Starting phenix.real_space_refine
on Fri Aug 22 15:50:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8exr_28660/08_2025/8exr_28660.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8exr_28660/08_2025/8exr_28660.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8exr_28660/08_2025/8exr_28660.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8exr_28660/08_2025/8exr_28660.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8exr_28660/08_2025/8exr_28660.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8exr_28660/08_2025/8exr_28660.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.014
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: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P       5      5.49       5
     S      20      5.16       5
     C    3438      2.51       5
     N     802      2.21       5
     O     844      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5111
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 2496
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 295, 2496
          Classifications: {'peptide': 295}
          Link IDs: {'PTRANS': 6, 'TRANS': 288}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 2051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 241, 2051
          Classifications: {'peptide': 241}
          Link IDs: {'PTRANS': 6, 'TRANS': 234}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 445
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 445
          Classifications: {'peptide': 54}
          Link IDs: {'TRANS': 53}
    Chain: "B"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 62
          Unusual residues: {' ZN': 1, 'P6L': 1, 'PO4': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "A"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 57
          Unusual residues: {' ZN': 1, 'P6L': 1, 'PO4': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.26, per 1000 atoms: 0.25
  Number of scatterers: 5111
  At special positions: 0
  Unit cell: (72.38, 85.47, 93.94, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      20     16.00
     P       5     15.00
     O     844      8.00
     N     802      7.00
     C    3438      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.50
  Conformation dependent library (CDL) restraints added in 135.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 701 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 205 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 201 "
      pdb="  ZN B 701 "
        pdb="ZN    ZN B 701 " - pdb=" NE2 HIS B 205 "
        pdb="ZN    ZN B 701 " - pdb=" NE2 HIS B 201 "


  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1164

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 2 sheets defined
      70.7% alpha, 3.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'B' and resid 2 through 29
      removed outlier: 3.858A  pdb=" N   TYR B  24 " --> pdb=" O   LEU B  20 " (cutoff:3.500A)
      removed outlier: 4.801A  pdb=" N   ILE B  25 " --> pdb=" O   PHE B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 38
    Processing helix  chain 'B' and resid 39 through 48
      removed outlier: 4.065A  pdb=" N   LEU B  43 " --> pdb=" O   TRP B  39 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 51
      No H-bonds generated for 'chain 'B' and resid 49 through 51'
    Processing helix  chain 'B' and resid 100 through 133
      removed outlier: 4.624A  pdb=" N   VAL B 108 " --> pdb=" O   ASN B 104 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   ILE B 111 " --> pdb=" O   THR B 107 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LYS B 133 " --> pdb=" O   LYS B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 151
    Processing helix  chain 'B' and resid 184 through 189
    Processing helix  chain 'B' and resid 194 through 208
      removed outlier: 4.327A  pdb=" N   LEU B 200 " --> pdb=" O   LYS B 196 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   ASN B 208 " --> pdb=" O   ALA B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 224
      removed outlier: 4.197A  pdb=" N   ILE B 215 " --> pdb=" O   THR B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 251
      removed outlier: 3.501A  pdb=" N   ILE B 232 " --> pdb=" O   PRO B 228 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   ILE B 238 " --> pdb=" O   LYS B 234 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   HIS B 239 " --> pdb=" O   ARG B 235 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ASP B 240 " --> pdb=" O   LYS B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 271
    Processing helix  chain 'B' and resid 289 through 300
    Processing helix  chain 'B' and resid 308 through 329
      removed outlier: 3.534A  pdb=" N   PHE B 328 " --> pdb=" O   ILE B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 336
    Processing helix  chain 'A' and resid 2 through 31
      removed outlier: 3.529A  pdb=" N   ILE A  15 " --> pdb=" O   SER A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 38
    Processing helix  chain 'A' and resid 39 through 47
      removed outlier: 4.125A  pdb=" N   LEU A  43 " --> pdb=" O   TRP A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 134
      removed outlier: 3.566A  pdb=" N   VAL A 108 " --> pdb=" O   ASN A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 151
    Processing helix  chain 'A' and resid 194 through 208
      removed outlier: 3.814A  pdb=" N   ASN A 208 " --> pdb=" O   ALA A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 224
    Processing helix  chain 'A' and resid 227 through 251
      removed outlier: 3.857A  pdb=" N   HIS A 231 " --> pdb=" O   ASN A 227 " (cutoff:3.500A)
      removed outlier: 4.631A  pdb=" N   LYS A 234 " --> pdb=" O   VAL A 230 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   ARG A 235 " --> pdb=" O   HIS A 231 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   LYS A 236 " --> pdb=" O   ILE A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 253
      No H-bonds generated for 'chain 'A' and resid 252 through 253'
    Processing helix  chain 'A' and resid 254 through 256
      No H-bonds generated for 'chain 'A' and resid 254 through 256'
    Processing helix  chain 'A' and resid 257 through 271
      removed outlier: 3.752A  pdb=" N   VAL A 269 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 289 through 299
      removed outlier: 3.734A  pdb=" N   LYS C 299 " --> pdb=" O   LEU C 295 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 307 through 329
      removed outlier: 4.354A  pdb=" N   LEU C 311 " --> pdb=" O   SER C 307 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 332 through 336
      removed outlier: 4.040A  pdb=" N   THR C 335 " --> pdb=" O   GLN C 332 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 160 through 164
    Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 164
      removed outlier: 6.685A  pdb=" N   VAL A 160 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 7.698A  pdb=" N   ILE A 182 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   ARG A 162 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)

    299 hydrogen bonds defined for protein.
    870 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.69

  Time building geometry restraints manager: 0.65 seconds

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

  Histogram of bond lengths:
        1.18 -     1.33: 1301
        1.33 -     1.47: 1570
        1.47 -     1.61: 2315
        1.61 -     1.75: 3
        1.75 -     1.89: 34
  Bond restraints: 5223
  Sorted by residual:
  bond pdb=" CB  HIS B 213 "
       pdb=" CG  HIS B 213 "
    ideal  model  delta    sigma   weight residual
    1.497  1.371  0.126 1.40e-02 5.10e+03 8.05e+01
  bond pdb=" CB  HIS B 153 "
       pdb=" CG  HIS B 153 "
    ideal  model  delta    sigma   weight residual
    1.497  1.372  0.125 1.40e-02 5.10e+03 7.94e+01
  bond pdb=" CB  PHE A 173 "
       pdb=" CG  PHE A 173 "
    ideal  model  delta    sigma   weight residual
    1.502  1.321  0.181 2.30e-02 1.89e+03 6.18e+01
  bond pdb=" NE1 TRP B  39 "
       pdb=" CE2 TRP B  39 "
    ideal  model  delta    sigma   weight residual
    1.370  1.285  0.085 1.10e-02 8.26e+03 6.00e+01
  bond pdb=" CB  HIS A 205 "
       pdb=" CG  HIS A 205 "
    ideal  model  delta    sigma   weight residual
    1.497  1.389  0.108 1.40e-02 5.10e+03 5.93e+01
  ... (remaining 5218 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.28: 6387
        3.28 -     6.57: 574
        6.57 -     9.85: 51
        9.85 -    13.13: 6
       13.13 -    16.42: 3
  Bond angle restraints: 7021
  Sorted by residual:
  angle pdb=" N   VAL A 160 "
        pdb=" CA  VAL A 160 "
        pdb=" C   VAL A 160 "
      ideal   model   delta    sigma   weight residual
     108.46  122.06  -13.60 1.49e+00 4.50e-01 8.33e+01
  angle pdb=" N   ARG A 194 "
        pdb=" CA  ARG A 194 "
        pdb=" C   ARG A 194 "
      ideal   model   delta    sigma   weight residual
     114.04  102.97   11.07 1.24e+00 6.50e-01 7.97e+01
  angle pdb=" N   VAL B 160 "
        pdb=" CA  VAL B 160 "
        pdb=" C   VAL B 160 "
      ideal   model   delta    sigma   weight residual
     108.46  121.66  -13.20 1.49e+00 4.50e-01 7.84e+01
  angle pdb=" CA  PHE B  30 "
        pdb=" CB  PHE B  30 "
        pdb=" CG  PHE B  30 "
      ideal   model   delta    sigma   weight residual
     113.80  105.18    8.62 1.00e+00 1.00e+00 7.44e+01
  angle pdb=" N   TRP B 174 "
        pdb=" CA  TRP B 174 "
        pdb=" C   TRP B 174 "
      ideal   model   delta    sigma   weight residual
     110.56  126.98  -16.42 1.94e+00 2.66e-01 7.16e+01
  ... (remaining 7016 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.09: 2907
       14.09 -    28.17: 148
       28.17 -    42.25: 49
       42.25 -    56.34: 30
       56.34 -    70.42: 11
  Dihedral angle restraints: 3145
    sinusoidal: 1362
      harmonic: 1783
  Sorted by residual:
  dihedral pdb=" C   PHE B 258 "
           pdb=" N   PHE B 258 "
           pdb=" CA  PHE B 258 "
           pdb=" CB  PHE B 258 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -114.82   -7.78     0      2.50e+00 1.60e-01 9.68e+00
  dihedral pdb=" N   TYR B 155 "
           pdb=" C   TYR B 155 "
           pdb=" CA  TYR B 155 "
           pdb=" CB  TYR B 155 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  130.57   -7.77     0      2.50e+00 1.60e-01 9.66e+00
  dihedral pdb=" CG  ARG A 235 "
           pdb=" CD  ARG A 235 "
           pdb=" NE  ARG A 235 "
           pdb=" CZ  ARG A 235 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  143.09   36.91     2      1.50e+01 4.44e-03 7.69e+00
  ... (remaining 3142 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.117: 564
       0.117 -    0.234: 200
       0.234 -    0.351: 31
       0.351 -    0.468: 4
       0.468 -    0.584: 1
  Chirality restraints: 800
  Sorted by residual:
  chirality pdb=" C5  P6L A 702 "
            pdb=" C6  P6L A 702 "
            pdb=" C7  P6L A 702 "
            pdb=" O4  P6L A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.31   -1.73   -0.58 2.00e-01 2.50e+01 8.54e+00
  chirality pdb=" CA  TRP B 174 "
            pdb=" N   TRP B 174 "
            pdb=" C   TRP B 174 "
            pdb=" CB  TRP B 174 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.30e+00
  chirality pdb=" CA  TYR B 155 "
            pdb=" N   TYR B 155 "
            pdb=" C   TYR B 155 "
            pdb=" CB  TYR B 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.12e+00
  ... (remaining 797 not shown)

  Planarity restraints: 823
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C21 P6L B 702 "    0.079 2.00e-02 2.50e+03   1.61e-01 2.59e+02
        pdb=" C22 P6L B 702 "   -0.213 2.00e-02 2.50e+03
        pdb=" C23 P6L B 702 "    0.213 2.00e-02 2.50e+03
        pdb=" C24 P6L B 702 "   -0.080 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C21 P6L A 702 "    0.077 2.00e-02 2.50e+03   1.53e-01 2.35e+02
        pdb=" C22 P6L A 702 "   -0.203 2.00e-02 2.50e+03
        pdb=" C23 P6L A 702 "    0.203 2.00e-02 2.50e+03
        pdb=" C24 P6L A 702 "   -0.077 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C32 P6L A 702 "   -0.074 2.00e-02 2.50e+03   1.48e-01 2.18e+02
        pdb=" C33 P6L A 702 "    0.195 2.00e-02 2.50e+03
        pdb=" C34 P6L A 702 "   -0.195 2.00e-02 2.50e+03
        pdb=" C35 P6L A 702 "    0.074 2.00e-02 2.50e+03
  ... (remaining 820 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.59: 76
        2.59 -     3.17: 5122
        3.17 -     3.75: 7615
        3.75 -     4.32: 10357
        4.32 -     4.90: 15033
  Nonbonded interactions: 38203
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 242 "
            pdb="ZN    ZN B 701 "
     model   vdw
     2.016 2.230
  nonbonded pdb=" OE2 GLU A 242 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.017 2.230
  nonbonded pdb=" OE1 GLU A 242 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.038 2.230
  nonbonded pdb=" OE1 GLU B 242 "
            pdb="ZN    ZN B 701 "
     model   vdw
     2.050 2.230
  nonbonded pdb=" O   GLY B 286 "
            pdb=" CG  LYS B 287 "
     model   vdw
     2.142 3.440
  ... (remaining 38198 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:             1.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.920
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6975
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      :  0.026   0.181   5227  Z= 1.487
  Angle     :  1.944  16.416   7021  Z= 1.328
  Chirality :  0.115   0.584    800
  Planarity :  0.013   0.161    823
  Dihedral  : 12.156  70.423   1981
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  2.76 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.66 (0.32), residues: 580
  helix: -0.13 (0.24), residues: 383
  sheet: -0.25 (0.87), residues: 26
  loop : -0.87 (0.46), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  23 
 TYR   0.099   0.012   TYR A 203 
 PHE   0.033   0.006   PHE B 284 
 TRP   0.043   0.009   TRP B  99 
 HIS   0.012   0.003   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.02593 ( 5223)
  covalent geometry    : angle       1.94400 ( 7021)
  hydrogen bonds       : bond        0.25172 (  299)
  hydrogen bonds       : angle       8.15000 (  870)
  metal coordination   : bond        0.05433 (    4)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   41 LEU cc_start: 0.8542 (mt) cc_final: 0.7864 (tt)
REVERT: B  136 LEU cc_start: 0.6840 (tp) cc_final: 0.6454 (tp)
REVERT: B  255 LYS cc_start: 0.8736 (mttt) cc_final: 0.8205 (mmtm)
REVERT: A  141 ASN cc_start: 0.7362 (m-40) cc_final: 0.6924 (p0)
REVERT: A  187 PHE cc_start: 0.8156 (m-80) cc_final: 0.7907 (m-80)
REVERT: A  219 ILE cc_start: 0.8605 (mm) cc_final: 0.8397 (mt)
REVERT: A  276 ASN cc_start: 0.6779 (p0) cc_final: 0.6314 (m-40)
REVERT: C  295 LEU cc_start: 0.8700 (mt) cc_final: 0.8423 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.0797
  time to fit residues: 18.6565
Evaluate side-chains
  119 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 26 optimal weight:    7.9990
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 50 optimal weight:    5.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
B 271 ASN
A 271 ASN
C 325 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.187138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.165502 restraints weight = 11117.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.169642 restraints weight = 6889.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.172658 restraints weight = 4792.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.174821 restraints weight = 3562.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.176418 restraints weight = 2801.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.4202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6722
moved from start:          0.3957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5227  Z= 0.199
  Angle     :  0.715   6.784   7021  Z= 0.403
  Chirality :  0.045   0.198    800
  Planarity :  0.005   0.049    823
  Dihedral  : 13.289  73.452    725
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  2.07 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 11.70 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.34), residues: 580
  helix:  1.43 (0.25), residues: 375
  sheet:  0.07 (1.02), residues: 35
  loop : -0.83 (0.47), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 247 
 TYR   0.019   0.002   TYR B 127 
 PHE   0.026   0.002   PHE B  16 
 TRP   0.011   0.002   TRP A 174 
 HIS   0.006   0.002   HIS B 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 5223)
  covalent geometry    : angle       0.71494 ( 7021)
  hydrogen bonds       : bond        0.08689 (  299)
  hydrogen bonds       : angle       5.18530 (  870)
  metal coordination   : bond        0.00316 (    4)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 154
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    7 MET cc_start: 0.7300 (mmt) cc_final: 0.6744 (ptp)
REVERT: B   22 PHE cc_start: 0.6941 (m-80) cc_final: 0.6687 (m-80)
REVERT: B  136 LEU cc_start: 0.7264 (tp) cc_final: 0.6597 (mp)
REVERT: B  168 GLN cc_start: 0.6719 (mp10) cc_final: 0.6204 (mm-40)
REVERT: B  240 ASP cc_start: 0.8468 (m-30) cc_final: 0.8066 (t0)
REVERT: A  122 LEU cc_start: 0.8381 (mt) cc_final: 0.8170 (tp)
REVERT: A  141 ASN cc_start: 0.7594 (m-40) cc_final: 0.7189 (p0)
REVERT: A  194 ARG cc_start: 0.6942 (ptt180) cc_final: 0.6648 (ptt180)
REVERT: C  295 LEU cc_start: 0.8553 (mt) cc_final: 0.7883 (tt)
  outliers start: 19
  outliers final: 8
  residues processed: 162
  average time/residue: 0.0669
  time to fit residues: 14.0043
Evaluate side-chains
  121 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain C residue  309 LEU
Chi-restraints excluded: chain C residue  328 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 5 optimal weight:    7.9990
   chunk 9 optimal weight:    0.8980
   chunk 23 optimal weight:    6.9990
   chunk 54 optimal weight:    0.0370
   chunk 34 optimal weight:    0.5980
   chunk 51 optimal weight:    0.5980
   chunk 50 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9990
   chunk 39 optimal weight:    4.9990
   overall best weight:    0.6260

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.185948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.164363 restraints weight = 10191.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.168690 restraints weight = 6441.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.171873 restraints weight = 4492.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.174288 restraints weight = 3307.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.176073 restraints weight = 2536.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.4187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6682
moved from start:          0.5104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5227  Z= 0.153
  Angle     :  0.632  10.371   7021  Z= 0.344
  Chirality :  0.042   0.206    800
  Planarity :  0.004   0.052    823
  Dihedral  : 11.768  85.487    725
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 16.13 %
    Favored  : 80.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.14 (0.34), residues: 580
  helix:  1.61 (0.25), residues: 374
  sheet: -0.33 (1.00), residues: 37
  loop : -0.88 (0.46), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 162 
 TYR   0.026   0.002   TYR A 186 
 PHE   0.020   0.002   PHE B  16 
 TRP   0.032   0.002   TRP A 174 
 HIS   0.003   0.001   HIS B 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 5223)
  covalent geometry    : angle       0.63212 ( 7021)
  hydrogen bonds       : bond        0.06930 (  299)
  hydrogen bonds       : angle       4.66667 (  870)
  metal coordination   : bond        0.00133 (    4)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 136
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   22 PHE cc_start: 0.6976 (m-80) cc_final: 0.6672 (m-80)
REVERT: B  136 LEU cc_start: 0.7492 (tp) cc_final: 0.7121 (mp)
REVERT: B  162 ARG cc_start: 0.6309 (mtt180) cc_final: 0.6079 (ttm170)
REVERT: B  240 ASP cc_start: 0.8546 (m-30) cc_final: 0.8119 (t0)
REVERT: B  266 MET cc_start: 0.6913 (tpt) cc_final: 0.6638 (tpt)
REVERT: A   22 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7847 (t80)
REVERT: A  100 ASP cc_start: 0.4968 (m-30) cc_final: 0.4428 (t0)
REVERT: A  141 ASN cc_start: 0.7549 (m-40) cc_final: 0.7272 (p0)
REVERT: A  165 GLU cc_start: 0.6868 (pm20) cc_final: 0.6583 (pt0)
REVERT: A  246 ASP cc_start: 0.7098 (m-30) cc_final: 0.6875 (t0)
REVERT: C  300 GLU cc_start: 0.8415 (tm-30) cc_final: 0.7969 (tm-30)
  outliers start: 17
  outliers final: 8
  residues processed: 142
  average time/residue: 0.0585
  time to fit residues: 10.9850
Evaluate side-chains
  126 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 117
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain A residue   22 PHE
Chi-restraints excluded: chain A residue  119 PHE
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  276 ASN
Chi-restraints excluded: chain C residue  309 LEU
Chi-restraints excluded: chain C residue  328 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 26 optimal weight:   10.0000
   chunk 18 optimal weight:    0.8980
   chunk 38 optimal weight:    7.9990
   chunk 53 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.3786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.184014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.162621 restraints weight = 9991.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.166937 restraints weight = 6260.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.170198 restraints weight = 4339.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.172541 restraints weight = 3167.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.174280 restraints weight = 2433.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.4161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6751
moved from start:          0.5506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5227  Z= 0.152
  Angle     :  0.621   9.257   7021  Z= 0.339
  Chirality :  0.042   0.198    800
  Planarity :  0.004   0.052    823
  Dihedral  : 11.084  81.003    725
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 17.02 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.34), residues: 580
  helix:  1.68 (0.25), residues: 374
  sheet: -0.76 (0.97), residues: 36
  loop : -1.14 (0.44), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 247 
 TYR   0.027   0.002   TYR B 127 
 PHE   0.020   0.002   PHE A 173 
 TRP   0.030   0.002   TRP A 174 
 HIS   0.005   0.001   HIS B 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 5223)
  covalent geometry    : angle       0.62056 ( 7021)
  hydrogen bonds       : bond        0.06325 (  299)
  hydrogen bonds       : angle       4.63473 (  870)
  metal coordination   : bond        0.00466 (    4)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 127
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
REVERT: B   22 PHE cc_start: 0.6892 (m-80) cc_final: 0.6597 (m-80)
REVERT: B  136 LEU cc_start: 0.7471 (tp) cc_final: 0.6612 (mp)
REVERT: B  240 ASP cc_start: 0.8582 (m-30) cc_final: 0.8262 (t0)
REVERT: A  165 GLU cc_start: 0.6915 (pm20) cc_final: 0.6668 (pt0)
REVERT: A  246 ASP cc_start: 0.7273 (m-30) cc_final: 0.7024 (t0)
REVERT: C  300 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8122 (tm-30)
REVERT: C  325 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8356 (tm-30)
  outliers start: 20
  outliers final: 13
  residues processed: 137
  average time/residue: 0.0609
  time to fit residues: 11.0142
Evaluate side-chains
  127 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  260 THR
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue  119 PHE
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain A residue  276 ASN
Chi-restraints excluded: chain C residue  296 ILE
Chi-restraints excluded: chain C residue  309 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    1.5386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.183378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.162736 restraints weight = 10474.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.166859 restraints weight = 6574.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.170087 restraints weight = 4595.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.172242 restraints weight = 3371.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.173822 restraints weight = 2605.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.4160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6776
moved from start:          0.5950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5227  Z= 0.156
  Angle     :  0.637   9.793   7021  Z= 0.345
  Chirality :  0.043   0.209    800
  Planarity :  0.005   0.051    823
  Dihedral  : 10.786  79.849    725
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 18.62 %
    Favored  : 77.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.34), residues: 580
  helix:  1.61 (0.26), residues: 373
  sheet: -0.93 (0.93), residues: 36
  loop : -1.46 (0.43), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  23 
 TYR   0.018   0.002   TYR A 186 
 PHE   0.021   0.002   PHE C 328 
 TRP   0.025   0.002   TRP A 174 
 HIS   0.006   0.001   HIS B 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 5223)
  covalent geometry    : angle       0.63740 ( 7021)
  hydrogen bonds       : bond        0.06061 (  299)
  hydrogen bonds       : angle       4.69282 (  870)
  metal coordination   : bond        0.00528 (    4)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 124
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  240 ASP cc_start: 0.8653 (m-30) cc_final: 0.8310 (t0)
REVERT: B  285 ASN cc_start: 0.6601 (m110) cc_final: 0.6064 (m-40)
REVERT: A  142 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7626 (mt-10)
REVERT: A  246 ASP cc_start: 0.7315 (m-30) cc_final: 0.7010 (t0)
REVERT: A  271 ASN cc_start: 0.6415 (m-40) cc_final: 0.6147 (p0)
REVERT: C  300 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8289 (tm-30)
  outliers start: 24
  outliers final: 16
  residues processed: 136
  average time/residue: 0.0638
  time to fit residues: 11.7226
Evaluate side-chains
  131 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  244 GLU
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue  119 PHE
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain A residue  276 ASN
Chi-restraints excluded: chain C residue  309 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 27 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   chunk 46 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 34 optimal weight:    0.2980
   chunk 17 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 152 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.188045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.166261 restraints weight = 10291.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.170776 restraints weight = 6404.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.174213 restraints weight = 4425.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.176529 restraints weight = 3235.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.178341 restraints weight = 2480.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.4200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6706
moved from start:          0.6395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5227  Z= 0.130
  Angle     :  0.595  11.957   7021  Z= 0.316
  Chirality :  0.042   0.178    800
  Planarity :  0.004   0.051    823
  Dihedral  : 10.072  71.922    725
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 21.81 %
    Favored  : 74.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.12 (0.35), residues: 580
  helix:  1.83 (0.26), residues: 371
  sheet: -0.99 (0.93), residues: 36
  loop : -1.31 (0.46), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  23 
 TYR   0.015   0.002   TYR A 261 
 PHE   0.026   0.001   PHE C 328 
 TRP   0.044   0.002   TRP A 174 
 HIS   0.004   0.001   HIS B 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 5223)
  covalent geometry    : angle       0.59539 ( 7021)
  hydrogen bonds       : bond        0.05213 (  299)
  hydrogen bonds       : angle       4.45731 (  870)
  metal coordination   : bond        0.00313 (    4)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  136 LEU cc_start: 0.7304 (tp) cc_final: 0.6773 (mp)
REVERT: B  240 ASP cc_start: 0.8716 (m-30) cc_final: 0.8358 (t0)
REVERT: B  266 MET cc_start: 0.6811 (tpt) cc_final: 0.6578 (tpt)
REVERT: A  165 GLU cc_start: 0.7162 (pm20) cc_final: 0.6813 (pt0)
REVERT: A  246 ASP cc_start: 0.7107 (m-30) cc_final: 0.6800 (t0)
REVERT: A  271 ASN cc_start: 0.6287 (m-40) cc_final: 0.6084 (p0)
REVERT: C  300 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8317 (tm-30)
  outliers start: 22
  outliers final: 15
  residues processed: 136
  average time/residue: 0.0603
  time to fit residues: 11.0940
Evaluate side-chains
  128 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue  119 PHE
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  220 PHE
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain C residue  287 LYS
Chi-restraints excluded: chain C residue  309 LEU
Chi-restraints excluded: chain C residue  334 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 11 optimal weight:    6.9990
   chunk 54 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
B 278 ASN
A 104 ASN
A 152 ASN
A 278 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.184736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.163375 restraints weight = 9959.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.167838 restraints weight = 6087.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.171068 restraints weight = 4115.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.173285 restraints weight = 3010.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.175012 restraints weight = 2327.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.4166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6807
moved from start:          0.6470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5227  Z= 0.159
  Angle     :  0.649  11.148   7021  Z= 0.346
  Chirality :  0.043   0.181    800
  Planarity :  0.005   0.053    823
  Dihedral  : 10.440  81.225    725
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 21.99 %
    Favored  : 73.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.74 (0.35), residues: 580
  helix:  1.57 (0.26), residues: 372
  sheet: -1.13 (0.91), residues: 36
  loop : -1.57 (0.46), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  23 
 TYR   0.018   0.002   TYR A 261 
 PHE   0.024   0.002   PHE B 151 
 TRP   0.040   0.002   TRP A 174 
 HIS   0.006   0.001   HIS B 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 5223)
  covalent geometry    : angle       0.64903 ( 7021)
  hydrogen bonds       : bond        0.05738 (  299)
  hydrogen bonds       : angle       4.60488 (  870)
  metal coordination   : bond        0.00596 (    4)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 116
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
REVERT: B   23 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7263 (ttm-80)
REVERT: B  240 ASP cc_start: 0.8758 (m-30) cc_final: 0.8455 (t0)
REVERT: B  285 ASN cc_start: 0.6666 (m110) cc_final: 0.6078 (m-40)
REVERT: A  142 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6986 (mt-10)
REVERT: A  271 ASN cc_start: 0.6395 (m-40) cc_final: 0.6077 (p0)
REVERT: C  300 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8449 (tm-30)
  outliers start: 27
  outliers final: 21
  residues processed: 133
  average time/residue: 0.0578
  time to fit residues: 10.3371
Evaluate side-chains
  134 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 113
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   11 SER
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  163 LYS
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  220 PHE
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain C residue  296 ILE
Chi-restraints excluded: chain C residue  309 LEU
Chi-restraints excluded: chain C residue  334 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 31 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 3 optimal weight:    0.0570
   chunk 54 optimal weight:    0.7980
   chunk 9 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.3704

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

Flipped N/Q/H residues before XYZ refinement:
B 278 ASN
B 306 GLN
A 152 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.186195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.164817 restraints weight = 9881.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.169462 restraints weight = 5916.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.172715 restraints weight = 3962.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.175016 restraints weight = 2850.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.176564 restraints weight = 2176.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.4176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6775
moved from start:          0.6680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5227  Z= 0.139
  Angle     :  0.607  10.923   7021  Z= 0.327
  Chirality :  0.043   0.179    800
  Planarity :  0.004   0.053    823
  Dihedral  : 10.324  89.504    725
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 22.34 %
    Favored  : 73.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.34), residues: 580
  helix:  1.61 (0.26), residues: 377
  sheet: -1.17 (0.91), residues: 36
  loop : -1.95 (0.43), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  23 
 TYR   0.019   0.002   TYR B 175 
 PHE   0.021   0.002   PHE B 151 
 TRP   0.037   0.002   TRP A 174 
 HIS   0.004   0.001   HIS B 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 5223)
  covalent geometry    : angle       0.60711 ( 7021)
  hydrogen bonds       : bond        0.05390 (  299)
  hydrogen bonds       : angle       4.54902 (  870)
  metal coordination   : bond        0.00498 (    4)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 118
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 ARG cc_start: 0.7968 (ttm-80) cc_final: 0.7209 (ttm-80)
REVERT: B  240 ASP cc_start: 0.8703 (m-30) cc_final: 0.8404 (t0)
REVERT: B  255 LYS cc_start: 0.8545 (mttt) cc_final: 0.8036 (mmtt)
REVERT: B  285 ASN cc_start: 0.6698 (m110) cc_final: 0.6303 (m-40)
REVERT: A  168 GLN cc_start: 0.6354 (pm20) cc_final: 0.6096 (pp30)
REVERT: A  271 ASN cc_start: 0.6301 (m-40) cc_final: 0.6087 (p0)
  outliers start: 26
  outliers final: 21
  residues processed: 133
  average time/residue: 0.0563
  time to fit residues: 9.9583
Evaluate side-chains
  135 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 114
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   11 SER
Chi-restraints excluded: chain B residue   33 MET
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  325 GLN
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue  119 PHE
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  173 PHE
Chi-restraints excluded: chain A residue  220 PHE
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain C residue  309 LEU
Chi-restraints excluded: chain C residue  334 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 44 optimal weight:    6.9990
   chunk 34 optimal weight:    6.9990
   chunk 12 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0000
   chunk 8 optimal weight:    3.9990
   chunk 43 optimal weight:    0.0270
   overall best weight:    0.5444

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

Flipped N/Q/H residues before XYZ refinement:
A 152 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.190017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.168707 restraints weight = 9737.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.173452 restraints weight = 5843.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.176821 restraints weight = 3896.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.179244 restraints weight = 2785.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.180809 restraints weight = 2109.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.4215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6700
moved from start:          0.7029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   5227  Z= 0.127
  Angle     :  0.618  14.086   7021  Z= 0.325
  Chirality :  0.042   0.183    800
  Planarity :  0.004   0.053    823
  Dihedral  :  9.851  87.672    725
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 23.23 %
    Favored  : 73.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.35), residues: 580
  helix:  1.84 (0.26), residues: 373
  sheet: -0.75 (0.96), residues: 36
  loop : -1.67 (0.46), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  23 
 TYR   0.014   0.001   TYR A 261 
 PHE   0.024   0.001   PHE B 151 
 TRP   0.035   0.002   TRP A 174 
 HIS   0.004   0.001   HIS B 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 5223)
  covalent geometry    : angle       0.61768 ( 7021)
  hydrogen bonds       : bond        0.04794 (  299)
  hydrogen bonds       : angle       4.40412 (  870)
  metal coordination   : bond        0.00228 (    4)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 122
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  186 TYR cc_start: 0.7550 (m-80) cc_final: 0.7040 (m-80)
REVERT: B  240 ASP cc_start: 0.8677 (m-30) cc_final: 0.8384 (t0)
REVERT: B  255 LYS cc_start: 0.8471 (mttt) cc_final: 0.7982 (mmtt)
REVERT: B  300 GLU cc_start: 0.6438 (mm-30) cc_final: 0.6013 (pp20)
REVERT: A   10 VAL cc_start: 0.8770 (m) cc_final: 0.8516 (p)
REVERT: A  211 THR cc_start: 0.8352 (p) cc_final: 0.8034 (p)
REVERT: A  246 ASP cc_start: 0.7171 (m-30) cc_final: 0.6846 (t0)
REVERT: A  266 MET cc_start: 0.5612 (ttm) cc_final: 0.5180 (ttm)
REVERT: A  271 ASN cc_start: 0.6232 (m-40) cc_final: 0.6022 (p0)
  outliers start: 18
  outliers final: 16
  residues processed: 133
  average time/residue: 0.0596
  time to fit residues: 10.5210
Evaluate side-chains
  126 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   33 MET
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  169 SER
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  244 GLU
Chi-restraints excluded: chain B residue  325 GLN
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  220 PHE
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain A residue  276 ASN
Chi-restraints excluded: chain C residue  334 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 11 optimal weight:    0.0470
   chunk 39 optimal weight:    0.7980
   chunk 14 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0870
   chunk 37 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0170
   chunk 45 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.3294

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

Flipped N/Q/H residues before XYZ refinement:
A 152 ASN

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 = 0.192427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.170149 restraints weight = 11101.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.174888 restraints weight = 6721.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.178214 restraints weight = 4550.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.180561 restraints weight = 3330.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.182126 restraints weight = 2583.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.4251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6661
moved from start:          0.7426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   5227  Z= 0.125
  Angle     :  0.621  14.932   7021  Z= 0.322
  Chirality :  0.042   0.176    800
  Planarity :  0.004   0.050    823
  Dihedral  :  9.209  87.439    725
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 26.06 %
    Favored  : 71.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.12 (0.35), residues: 580
  helix:  1.88 (0.26), residues: 374
  sheet: -0.43 (1.03), residues: 36
  loop : -1.63 (0.44), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  23 
 TYR   0.013   0.001   TYR A 261 
 PHE   0.021   0.001   PHE B 151 
 TRP   0.034   0.002   TRP A 174 
 HIS   0.003   0.001   HIS B 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 5223)
  covalent geometry    : angle       0.62142 ( 7021)
  hydrogen bonds       : bond        0.04314 (  299)
  hydrogen bonds       : angle       4.35954 (  870)
  metal coordination   : bond        0.00130 (    4)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  110 TRP cc_start: 0.7971 (t60) cc_final: 0.7759 (t60)
REVERT: B  162 ARG cc_start: 0.6053 (ttt180) cc_final: 0.5439 (ttt90)
REVERT: B  186 TYR cc_start: 0.7453 (m-80) cc_final: 0.7193 (m-80)
REVERT: B  240 ASP cc_start: 0.8661 (m-30) cc_final: 0.8396 (t0)
REVERT: B  300 GLU cc_start: 0.6529 (mm-30) cc_final: 0.6085 (pp20)
REVERT: A    7 MET cc_start: 0.7327 (mtt) cc_final: 0.7033 (mtm)
REVERT: A  211 THR cc_start: 0.8350 (p) cc_final: 0.8058 (p)
REVERT: A  246 ASP cc_start: 0.7120 (m-30) cc_final: 0.6822 (t0)
REVERT: A  271 ASN cc_start: 0.6185 (m-40) cc_final: 0.5973 (p0)
  outliers start: 13
  outliers final: 10
  residues processed: 127
  average time/residue: 0.0562
  time to fit residues: 9.4161
Evaluate side-chains
  118 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   33 MET
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  325 GLN
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  173 PHE
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain A residue  276 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 43 optimal weight:    0.0070
   chunk 28 optimal weight:    0.0770
   chunk 53 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 38 optimal weight:    6.9990
   chunk 7 optimal weight:    1.9990
   chunk 50 optimal weight:    7.9990
   chunk 3 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0370
   chunk 5 optimal weight:    3.9990
   overall best weight:    1.0238

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

Flipped N/Q/H residues before XYZ refinement:
A 152 ASN
** A 168 GLN ** 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 = 0.4328 r_free = 0.4328 target = 0.189453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.166920 restraints weight = 11114.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.171446 restraints weight = 6739.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.174704 restraints weight = 4605.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.177013 restraints weight = 3392.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.178701 restraints weight = 2655.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.4214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6729
moved from start:          0.7444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5227  Z= 0.134
  Angle     :  0.633  14.054   7021  Z= 0.334
  Chirality :  0.043   0.180    800
  Planarity :  0.004   0.050    823
  Dihedral  :  9.335  88.900    725
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 13.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 25.71 %
    Favored  : 71.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.13 (0.35), residues: 580
  helix:  1.84 (0.26), residues: 374
  sheet: -0.52 (1.02), residues: 36
  loop : -1.50 (0.46), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  23 
 TYR   0.016   0.001   TYR A 261 
 PHE   0.022   0.001   PHE B 151 
 TRP   0.030   0.002   TRP A 174 
 HIS   0.004   0.001   HIS B 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 5223)
  covalent geometry    : angle       0.63264 ( 7021)
  hydrogen bonds       : bond        0.04684 (  299)
  hydrogen bonds       : angle       4.40020 (  870)
  metal coordination   : bond        0.00378 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 955.88 seconds
wall clock time: 17 minutes 8.14 seconds (1028.14 seconds total)