Starting phenix.real_space_refine
on Fri Aug 22 14:26:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hfc_34717/08_2025/8hfc_34717.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hfc_34717/08_2025/8hfc_34717.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hfc_34717/08_2025/8hfc_34717.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hfc_34717/08_2025/8hfc_34717.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hfc_34717/08_2025/8hfc_34717.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hfc_34717/08_2025/8hfc_34717.cif"
  }
  resolution = 3.5
  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=   0.004 sd=   0.145
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      22      5.16       5
     C    2590      2.51       5
     N     694      2.21       5
     O     699      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  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: 4007
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2234
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2234
          Classifications: {'peptide': 276}
          Link IDs: {'PTRANS': 16, 'TRANS': 259}
    Chain: "B"
      Number of atoms: 1756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1756
          Classifications: {'peptide': 222}
          Link IDs: {'PTRANS': 13, 'TRANS': 208}
    Chain: "A"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 17
          Unusual residues: {' ZN': 2, 'PLM': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'PLM:plan-1': 1}
          Unresolved non-hydrogen planarities: 1

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    953  SG  CYS A 189      39.293  32.069  58.239  1.00 43.49           S
  ATOM    972  SG  CYS A 192      39.223  35.988  57.314  1.00 49.55           S
  ATOM   1110  SG  CYS A 209      36.468  33.802  57.411  1.00 32.51           S
  ATOM    837  SG  CYS A 175      39.498  31.365  69.663  1.00 35.51           S
  ATOM    856  SG  CYS A 178      38.830  35.231  68.292  1.00 36.69           S
  ATOM    993  SG  CYS A 195      36.831  32.303  67.459  1.00 31.03           S

  Time building chain proxies: 1.28, per 1000 atoms: 0.32
  Number of scatterers: 4007
  At special positions: 0
  Unit cell: (60.872, 65.22, 117.396, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      2     29.99
     S      22     16.00
     O     699      8.00
     N     694      7.00
     C    2590      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 114 " - pdb=" SG  CYS B 126 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.37
  Conformation dependent library (CDL) restraints added in 173.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 402 "
        pdb="ZN    ZN A 402 " - pdb=" ND1 HIS A 202 "
        pdb="ZN    ZN A 402 " - pdb=" SG  CYS A 209 "
        pdb="ZN    ZN A 402 " - pdb=" SG  CYS A 189 "
        pdb="ZN    ZN A 402 " - pdb=" SG  CYS A 192 "
      pdb="  ZN A 403 "
        pdb="ZN    ZN A 403 " - pdb=" ND1 HIS A 188 "
        pdb="ZN    ZN A 403 " - pdb=" SG  CYS A 175 "
        pdb="ZN    ZN A 403 " - pdb=" SG  CYS A 178 "
        pdb="ZN    ZN A 403 " - pdb=" SG  CYS A 195 "
      Number of angles added : 6


  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  928

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 7 sheets defined
      41.2% alpha, 5.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 76 through 94
      removed outlier: 3.807A  pdb=" N   VAL A  80 " --> pdb=" O   LEU A  76 " (cutoff:3.500A)
      Proline residue:  A  87  - end of helix
      removed outlier: 3.874A  pdb=" N   PHE A  94 " --> pdb=" O   LEU A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 129
    Processing helix  chain 'A' and resid 214 through 243
    Processing helix  chain 'A' and resid 246 through 249
    Processing helix  chain 'A' and resid 250 through 264
      removed outlier: 4.000A  pdb=" N   ILE A 254 " --> pdb=" O   CYS A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 279
      removed outlier: 3.606A  pdb=" N   ALA A 268 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 291
    Processing helix  chain 'A' and resid 313 through 323
    Processing helix  chain 'B' and resid 45 through 49
    Processing helix  chain 'B' and resid 65 through 69
    Processing helix  chain 'B' and resid 130 through 135
    Processing helix  chain 'B' and resid 137 through 157
    Processing helix  chain 'B' and resid 161 through 174
    Processing helix  chain 'B' and resid 188 through 190
      No H-bonds generated for 'chain 'B' and resid 188 through 190'
    Processing helix  chain 'B' and resid 191 through 206
      removed outlier: 3.864A  pdb=" N   LEU B 195 " --> pdb=" O   PHE B 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 215
      removed outlier: 3.643A  pdb=" N   ARG B 214 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 160
    Processing sheet with id=AA2, first strand: chain 'A' and resid 174 through 175
      removed outlier: 3.825A  pdb=" N   ILE A 180 " --> pdb=" O   CYS A 175 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 187 through 189
      removed outlier: 3.774A  pdb=" N   VAL A 194 " --> pdb=" O   CYS A 189 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 202 through 203
    Processing sheet with id=AA5, first strand: chain 'B' and resid 27 through 28
    Processing sheet with id=AA6, first strand: chain 'B' and resid 32 through 33
    Processing sheet with id=AA7, first strand: chain 'B' and resid 70 through 75

    160 hydrogen bonds defined for protein.
    435 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: 0.57

  Time building geometry restraints manager: 0.48 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1281
        1.34 -     1.46: 843
        1.46 -     1.58: 1967
        1.58 -     1.70: 1
        1.70 -     1.82: 29
  Bond restraints: 4121
  Sorted by residual:
  bond pdb=" C1  PLM A 401 "
       pdb=" C2  PLM A 401 "
    ideal  model  delta    sigma   weight residual
    1.542  1.599 -0.057 2.00e-02 2.50e+03 8.25e+00
  bond pdb=" CA  VAL B 233 "
       pdb=" CB  VAL B 233 "
    ideal  model  delta    sigma   weight residual
    1.546  1.534  0.012 8.80e-03 1.29e+04 1.95e+00
  bond pdb=" C6  PLM A 401 "
       pdb=" C7  PLM A 401 "
    ideal  model  delta    sigma   weight residual
    1.525  1.552 -0.027 2.00e-02 2.50e+03 1.87e+00
  bond pdb=" C2  PLM A 401 "
       pdb=" C3  PLM A 401 "
    ideal  model  delta    sigma   weight residual
    1.522  1.549 -0.027 2.00e-02 2.50e+03 1.84e+00
  bond pdb=" CB  TRP A 117 "
       pdb=" CG  TRP A 117 "
    ideal  model  delta    sigma   weight residual
    1.498  1.456  0.042 3.10e-02 1.04e+03 1.84e+00
  ... (remaining 4116 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 5343
        1.41 -     2.82: 207
        2.82 -     4.23: 36
        4.23 -     5.64: 4
        5.64 -     7.05: 5
  Bond angle restraints: 5595
  Sorted by residual:
  angle pdb=" C   TYR B 117 "
        pdb=" N   ASP B 118 "
        pdb=" CA  ASP B 118 "
      ideal   model   delta    sigma   weight residual
     121.54  128.59   -7.05 1.91e+00 2.74e-01 1.36e+01
  angle pdb=" N   ILE A  93 "
        pdb=" CA  ILE A  93 "
        pdb=" C   ILE A  93 "
      ideal   model   delta    sigma   weight residual
     111.81  108.81    3.00 8.60e-01 1.35e+00 1.22e+01
  angle pdb=" C   ARG B 116 "
        pdb=" N   TYR B 117 "
        pdb=" CA  TYR B 117 "
      ideal   model   delta    sigma   weight residual
     121.54  127.66   -6.12 1.91e+00 2.74e-01 1.03e+01
  angle pdb=" C   ASP A 341 "
        pdb=" N   TRP A 342 "
        pdb=" CA  TRP A 342 "
      ideal   model   delta    sigma   weight residual
     121.54  125.75   -4.21 1.91e+00 2.74e-01 4.86e+00
  angle pdb=" N   ARG B 188 "
        pdb=" CA  ARG B 188 "
        pdb=" C   ARG B 188 "
      ideal   model   delta    sigma   weight residual
     109.81  114.56   -4.75 2.21e+00 2.05e-01 4.61e+00
  ... (remaining 5590 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.51: 2036
       17.51 -    35.01: 288
       35.01 -    52.52: 78
       52.52 -    70.03: 16
       70.03 -    87.53: 7
  Dihedral angle restraints: 2425
    sinusoidal: 982
      harmonic: 1443
  Sorted by residual:
  dihedral pdb=" CA  ARG B 188 "
           pdb=" C   ARG B 188 "
           pdb=" N   PRO B 189 "
           pdb=" CA  PRO B 189 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.89  -19.11     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  GLY B 176 "
           pdb=" C   GLY B 176 "
           pdb=" N   LEU B 177 "
           pdb=" CA  LEU B 177 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.92  -19.08     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  LEU B 185 "
           pdb=" C   LEU B 185 "
           pdb=" N   LEU B 186 "
           pdb=" CA  LEU B 186 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.50  -18.50     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 2422 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 275
       0.027 -    0.053: 184
       0.053 -    0.079: 92
       0.079 -    0.106: 43
       0.106 -    0.132: 12
  Chirality restraints: 606
  Sorted by residual:
  chirality pdb=" CA  VAL B 233 "
            pdb=" N   VAL B 233 "
            pdb=" C   VAL B 233 "
            pdb=" CB  VAL B 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.39e-01
  chirality pdb=" CA  VAL B 216 "
            pdb=" N   VAL B 216 "
            pdb=" C   VAL B 216 "
            pdb=" CB  VAL B 216 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.07e-01
  chirality pdb=" CA  PRO A 267 "
            pdb=" N   PRO A 267 "
            pdb=" C   PRO A 267 "
            pdb=" CB  PRO A 267 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.01e-01
  ... (remaining 603 not shown)

  Planarity restraints: 713
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 266 "    0.032 5.00e-02 4.00e+02   4.78e-02 3.65e+00
        pdb=" N   PRO A 267 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO A 267 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 267 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B  88 "    0.023 5.00e-02 4.00e+02   3.53e-02 2.00e+00
        pdb=" N   PRO B  89 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO B  89 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B  89 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B  55 "    0.019 5.00e-02 4.00e+02   2.85e-02 1.30e+00
        pdb=" N   PRO B  56 "   -0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO B  56 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B  56 "    0.016 5.00e-02 4.00e+02
  ... (remaining 710 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 186
        2.71 -     3.26: 3917
        3.26 -     3.81: 6278
        3.81 -     4.35: 7274
        4.35 -     4.90: 13142
  Nonbonded interactions: 30797
  Sorted by model distance:
  nonbonded pdb=" O   SER B 224 "
            pdb=" OG  SER B 224 "
     model   vdw
     2.164 3.040
  nonbonded pdb=" OH  TYR B  59 "
            pdb=" OD2 ASP B 230 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" O   TYR B 135 "
            pdb=" NH1 ARG B 214 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" O   ALA A  83 "
            pdb=" OH  TYR A 259 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OE2 GLU B 155 "
            pdb=" OG  SER B 194 "
     model   vdw
     2.238 3.040
  ... (remaining 30792 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.620
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.670
  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:1.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
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      :  0.008   0.121   4131  Z= 0.315
  Angle     :  0.781  19.255   5603  Z= 0.385
  Chirality :  0.046   0.132    606
  Planarity :  0.004   0.048    713
  Dihedral  : 18.011  87.532   1494
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.48 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 24.20 %
    Favored  : 71.92 %
  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: -2.90 (0.33), residues: 494
  helix: -0.85 (0.34), residues: 175
  sheet: -2.79 (0.61), residues: 40
  loop : -2.60 (0.34), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  83 
 TYR   0.011   0.002   TYR B 117 
 PHE   0.013   0.002   PHE A 218 
 TRP   0.011   0.002   TRP B 162 
 HIS   0.003   0.001   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00699 ( 4121)
  covalent geometry    : angle       0.67102 ( 5595)
  SS BOND              : bond        0.00046 (    1)
  SS BOND              : angle       0.60188 (    2)
  hydrogen bonds       : bond        0.11184 (  160)
  hydrogen bonds       : angle       5.51198 (  435)
  metal coordination   : bond        0.06666 (    8)
  metal coordination   : angle      12.21092 (    6)
  Misc. bond           : bond        0.03646 (    1)

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

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

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 68
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A  153 GLU cc_start: 0.8224 (mp0) cc_final: 0.7936 (mp0)
REVERT: A  287 PHE cc_start: 0.8232 (t80) cc_final: 0.8031 (t80)
REVERT: B  116 ARG cc_start: 0.7613 (mtm-85) cc_final: 0.7324 (mmm-85)
REVERT: B  222 ARG cc_start: 0.8421 (tmt170) cc_final: 0.8093 (tmt170)
  outliers start: 17
  outliers final: 12
  residues processed: 82
  average time/residue: 0.0766
  time to fit residues: 7.8212
Evaluate side-chains
  70 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue   86 CYS
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  192 CYS
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain B residue  126 CYS
Chi-restraints excluded: chain B residue  166 SER
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  232 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    0.3980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:   40.0000
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 199 HIS
A 282 GLN
A 296 ASN
A 300 HIS
A 307 ASN
A 320 HIS
** B  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 149 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.169684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.124720 restraints weight = 4604.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.126652 restraints weight = 3694.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.126688 restraints weight = 3181.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.127229 restraints weight = 2852.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.127852 restraints weight = 2610.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.1166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4131  Z= 0.130
  Angle     :  0.547   6.909   5603  Z= 0.282
  Chirality :  0.042   0.137    606
  Planarity :  0.004   0.034    713
  Dihedral  :  7.174  59.948    575
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 24.43 %
    Favored  : 70.78 %
  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: -1.31 (0.37), residues: 494
  helix:  0.59 (0.37), residues: 188
  sheet: -1.31 (0.78), residues: 34
  loop : -1.96 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 242 
 TYR   0.015   0.001   TYR B 200 
 PHE   0.009   0.001   PHE B 231 
 TRP   0.013   0.001   TRP B 178 
 HIS   0.004   0.001   HIS B 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 4121)
  covalent geometry    : angle       0.54114 ( 5595)
  SS BOND              : bond        0.00267 (    1)
  SS BOND              : angle       0.29440 (    2)
  hydrogen bonds       : bond        0.04168 (  160)
  hydrogen bonds       : angle       4.37927 (  435)
  metal coordination   : bond        0.00942 (    8)
  metal coordination   : angle       2.41505 (    6)
  Misc. bond           : bond        0.00014 (    1)

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

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

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 71
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A   88 MET cc_start: 0.7466 (tmm) cc_final: 0.7239 (tmm)
REVERT: A  153 GLU cc_start: 0.8334 (mp0) cc_final: 0.7827 (mp0)
REVERT: A  291 ILE cc_start: 0.6062 (OUTLIER) cc_final: 0.5782 (tt)
REVERT: B  116 ARG cc_start: 0.7556 (mtm-85) cc_final: 0.7219 (mmm-85)
REVERT: B  218 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8385 (tt)
REVERT: B  222 ARG cc_start: 0.8423 (tmt170) cc_final: 0.8156 (tmt170)
  outliers start: 21
  outliers final: 9
  residues processed: 86
  average time/residue: 0.0689
  time to fit residues: 7.3969
Evaluate side-chains
  76 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  243 GLU
Chi-restraints excluded: chain A residue  273 TYR
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain B residue   25 GLU
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  218 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0050
   chunk 11 optimal weight:    6.9990
   chunk 12 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 35 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.9398

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

Flipped N/Q/H residues before XYZ refinement:
A 239 HIS
** B  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.169976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.124516 restraints weight = 4560.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.126825 restraints weight = 3679.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.126807 restraints weight = 3141.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.127354 restraints weight = 2805.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.128038 restraints weight = 2558.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.1509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4131  Z= 0.138
  Angle     :  0.548   7.520   5603  Z= 0.276
  Chirality :  0.042   0.133    606
  Planarity :  0.004   0.032    713
  Dihedral  :  5.487  45.280    563
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  6.16 %
    Allowed  : 23.97 %
    Favored  : 69.86 %
  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: -0.67 (0.38), residues: 494
  helix:  1.22 (0.38), residues: 189
  sheet: -0.74 (0.81), residues: 34
  loop : -1.71 (0.37), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 242 
 TYR   0.012   0.001   TYR B 200 
 PHE   0.009   0.001   PHE A 287 
 TRP   0.015   0.001   TRP B 178 
 HIS   0.011   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 4121)
  covalent geometry    : angle       0.54269 ( 5595)
  SS BOND              : bond        0.01011 (    1)
  SS BOND              : angle       1.04154 (    2)
  hydrogen bonds       : bond        0.04019 (  160)
  hydrogen bonds       : angle       4.13927 (  435)
  metal coordination   : bond        0.01003 (    8)
  metal coordination   : angle       2.28121 (    6)
  Misc. bond           : bond        0.00003 (    1)

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

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

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 71
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A   76 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8754 (tt)
REVERT: A   88 MET cc_start: 0.7381 (tmm) cc_final: 0.7116 (tmm)
REVERT: A  153 GLU cc_start: 0.8324 (mp0) cc_final: 0.7794 (mp0)
REVERT: A  291 ILE cc_start: 0.6091 (OUTLIER) cc_final: 0.5789 (tt)
REVERT: B  116 ARG cc_start: 0.7561 (mtm-85) cc_final: 0.7109 (mmm-85)
REVERT: B  205 ASN cc_start: 0.7604 (m-40) cc_final: 0.7234 (m-40)
REVERT: B  222 ARG cc_start: 0.8372 (tmt170) cc_final: 0.8165 (tmt170)
  outliers start: 27
  outliers final: 13
  residues processed: 92
  average time/residue: 0.0646
  time to fit residues: 7.4481
Evaluate side-chains
  86 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  239 HIS
Chi-restraints excluded: chain A residue  243 GLU
Chi-restraints excluded: chain A residue  258 CYS
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain B residue   25 GLU
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  232 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 17 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 44 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
A 239 HIS
** B  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.170041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.119266 restraints weight = 4532.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.122773 restraints weight = 3147.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.125076 restraints weight = 2556.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.126316 restraints weight = 2268.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.126858 restraints weight = 2119.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.1692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4131  Z= 0.136
  Angle     :  0.532   6.821   5603  Z= 0.272
  Chirality :  0.042   0.138    606
  Planarity :  0.004   0.033    713
  Dihedral  :  4.985  33.944    561
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 25.57 %
    Favored  : 69.86 %
  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: -0.47 (0.38), residues: 494
  helix:  1.37 (0.38), residues: 190
  sheet: -0.65 (0.80), residues: 34
  loop : -1.59 (0.37), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 242 
 TYR   0.013   0.001   TYR B 200 
 PHE   0.009   0.001   PHE B 231 
 TRP   0.013   0.001   TRP B 178 
 HIS   0.015   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 4121)
  covalent geometry    : angle       0.52879 ( 5595)
  SS BOND              : bond        0.00493 (    1)
  SS BOND              : angle       0.16625 (    2)
  hydrogen bonds       : bond        0.03982 (  160)
  hydrogen bonds       : angle       3.98435 (  435)
  metal coordination   : bond        0.00872 (    8)
  metal coordination   : angle       1.96057 (    6)
  Misc. bond           : bond        0.00001 (    1)

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

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

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 72
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A   76 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8728 (tt)
REVERT: A   88 MET cc_start: 0.7315 (tmm) cc_final: 0.7028 (tmm)
REVERT: A  102 THR cc_start: 0.8209 (p) cc_final: 0.6998 (t)
REVERT: A  152 GLN cc_start: 0.8102 (tp-100) cc_final: 0.7744 (tp-100)
REVERT: A  153 GLU cc_start: 0.8342 (mp0) cc_final: 0.7791 (mp0)
REVERT: A  291 ILE cc_start: 0.6052 (OUTLIER) cc_final: 0.5745 (tt)
REVERT: B  116 ARG cc_start: 0.7587 (mtm-85) cc_final: 0.7016 (mmm-85)
REVERT: B  205 ASN cc_start: 0.7647 (m-40) cc_final: 0.7226 (m-40)
REVERT: B  218 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8341 (tt)
  outliers start: 20
  outliers final: 13
  residues processed: 88
  average time/residue: 0.0579
  time to fit residues: 6.5048
Evaluate side-chains
  83 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain B residue   25 GLU
Chi-restraints excluded: chain B residue   30 PHE
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  156 GLU
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  232 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 31 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 9 optimal weight:    5.9990
   chunk 38 optimal weight:    0.0980
   chunk 18 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 46 optimal weight:    5.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.169685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.123174 restraints weight = 4505.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.125996 restraints weight = 3360.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.125933 restraints weight = 2737.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.126623 restraints weight = 2395.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.126969 restraints weight = 2200.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.1968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4131  Z= 0.115
  Angle     :  0.529   8.003   5603  Z= 0.265
  Chirality :  0.041   0.163    606
  Planarity :  0.004   0.034    713
  Dihedral  :  4.795  33.888    561
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 3.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 25.80 %
    Favored  : 69.63 %
  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: -0.16 (0.38), residues: 494
  helix:  1.76 (0.39), residues: 184
  sheet: -0.60 (0.78), residues: 34
  loop : -1.41 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 242 
 TYR   0.010   0.001   TYR A 115 
 PHE   0.009   0.001   PHE B 231 
 TRP   0.014   0.001   TRP B 178 
 HIS   0.005   0.001   HIS B 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 4121)
  covalent geometry    : angle       0.52631 ( 5595)
  SS BOND              : bond        0.00033 (    1)
  SS BOND              : angle       0.29526 (    2)
  hydrogen bonds       : bond        0.03597 (  160)
  hydrogen bonds       : angle       3.88173 (  435)
  metal coordination   : bond        0.00648 (    8)
  metal coordination   : angle       1.78734 (    6)
  Misc. bond           : bond        0.00004 (    1)

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

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

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A   76 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8725 (tt)
REVERT: A   88 MET cc_start: 0.7419 (tmm) cc_final: 0.7161 (tmm)
REVERT: A  102 THR cc_start: 0.8023 (p) cc_final: 0.7613 (t)
REVERT: A  152 GLN cc_start: 0.8092 (tp-100) cc_final: 0.7740 (tp-100)
REVERT: A  153 GLU cc_start: 0.8306 (mp0) cc_final: 0.7810 (mp0)
REVERT: B  116 ARG cc_start: 0.7711 (mtm-85) cc_final: 0.7247 (mmm-85)
REVERT: B  205 ASN cc_start: 0.7747 (m-40) cc_final: 0.7355 (m-40)
  outliers start: 20
  outliers final: 15
  residues processed: 84
  average time/residue: 0.0554
  time to fit residues: 6.0174
Evaluate side-chains
  82 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  258 CYS
Chi-restraints excluded: chain A residue  318 MET
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain B residue   25 GLU
Chi-restraints excluded: chain B residue   30 PHE
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  156 GLU
Chi-restraints excluded: chain B residue  232 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0470
   chunk 19 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 1 optimal weight:    0.3980
   chunk 24 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  68 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.170664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.124023 restraints weight = 4602.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.126674 restraints weight = 3457.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.126723 restraints weight = 2746.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.127420 restraints weight = 2406.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.128006 restraints weight = 2203.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.2160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4131  Z= 0.113
  Angle     :  0.526   6.147   5603  Z= 0.266
  Chirality :  0.041   0.163    606
  Planarity :  0.004   0.034    713
  Dihedral  :  4.737  33.219    561
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 3.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 27.17 %
    Favored  : 69.41 %
  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:  0.02 (0.38), residues: 494
  helix:  1.90 (0.38), residues: 184
  sheet: -0.53 (0.77), residues: 34
  loop : -1.31 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 242 
 TYR   0.010   0.001   TYR A 115 
 PHE   0.009   0.001   PHE A 287 
 TRP   0.013   0.001   TRP B 178 
 HIS   0.004   0.001   HIS B 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 4121)
  covalent geometry    : angle       0.52328 ( 5595)
  SS BOND              : bond        0.00309 (    1)
  SS BOND              : angle       1.11540 (    2)
  hydrogen bonds       : bond        0.03520 (  160)
  hydrogen bonds       : angle       3.79900 (  435)
  metal coordination   : bond        0.00636 (    8)
  metal coordination   : angle       1.71427 (    6)
  Misc. bond           : bond        0.00006 (    1)

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

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

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.099 
Fit side-chains
REVERT: A   76 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8698 (tt)
REVERT: A   88 MET cc_start: 0.7396 (tmm) cc_final: 0.7130 (tmm)
REVERT: A  152 GLN cc_start: 0.8045 (tp-100) cc_final: 0.7669 (tp-100)
REVERT: A  153 GLU cc_start: 0.8275 (mp0) cc_final: 0.7755 (mp0)
REVERT: A  242 ARG cc_start: 0.8886 (tpp80) cc_final: 0.8660 (tpp80)
REVERT: B  116 ARG cc_start: 0.7548 (mtm-85) cc_final: 0.7113 (mmm-85)
REVERT: B  205 ASN cc_start: 0.7865 (m-40) cc_final: 0.7446 (m-40)
  outliers start: 15
  outliers final: 14
  residues processed: 76
  average time/residue: 0.0489
  time to fit residues: 4.7685
Evaluate side-chains
  77 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  318 MET
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain B residue   25 GLU
Chi-restraints excluded: chain B residue   30 PHE
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  156 GLU
Chi-restraints excluded: chain B residue  232 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0470
   chunk 7 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.6880

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.170995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.124863 restraints weight = 4560.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.127290 restraints weight = 3850.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.127427 restraints weight = 3112.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.127956 restraints weight = 2736.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.128365 restraints weight = 2499.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.2267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4131  Z= 0.113
  Angle     :  0.549   9.423   5603  Z= 0.267
  Chirality :  0.041   0.161    606
  Planarity :  0.004   0.034    713
  Dihedral  :  4.687  33.170    561
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 26.71 %
    Favored  : 69.63 %
  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:  0.12 (0.38), residues: 494
  helix:  1.99 (0.38), residues: 184
  sheet: -0.45 (0.78), residues: 34
  loop : -1.26 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 242 
 TYR   0.015   0.001   TYR B 200 
 PHE   0.010   0.001   PHE B 231 
 TRP   0.013   0.001   TRP B 178 
 HIS   0.003   0.001   HIS B 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 4121)
  covalent geometry    : angle       0.54642 ( 5595)
  SS BOND              : bond        0.00371 (    1)
  SS BOND              : angle       0.14182 (    2)
  hydrogen bonds       : bond        0.03488 (  160)
  hydrogen bonds       : angle       3.74614 (  435)
  metal coordination   : bond        0.00637 (    8)
  metal coordination   : angle       1.67277 (    6)
  Misc. bond           : bond        0.00006 (    1)

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

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

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A   76 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8770 (tt)
REVERT: A   88 MET cc_start: 0.7433 (tmm) cc_final: 0.7173 (tmm)
REVERT: A  152 GLN cc_start: 0.8025 (tp-100) cc_final: 0.7734 (tp-100)
REVERT: A  153 GLU cc_start: 0.8216 (mp0) cc_final: 0.7758 (mp0)
REVERT: B  116 ARG cc_start: 0.7652 (mtm-85) cc_final: 0.7368 (mmm-85)
REVERT: B  205 ASN cc_start: 0.7945 (m-40) cc_final: 0.7528 (m-40)
  outliers start: 16
  outliers final: 14
  residues processed: 73
  average time/residue: 0.0496
  time to fit residues: 4.7872
Evaluate side-chains
  77 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  318 MET
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain B residue   25 GLU
Chi-restraints excluded: chain B residue   30 PHE
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  156 GLU
Chi-restraints excluded: chain B residue  232 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 14 optimal weight:    0.5980
   chunk 9 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 6 optimal weight:    0.0570
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.171333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.124847 restraints weight = 4516.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.127374 restraints weight = 3439.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.127495 restraints weight = 2740.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.128210 restraints weight = 2390.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.128474 restraints weight = 2198.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.2389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4131  Z= 0.103
  Angle     :  0.529   8.650   5603  Z= 0.261
  Chirality :  0.041   0.178    606
  Planarity :  0.004   0.034    713
  Dihedral  :  4.575  32.348    561
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 26.71 %
    Favored  : 69.63 %
  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:  0.21 (0.38), residues: 494
  helix:  2.07 (0.38), residues: 184
  sheet: -0.39 (0.79), residues: 34
  loop : -1.21 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 242 
 TYR   0.010   0.001   TYR A 115 
 PHE   0.010   0.001   PHE B 231 
 TRP   0.013   0.001   TRP B 178 
 HIS   0.006   0.001   HIS B 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 4121)
  covalent geometry    : angle       0.52701 ( 5595)
  SS BOND              : bond        0.00105 (    1)
  SS BOND              : angle       0.14261 (    2)
  hydrogen bonds       : bond        0.03286 (  160)
  hydrogen bonds       : angle       3.64709 (  435)
  metal coordination   : bond        0.00545 (    8)
  metal coordination   : angle       1.57549 (    6)
  Misc. bond           : bond        0.00006 (    1)

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

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

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.121 
Fit side-chains
REVERT: A   76 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8756 (tt)
REVERT: A   88 MET cc_start: 0.7524 (tmm) cc_final: 0.7247 (tmm)
REVERT: A  152 GLN cc_start: 0.8010 (tp-100) cc_final: 0.7690 (tp-100)
REVERT: A  153 GLU cc_start: 0.8226 (mp0) cc_final: 0.7771 (mp0)
REVERT: B  116 ARG cc_start: 0.7713 (mtm-85) cc_final: 0.7440 (mmm-85)
REVERT: B  205 ASN cc_start: 0.7749 (m-40) cc_final: 0.7506 (m-40)
  outliers start: 16
  outliers final: 13
  residues processed: 79
  average time/residue: 0.0541
  time to fit residues: 5.4430
Evaluate side-chains
  76 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  318 MET
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain B residue   25 GLU
Chi-restraints excluded: chain B residue   30 PHE
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  156 GLU
Chi-restraints excluded: chain B residue  232 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0570
   chunk 19 optimal weight:    0.5980
   chunk 7 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.176317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.125153 restraints weight = 4753.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.128851 restraints weight = 3267.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.130715 restraints weight = 2653.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.132578 restraints weight = 2371.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.133137 restraints weight = 2204.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4131  Z= 0.110
  Angle     :  0.567   9.392   5603  Z= 0.278
  Chirality :  0.041   0.169    606
  Planarity :  0.004   0.034    713
  Dihedral  :  4.516  32.926    561
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 28.08 %
    Favored  : 68.72 %
  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:  0.30 (0.38), residues: 494
  helix:  2.14 (0.38), residues: 184
  sheet: -0.35 (0.80), residues: 34
  loop : -1.15 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 242 
 TYR   0.017   0.001   TYR B 200 
 PHE   0.010   0.001   PHE B 231 
 TRP   0.012   0.001   TRP B 178 
 HIS   0.005   0.001   HIS B 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 4121)
  covalent geometry    : angle       0.56516 ( 5595)
  SS BOND              : bond        0.00109 (    1)
  SS BOND              : angle       0.20629 (    2)
  hydrogen bonds       : bond        0.03328 (  160)
  hydrogen bonds       : angle       3.67773 (  435)
  metal coordination   : bond        0.00581 (    8)
  metal coordination   : angle       1.57151 (    6)
  Misc. bond           : bond        0.00008 (    1)

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

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

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.092 
Fit side-chains
REVERT: A   76 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8739 (tt)
REVERT: A   88 MET cc_start: 0.7547 (tmm) cc_final: 0.7270 (tmm)
REVERT: A  152 GLN cc_start: 0.7996 (tp-100) cc_final: 0.7668 (tp-100)
REVERT: A  153 GLU cc_start: 0.8200 (mp0) cc_final: 0.7728 (mp0)
REVERT: B  116 ARG cc_start: 0.7660 (mtm-85) cc_final: 0.7431 (mmm-85)
REVERT: B  198 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8358 (mt-10)
REVERT: B  205 ASN cc_start: 0.7709 (m-40) cc_final: 0.7479 (m-40)
  outliers start: 14
  outliers final: 12
  residues processed: 74
  average time/residue: 0.0607
  time to fit residues: 5.7096
Evaluate side-chains
  76 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  318 MET
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain B residue   25 GLU
Chi-restraints excluded: chain B residue   30 PHE
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  232 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    6.9990
   chunk 3 optimal weight:    1.9990
   chunk 23 optimal weight:    0.3980
   chunk 16 optimal weight:    0.0970
   chunk 27 optimal weight:    1.9990
   chunk 22 optimal weight:    9.9990
   chunk 31 optimal weight:    0.8980
   chunk 10 optimal weight:    0.1980
   chunk 8 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.174731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.129551 restraints weight = 4655.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.131572 restraints weight = 3997.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.131726 restraints weight = 3318.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.132224 restraints weight = 2997.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.132916 restraints weight = 2641.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.2602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   4131  Z= 0.103
  Angle     :  0.553   9.383   5603  Z= 0.274
  Chirality :  0.041   0.185    606
  Planarity :  0.004   0.034    713
  Dihedral  :  4.459  32.925    561
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 28.08 %
    Favored  : 68.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.40 (0.39), residues: 494
  helix:  2.22 (0.38), residues: 184
  sheet: -0.28 (0.80), residues: 34
  loop : -1.09 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 242 
 TYR   0.010   0.001   TYR A 115 
 PHE   0.010   0.001   PHE A 287 
 TRP   0.013   0.001   TRP B 178 
 HIS   0.007   0.001   HIS B 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 4121)
  covalent geometry    : angle       0.55021 ( 5595)
  SS BOND              : bond        0.01497 (    1)
  SS BOND              : angle       1.43461 (    2)
  hydrogen bonds       : bond        0.03159 (  160)
  hydrogen bonds       : angle       3.61991 (  435)
  metal coordination   : bond        0.00491 (    8)
  metal coordination   : angle       1.46728 (    6)
  Misc. bond           : bond        0.00007 (    1)

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

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

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.204 
Fit side-chains
REVERT: A   76 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8739 (tt)
REVERT: A   88 MET cc_start: 0.7569 (tmm) cc_final: 0.7299 (tmm)
REVERT: A  152 GLN cc_start: 0.7922 (tp-100) cc_final: 0.7675 (tp-100)
REVERT: A  153 GLU cc_start: 0.8159 (mp0) cc_final: 0.7753 (mp0)
REVERT: B  126 CYS cc_start: 0.5882 (p) cc_final: 0.5425 (p)
REVERT: B  205 ASN cc_start: 0.7857 (m-40) cc_final: 0.7641 (m110)
  outliers start: 13
  outliers final: 12
  residues processed: 71
  average time/residue: 0.0576
  time to fit residues: 5.2419
Evaluate side-chains
  71 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  318 MET
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain B residue   25 GLU
Chi-restraints excluded: chain B residue   30 PHE
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  232 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   chunk 20 optimal weight:    0.1980
   chunk 29 optimal weight:    4.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.176384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.130705 restraints weight = 4683.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.131970 restraints weight = 4020.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.132367 restraints weight = 3324.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.133018 restraints weight = 2863.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.133834 restraints weight = 2612.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.2693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4131  Z= 0.115
  Angle     :  0.569   9.322   5603  Z= 0.279
  Chirality :  0.041   0.179    606
  Planarity :  0.004   0.034    713
  Dihedral  :  4.455  33.757    561
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 27.85 %
    Favored  : 68.72 %
  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:  0.36 (0.38), residues: 494
  helix:  2.19 (0.38), residues: 184
  sheet: -0.28 (0.79), residues: 34
  loop : -1.11 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 116 
 TYR   0.017   0.001   TYR B 200 
 PHE   0.010   0.001   PHE A 287 
 TRP   0.012   0.001   TRP B 178 
 HIS   0.007   0.001   HIS B 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 4121)
  covalent geometry    : angle       0.56687 ( 5595)
  SS BOND              : bond        0.00650 (    1)
  SS BOND              : angle       1.20128 (    2)
  hydrogen bonds       : bond        0.03294 (  160)
  hydrogen bonds       : angle       3.63703 (  435)
  metal coordination   : bond        0.00641 (    8)
  metal coordination   : angle       1.62652 (    6)
  Misc. bond           : bond        0.00004 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 819.90 seconds
wall clock time: 14 minutes 48.44 seconds (888.44 seconds total)