   GLY A 502 "    0.034 2.00e-02 2.50e+03
        pdb=" O   GLY A 502 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   VAL A 503 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU a 152 "    0.030 5.00e-02 4.00e+02   4.55e-02 3.31e+00
        pdb=" N   PRO a 153 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO a 153 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO a 153 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 490 "    0.028 5.00e-02 4.00e+02   4.26e-02 2.91e+00
        pdb=" N   PRO A 491 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 491 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 491 "    0.025 5.00e-02 4.00e+02
  ... (remaining 872 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.35: 5
        2.35 -     2.99: 2317
        2.99 -     3.63: 6348
        3.63 -     4.26: 10307
        4.26 -     4.90: 17217
  Nonbonded interactions: 36194
  Sorted by model distance:
  nonbonded pdb=" CD1 LEU A 455 "
            pdb=" OE1 GLN A 493 "
     model   vdw
     1.713 3.460
  nonbonded pdb=" CD1 LEU A 455 "
            pdb=" CD  GLN A 493 "
     model   vdw
     1.960 3.690
  nonbonded pdb=" CD1 LEU A 455 "
            pdb=" NE2 GLN A 493 "
     model   vdw
     2.206 3.540
  nonbonded pdb=" OH  TYR A 453 "
            pdb=" OE1 GLN A 493 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OD1 ASP b  88 "
            pdb=" OH  TYR b  92 "
     model   vdw
     2.314 3.040
  ... (remaining 36189 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:             5.120
  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:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.610
  Find NCS groups from input model:        0.080
  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:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6318
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      :  0.003   0.031   5007  Z= 0.197
  Angle     :  0.708   7.512   6825  Z= 0.420
  Chirality :  0.046   0.248    755
  Planarity :  0.006   0.046    875
  Dihedral  : 12.878  77.314   1776
  Min Nonbonded Distance : 1.713

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  2.73 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  5.65 %
    Favored  : 93.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.76 (0.28), residues: 622
  helix: -5.01 (0.15), residues: 42
  sheet: -0.54 (0.32), residues: 223
  loop : -2.37 (0.26), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 436 
 HIS   0.003   0.001   HIS A 519 
 PHE   0.011   0.001   PHE b 144 
 TYR   0.010   0.001   TYR A 501 
 ARG   0.001   0.000   ARG b  18 

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 182
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  468 ILE cc_start: 0.7911 (mp) cc_final: 0.7528 (pt)
REVERT: b   42 TYR cc_start: 0.7893 (m-80) cc_final: 0.7493 (m-80)
  outliers start: 7
  outliers final: 5
  residues processed: 186
  average time/residue: 0.1734
  time to fit residues: 40.4641
Evaluate side-chains
  140 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 135
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  489 TYR
Chi-restraints excluded: chain A residue  493 GLN
Chi-restraints excluded: chain a residue   52 ASN
Chi-restraints excluded: chain a residue   55 ILE
Chi-restraints excluded: chain a residue   59 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0070
   chunk 18 optimal weight:    0.0870
   chunk 29 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0170
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.3814

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN
** a   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  43 GLN
b  34 ASN
b  43 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.207229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.184782 restraints weight = 8415.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.189448 restraints weight = 4869.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.192664 restraints weight = 3236.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.4297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6499
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5007  Z= 0.193
  Angle     :  0.575   7.915   6825  Z= 0.297
  Chirality :  0.043   0.175    755
  Planarity :  0.005   0.056    875
  Dihedral  :  5.414  55.223    694
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 14.21 %
    Favored  : 82.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    Cis-general     : 0.17 %
    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: -1.87 (0.30), residues: 622
  helix: -4.25 (0.32), residues: 42
  sheet:  0.01 (0.32), residues: 232
  loop : -1.78 (0.29), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP a  36 
 HIS   0.005   0.001   HIS b 203 
 PHE   0.015   0.001   PHE b  77 
 TYR   0.017   0.002   TYR a 179 
 ARG   0.006   0.001   ARG b 113 

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 139
  time to evaluate  : 0.601 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 TYR cc_start: 0.8059 (p90) cc_final: 0.7787 (p90)
REVERT: A  448 ASN cc_start: 0.6582 (t0) cc_final: 0.6076 (m-40)
REVERT: A  468 ILE cc_start: 0.7995 (mp) cc_final: 0.7765 (mp)
REVERT: a   10 GLU cc_start: 0.7232 (mp0) cc_final: 0.7019 (mp0)
REVERT: a   19 LYS cc_start: 0.7453 (mttt) cc_final: 0.6958 (pttm)
REVERT: a   90 ASP cc_start: 0.7575 (m-30) cc_final: 0.7295 (m-30)
REVERT: a  185 VAL cc_start: 0.7242 (m) cc_final: 0.6940 (t)
REVERT: a  195 GLU cc_start: 0.6295 (tp30) cc_final: 0.5825 (mt-10)
REVERT: b    4 MET cc_start: 0.6583 (mtt) cc_final: 0.6192 (mtt)
REVERT: b   42 TYR cc_start: 0.8101 (m-80) cc_final: 0.7718 (m-80)
REVERT: b  147 LYS cc_start: 0.7165 (pttt) cc_final: 0.6958 (pttt)
REVERT: b  210 ILE cc_start: 0.7702 (mt) cc_final: 0.7491 (pt)
  outliers start: 16
  outliers final: 11
  residues processed: 146
  average time/residue: 0.1561
  time to fit residues: 29.7882
Evaluate side-chains
  134 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 123
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  489 TYR
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain a residue   55 ILE
Chi-restraints excluded: chain a residue   58 THR
Chi-restraints excluded: chain a residue   59 THR
Chi-restraints excluded: chain a residue  183 SER
Chi-restraints excluded: chain b residue   19 VAL
Chi-restraints excluded: chain b residue   34 ASN
Chi-restraints excluded: chain b residue  112 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 35 optimal weight:    0.0170
   chunk 60 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.7620

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

Flipped N/Q/H residues before XYZ refinement:
a   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.199449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.177255 restraints weight = 8448.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.181631 restraints weight = 5014.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.184696 restraints weight = 3397.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.4225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6687
moved from start:          0.3473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   5007  Z= 0.252
  Angle     :  0.594   6.645   6825  Z= 0.310
  Chirality :  0.044   0.170    755
  Planarity :  0.005   0.047    875
  Dihedral  :  5.054  48.684    689
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 16.76 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    Cis-general     : 0.17 %
    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: -1.27 (0.32), residues: 622
  helix: -3.36 (0.62), residues: 36
  sheet:  0.33 (0.33), residues: 238
  loop : -1.45 (0.30), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP a  36 
 HIS   0.003   0.001   HIS b 203 
 PHE   0.021   0.002   PHE b  77 
 TYR   0.017   0.002   TYR A 453 
 ARG   0.005   0.001   ARG b 113 

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 130
  time to evaluate  : 0.585 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 TYR cc_start: 0.8131 (p90) cc_final: 0.7856 (p90)
REVERT: A  380 TYR cc_start: 0.5499 (m-80) cc_final: 0.5196 (m-10)
REVERT: A  468 ILE cc_start: 0.8022 (mp) cc_final: 0.7776 (mp)
REVERT: a   19 LYS cc_start: 0.7550 (mttt) cc_final: 0.7086 (pttm)
REVERT: a   90 ASP cc_start: 0.7590 (m-30) cc_final: 0.7190 (m-30)
REVERT: a  195 GLU cc_start: 0.6632 (tp30) cc_final: 0.6190 (mt-10)
REVERT: b  200 GLU cc_start: 0.7898 (tt0) cc_final: 0.7358 (tp30)
REVERT: b  210 ILE cc_start: 0.7734 (mt) cc_final: 0.7462 (pt)
  outliers start: 19
  outliers final: 15
  residues processed: 139
  average time/residue: 0.1557
  time to fit residues: 28.1022
Evaluate side-chains
  132 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  489 TYR
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain a residue   41 HIS
Chi-restraints excluded: chain a residue   55 ILE
Chi-restraints excluded: chain a residue  128 LEU
Chi-restraints excluded: chain a residue  210 VAL
Chi-restraints excluded: chain b residue   19 VAL
Chi-restraints excluded: chain b residue   84 VAL
Chi-restraints excluded: chain b residue  112 LEU
Chi-restraints excluded: chain b residue  175 ASP
Chi-restraints excluded: chain b residue  197 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 19 optimal weight:    0.0980
   chunk 43 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 54 optimal weight:    0.4980
   chunk 35 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0070
   chunk 23 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.4198

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

Flipped N/Q/H residues before XYZ refinement:
a  62 GLN
b  34 ASN
b  44 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.200256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.178406 restraints weight = 8442.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.182846 restraints weight = 4965.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.185867 restraints weight = 3332.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.4237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6673
moved from start:          0.3821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5007  Z= 0.173
  Angle     :  0.549   6.975   6825  Z= 0.283
  Chirality :  0.043   0.168    755
  Planarity :  0.004   0.045    875
  Dihedral  :  4.802  48.280    688
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 19.31 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    Cis-general     : 0.17 %
    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: -1.06 (0.32), residues: 622
  helix: -2.81 (0.76), residues: 36
  sheet:  0.49 (0.33), residues: 238
  loop : -1.37 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP a  36 
 HIS   0.005   0.001   HIS a 203 
 PHE   0.018   0.001   PHE b  77 
 TYR   0.017   0.001   TYR A 449 
 ARG   0.004   0.000   ARG b 113 

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 TYR cc_start: 0.8132 (p90) cc_final: 0.7864 (p90)
REVERT: A  380 TYR cc_start: 0.5805 (m-80) cc_final: 0.5566 (m-10)
REVERT: A  468 ILE cc_start: 0.7992 (mp) cc_final: 0.7747 (mp)
REVERT: a   19 LYS cc_start: 0.7500 (mttt) cc_final: 0.7074 (pttm)
REVERT: a   90 ASP cc_start: 0.7661 (m-30) cc_final: 0.7234 (m-30)
REVERT: a  154 VAL cc_start: 0.6740 (m) cc_final: 0.6354 (m)
REVERT: b   42 TYR cc_start: 0.8123 (m-80) cc_final: 0.7788 (m-80)
REVERT: b  210 ILE cc_start: 0.7861 (mt) cc_final: 0.7580 (tp)
  outliers start: 16
  outliers final: 13
  residues processed: 127
  average time/residue: 0.1426
  time to fit residues: 23.9203
Evaluate side-chains
  121 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  489 TYR
Chi-restraints excluded: chain a residue   41 HIS
Chi-restraints excluded: chain a residue   55 ILE
Chi-restraints excluded: chain a residue  128 LEU
Chi-restraints excluded: chain a residue  160 SER
Chi-restraints excluded: chain a residue  181 LEU
Chi-restraints excluded: chain b residue   19 VAL
Chi-restraints excluded: chain b residue   84 VAL
Chi-restraints excluded: chain b residue  112 LEU
Chi-restraints excluded: chain b residue  197 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0470
   chunk 9 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.2980
   chunk 44 optimal weight:    0.5980
   chunk 47 optimal weight:    0.4980
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.4678

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

Flipped N/Q/H residues before XYZ refinement:
a  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.199104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.177685 restraints weight = 8809.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.181898 restraints weight = 5240.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.184824 restraints weight = 3556.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.4212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6729
moved from start:          0.4155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5007  Z= 0.179
  Angle     :  0.552   8.673   6825  Z= 0.282
  Chirality :  0.043   0.168    755
  Planarity :  0.004   0.044    875
  Dihedral  :  4.911  47.182    688
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 18.03 %
    Favored  : 77.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    Cis-general     : 0.17 %
    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: -0.80 (0.33), residues: 622
  helix: -2.74 (0.72), residues: 42
  sheet:  0.76 (0.33), residues: 237
  loop : -1.21 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP a 158 
 HIS   0.002   0.000   HIS a 203 
 PHE   0.018   0.001   PHE b  77 
 TYR   0.013   0.001   TYR A 449 
 ARG   0.002   0.000   ARG b 113 

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 116
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 TYR cc_start: 0.8218 (p90) cc_final: 0.7951 (p90)
REVERT: A  468 ILE cc_start: 0.8053 (mp) cc_final: 0.7800 (mp)
REVERT: a   19 LYS cc_start: 0.7450 (mttt) cc_final: 0.7091 (pttm)
REVERT: a   90 ASP cc_start: 0.7811 (m-30) cc_final: 0.7433 (m-30)
REVERT: a  139 MET cc_start: 0.5261 (mmm) cc_final: 0.4601 (mtm)
REVERT: b   42 TYR cc_start: 0.8102 (m-80) cc_final: 0.7814 (m-80)
REVERT: b   97 TYR cc_start: 0.3401 (OUTLIER) cc_final: 0.2352 (m-80)
REVERT: b  200 GLU cc_start: 0.7737 (tt0) cc_final: 0.7440 (tp30)
REVERT: b  210 ILE cc_start: 0.7982 (mt) cc_final: 0.7761 (pt)
  outliers start: 22
  outliers final: 15
  residues processed: 128
  average time/residue: 0.1544
  time to fit residues: 25.8499
Evaluate side-chains
  128 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  489 TYR
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain a residue   41 HIS
Chi-restraints excluded: chain a residue   55 ILE
Chi-restraints excluded: chain a residue  160 SER
Chi-restraints excluded: chain a residue  181 LEU
Chi-restraints excluded: chain b residue   19 VAL
Chi-restraints excluded: chain b residue   84 VAL
Chi-restraints excluded: chain b residue   97 TYR
Chi-restraints excluded: chain b residue  112 LEU
Chi-restraints excluded: chain b residue  119 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 20 optimal weight:    0.4980
   chunk 60 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  62 GLN
b  34 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.195328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.173705 restraints weight = 8682.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.177774 restraints weight = 5223.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.180624 restraints weight = 3605.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.4168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6806
moved from start:          0.4538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   5007  Z= 0.225
  Angle     :  0.572   6.649   6825  Z= 0.297
  Chirality :  0.043   0.170    755
  Planarity :  0.004   0.043    875
  Dihedral  :  5.102  49.265    688
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 19.49 %
    Favored  : 77.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    Cis-general     : 0.17 %
    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: -0.59 (0.33), residues: 622
  helix: -1.89 (0.98), residues: 30
  sheet:  0.77 (0.33), residues: 237
  loop : -1.12 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP a 192 
 HIS   0.001   0.000   HIS b 194 
 PHE   0.018   0.002   PHE b  77 
 TYR   0.011   0.002   TYR A 451 
 ARG   0.003   0.000   ARG A 509 

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.586 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  458 LYS cc_start: 0.8358 (ptmt) cc_final: 0.7242 (mmtm)
REVERT: A  468 ILE cc_start: 0.8137 (mp) cc_final: 0.7874 (mp)
REVERT: a   19 LYS cc_start: 0.7418 (mttt) cc_final: 0.7118 (pttm)
REVERT: a   90 ASP cc_start: 0.7730 (m-30) cc_final: 0.7374 (m-30)
REVERT: a  139 MET cc_start: 0.5294 (mmm) cc_final: 0.4820 (mtm)
REVERT: b   42 TYR cc_start: 0.8159 (m-80) cc_final: 0.7936 (m-80)
REVERT: b   97 TYR cc_start: 0.3557 (OUTLIER) cc_final: 0.2742 (m-80)
REVERT: b  210 ILE cc_start: 0.7993 (mt) cc_final: 0.7757 (pt)
  outliers start: 18
  outliers final: 17
  residues processed: 126
  average time/residue: 0.1569
  time to fit residues: 25.9858
Evaluate side-chains
  132 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  489 TYR
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain a residue   41 HIS
Chi-restraints excluded: chain a residue   55 ILE
Chi-restraints excluded: chain a residue  160 SER
Chi-restraints excluded: chain a residue  181 LEU
Chi-restraints excluded: chain b residue   19 VAL
Chi-restraints excluded: chain b residue   84 VAL
Chi-restraints excluded: chain b residue   97 TYR
Chi-restraints excluded: chain b residue  112 LEU
Chi-restraints excluded: chain b residue  119 THR
Chi-restraints excluded: chain b residue  197 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 18 optimal weight:    0.2980
   chunk 56 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 34 optimal weight:    0.3980
   chunk 16 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 57 optimal weight:    4.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.193973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.172862 restraints weight = 8734.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.176849 restraints weight = 5236.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.179693 restraints weight = 3611.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.4161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6823
moved from start:          0.4798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5007  Z= 0.230
  Angle     :  0.582   8.215   6825  Z= 0.303
  Chirality :  0.043   0.169    755
  Planarity :  0.004   0.039    875
  Dihedral  :  5.219  53.212    688
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 19.13 %
    Favored  : 76.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    Cis-general     : 0.17 %
    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: -0.56 (0.34), residues: 622
  helix: -1.61 (1.14), residues: 24
  sheet:  0.98 (0.34), residues: 225
  loop : -1.21 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP a 192 
 HIS   0.003   0.001   HIS a 203 
 PHE   0.018   0.002   PHE b  77 
 TYR   0.011   0.002   TYR a 179 
 ARG   0.002   0.000   ARG b 160 

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 122
  time to evaluate  : 0.563 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 TYR cc_start: 0.8230 (p90) cc_final: 0.7959 (p90)
REVERT: A  458 LYS cc_start: 0.8292 (ptmt) cc_final: 0.7420 (mmmt)
REVERT: A  468 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7825 (mp)
REVERT: a   19 LYS cc_start: 0.7405 (mttt) cc_final: 0.7116 (pttm)
REVERT: a   90 ASP cc_start: 0.7710 (m-30) cc_final: 0.7370 (m-30)
REVERT: a  139 MET cc_start: 0.5499 (mmm) cc_final: 0.4930 (mtm)
REVERT: a  178 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6764 (mt)
REVERT: a  192 TRP cc_start: 0.5125 (t-100) cc_final: 0.4917 (t-100)
REVERT: b   42 TYR cc_start: 0.8156 (m-80) cc_final: 0.7916 (m-80)
REVERT: b   97 TYR cc_start: 0.3601 (OUTLIER) cc_final: 0.2758 (m-80)
REVERT: b  210 ILE cc_start: 0.8067 (mt) cc_final: 0.7805 (pt)
  outliers start: 22
  outliers final: 17
  residues processed: 132
  average time/residue: 0.1523
  time to fit residues: 26.2599
Evaluate side-chains
  136 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  489 TYR
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain a residue   41 HIS
Chi-restraints excluded: chain a residue   55 ILE
Chi-restraints excluded: chain a residue  178 LEU
Chi-restraints excluded: chain a residue  181 LEU
Chi-restraints excluded: chain a residue  210 VAL
Chi-restraints excluded: chain b residue   19 VAL
Chi-restraints excluded: chain b residue   84 VAL
Chi-restraints excluded: chain b residue   97 TYR
Chi-restraints excluded: chain b residue  112 LEU
Chi-restraints excluded: chain b residue  197 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 57 optimal weight:    4.9990
   chunk 16 optimal weight:    0.4980
   chunk 42 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.192579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.171411 restraints weight = 8749.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.175423 restraints weight = 5270.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.178141 restraints weight = 3646.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.4150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6862
moved from start:          0.5130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   5007  Z= 0.251
  Angle     :  0.603   8.967   6825  Z= 0.316
  Chirality :  0.044   0.168    755
  Planarity :  0.004   0.038    875
  Dihedral  :  5.504  58.654    688
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 19.49 %
    Favored  : 75.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    Cis-general     : 0.17 %
    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: -0.60 (0.34), residues: 622
  helix: -2.36 (0.95), residues: 30
  sheet:  0.99 (0.34), residues: 225
  loop : -1.18 (0.32), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP b 153 
 HIS   0.001   0.000   HIS a 203 
 PHE   0.018   0.002   PHE b  77 
 TYR   0.012   0.002   TYR b 100 
 ARG   0.002   0.000   ARG A 454 

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 118
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 TYR cc_start: 0.8231 (p90) cc_final: 0.7927 (p90)
REVERT: A  379 CYS cc_start: 0.5653 (m) cc_final: 0.5319 (m)
REVERT: A  458 LYS cc_start: 0.8386 (ptmt) cc_final: 0.7482 (mmmt)
REVERT: A  468 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7828 (mp)
REVERT: a   19 LYS cc_start: 0.7517 (mttt) cc_final: 0.7186 (pttm)
REVERT: a   41 HIS cc_start: 0.5098 (OUTLIER) cc_final: 0.4833 (m170)
REVERT: a   90 ASP cc_start: 0.7746 (m-30) cc_final: 0.7394 (m-30)
REVERT: a  139 MET cc_start: 0.5516 (mmm) cc_final: 0.4923 (mtt)
REVERT: a  178 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6921 (mt)
REVERT: b   97 TYR cc_start: 0.3693 (OUTLIER) cc_final: 0.2596 (m-80)
  outliers start: 25
  outliers final: 20
  residues processed: 128
  average time/residue: 0.1545
  time to fit residues: 25.8228
Evaluate side-chains
  139 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  489 TYR
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain a residue   11 LEU
Chi-restraints excluded: chain a residue   41 HIS
Chi-restraints excluded: chain a residue   55 ILE
Chi-restraints excluded: chain a residue  178 LEU
Chi-restraints excluded: chain a residue  181 LEU
Chi-restraints excluded: chain a residue  210 VAL
Chi-restraints excluded: chain b residue   19 VAL
Chi-restraints excluded: chain b residue   84 VAL
Chi-restraints excluded: chain b residue   97 TYR
Chi-restraints excluded: chain b residue  112 LEU
Chi-restraints excluded: chain b residue  149 ILE
Chi-restraints excluded: chain b residue  197 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 37 optimal weight:    0.0010
   chunk 23 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.7188

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

Flipped N/Q/H residues before XYZ refinement:
** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  62 GLN
a 168 HIS
** a 203 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 = 0.4294 r_free = 0.4294 target = 0.193062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.172092 restraints weight = 8588.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.176099 restraints weight = 5190.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.178854 restraints weight = 3592.905|
|-----------------------------------------------------------------------------|
r_work (final): 0.4149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6853
moved from start:          0.5313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5007  Z= 0.229
  Angle     :  0.596   8.452   6825  Z= 0.312
  Chirality :  0.044   0.166    755
  Planarity :  0.004   0.036    875
  Dihedral  :  5.284  49.084    688
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 20.40 %
    Favored  : 75.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    Cis-general     : 0.17 %
    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: -0.60 (0.34), residues: 622
  helix: -2.46 (0.94), residues: 30
  sheet:  1.06 (0.35), residues: 220
  loop : -1.20 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP a 192 
 HIS   0.003   0.001   HIS a 203 
 PHE   0.017   0.001   PHE b  77 
 TYR   0.012   0.002   TYR A 495 
 ARG   0.001   0.000   ARG A 357 

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 0.853 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 TYR cc_start: 0.8221 (p90) cc_final: 0.7951 (p90)
REVERT: A  458 LYS cc_start: 0.8475 (ptmt) cc_final: 0.7491 (mmmt)
REVERT: A  468 ILE cc_start: 0.8065 (mp) cc_final: 0.7773 (mp)
REVERT: A  495 TYR cc_start: 0.6843 (t80) cc_final: 0.6630 (t80)
REVERT: a   19 LYS cc_start: 0.7543 (mttt) cc_final: 0.7173 (pttm)
REVERT: a   41 HIS cc_start: 0.5064 (OUTLIER) cc_final: 0.4859 (m-70)
REVERT: a   90 ASP cc_start: 0.7777 (m-30) cc_final: 0.7436 (m-30)
REVERT: a  139 MET cc_start: 0.5543 (mmm) cc_final: 0.5147 (mtt)
REVERT: a  178 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6929 (mt)
REVERT: b   97 TYR cc_start: 0.3682 (OUTLIER) cc_final: 0.2648 (m-80)
  outliers start: 24
  outliers final: 19
  residues processed: 136
  average time/residue: 0.1709
  time to fit residues: 30.6098
Evaluate side-chains
  140 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 118
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  489 TYR
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain a residue   11 LEU
Chi-restraints excluded: chain a residue   41 HIS
Chi-restraints excluded: chain a residue   55 ILE
Chi-restraints excluded: chain a residue  178 LEU
Chi-restraints excluded: chain a residue  181 LEU
Chi-restraints excluded: chain a residue  210 VAL
Chi-restraints excluded: chain b residue   19 VAL
Chi-restraints excluded: chain b residue   84 VAL
Chi-restraints excluded: chain b residue   97 TYR
Chi-restraints excluded: chain b residue  112 LEU
Chi-restraints excluded: chain b residue  149 ILE
Chi-restraints excluded: chain b residue  197 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 29 optimal weight:    0.7980
   chunk 49 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0670
   chunk 42 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.6718

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  62 GLN
a 168 HIS
** a 203 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 = 0.4290 r_free = 0.4290 target = 0.192567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.171035 restraints weight = 8727.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.175317 restraints weight = 5098.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.178178 restraints weight = 3441.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.4143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6837
moved from start:          0.5465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5007  Z= 0.224
  Angle     :  0.604   8.384   6825  Z= 0.316
  Chirality :  0.044   0.177    755
  Planarity :  0.004   0.038    875
  Dihedral  :  5.101  49.501    688
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 21.86 %
    Favored  : 74.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    Cis-general     : 0.17 %
    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: -0.61 (0.33), residues: 622
  helix: -2.55 (0.91), residues: 30
  sheet:  1.06 (0.34), residues: 219
  loop : -1.19 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP a 192 
 HIS   0.002   0.001   HIS a 203 
 PHE   0.017   0.001   PHE b  77 
 TYR   0.013   0.002   TYR A 380 
 ARG   0.002   0.000   ARG a  98 

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 TYR cc_start: 0.8243 (p90) cc_final: 0.7904 (p90)
REVERT: A  380 TYR cc_start: 0.6253 (m-80) cc_final: 0.5829 (m-10)
REVERT: A  451 TYR cc_start: 0.8419 (m-80) cc_final: 0.8174 (m-10)
REVERT: A  458 LYS cc_start: 0.8415 (ptmt) cc_final: 0.7320 (mmmt)
REVERT: A  468 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7748 (mp)
REVERT: A  495 TYR cc_start: 0.7032 (t80) cc_final: 0.6712 (t80)
REVERT: a   19 LYS cc_start: 0.7696 (mttt) cc_final: 0.7250 (pttm)
REVERT: a   41 HIS cc_start: 0.5195 (OUTLIER) cc_final: 0.4972 (m-70)
REVERT: a   90 ASP cc_start: 0.7774 (m-30) cc_final: 0.7380 (m-30)
REVERT: a  139 MET cc_start: 0.5646 (mmm) cc_final: 0.5347 (mtt)
REVERT: a  178 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7035 (mt)
REVERT: b   97 TYR cc_start: 0.3574 (OUTLIER) cc_final: 0.2526 (m-80)
  outliers start: 21
  outliers final: 17
  residues processed: 128
  average time/residue: 0.1576
  time to fit residues: 26.6007
Evaluate side-chains
  139 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  489 TYR
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain a residue   11 LEU
Chi-restraints excluded: chain a residue   41 HIS
Chi-restraints excluded: chain a residue   55 ILE
Chi-restraints excluded: chain a residue  178 LEU
Chi-restraints excluded: chain a residue  181 LEU
Chi-restraints excluded: chain a residue  210 VAL
Chi-restraints excluded: chain b residue   19 VAL
Chi-restraints excluded: chain b residue   84 VAL
Chi-restraints excluded: chain b residue   97 TYR
Chi-restraints excluded: chain b residue  112 LEU
Chi-restraints excluded: chain b residue  149 ILE
Chi-restraints excluded: chain b residue  197 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   chunk 47 optimal weight:    0.5980
   chunk 49 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9980
   chunk 59 optimal weight:    7.9990
   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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  62 GLN
a 168 HIS
** a 203 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 = 0.4271 r_free = 0.4271 target = 0.191054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.170154 restraints weight = 8784.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.173997 restraints weight = 5301.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.176698 restraints weight = 3688.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.4125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6896
moved from start:          0.5655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   5007  Z= 0.258
  Angle     :  0.622   8.772   6825  Z= 0.327
  Chirality :  0.044   0.157    755
  Planarity :  0.004   0.039    875
  Dihedral  :  5.284  49.750    688
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 21.86 %
    Favored  : 74.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    Cis-general     : 0.17 %
    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: -0.67 (0.33), residues: 622
  helix: -2.58 (0.91), residues: 30
  sheet:  0.96 (0.34), residues: 220
  loop : -1.20 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP b 153 
 HIS   0.002   0.001   HIS a 203 
 PHE   0.016   0.002   PHE b  77 
 TYR   0.014   0.002   TYR A 501 
 ARG   0.003   0.000   ARG a  98 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2145.57 seconds
wall clock time: 40 minutes 29.33 seconds (2429.33 seconds total)