Starting phenix.real_space_refine
on Tue Mar  3 12:25:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f9w_31499/03_2026/7f9w_31499.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f9w_31499/03_2026/7f9w_31499.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f9w_31499/03_2026/7f9w_31499.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f9w_31499/03_2026/7f9w_31499.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f9w_31499/03_2026/7f9w_31499.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f9w_31499/03_2026/7f9w_31499.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      22      5.16       5
     C    2654      2.51       5
     N     713      2.21       5
     O     828      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4217
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 854
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 106, 846
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 9, 'TRANS': 96}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 106, 846
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 9, 'TRANS': 96}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 863
    Chain: "C"
      Number of atoms: 1694
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1694
          Classifications: {'peptide': 218}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206}
    Chain: "B"
      Number of atoms: 1669
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1669
          Classifications: {'peptide': 223}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 210}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AMET A  25 " occ=0.50
      ... (14 atoms not shown)
      pdb=" CE BMET A  25 " occ=0.50
  Time building chain proxies: 1.10, per 1000 atoms: 0.26
  Number of scatterers: 4217
  At special positions: 0
  Unit cell: (64.26, 64.8, 116.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      22     16.00
     O     828      8.00
     N     713      7.00
     C    2654      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  46 " - pdb=" SG  CYS A 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 163 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  94 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 140 " - pdb=" SG  CYS C 200 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 149 " - pdb=" SG  CYS B 205 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.27
  Conformation dependent library (CDL) restraints added in 143.0 milliseconds
  

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1016

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 15 sheets defined
      5.9% alpha, 37.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'C' and resid 85 through 89
      removed outlier: 3.834A  pdb=" N   VAL C  89 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 127 through 134
      removed outlier: 3.700A  pdb=" N   LEU C 131 " --> pdb=" O   SER C 127 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 189 through 195
      removed outlier: 3.727A  pdb=" N   LYS C 194 " --> pdb=" O   ALA C 190 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   HIS C 195 " --> pdb=" O   ASP C 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 167
      No H-bonds generated for 'chain 'B' and resid 165 through 167'
    Processing helix  chain 'B' and resid 194 through 198
    Processing helix  chain 'B' and resid 210 through 213
    Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16
      removed outlier: 3.705A  pdb=" N   GLN A 130 " --> pdb=" O   THR A  14 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   SER A 145 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 21
      removed outlier: 3.612A  pdb=" N   TYR A  20 " --> pdb=" O   CYS A 104 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 45 through 48
      removed outlier: 3.878A  pdb=" N   LEU A  45 " --> pdb=" O   ASP A  56 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 136 through 137
    Processing sheet with id=AA5, first strand: chain 'C' and resid 10 through 13
      removed outlier: 6.136A  pdb=" N   LEU C  11 " --> pdb=" O   GLU C 111 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ALA C  90 " --> pdb=" O   VAL C 110 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   VAL C  91 " --> pdb=" O   GLN C  44 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   TRP C  41 " --> pdb=" O   LEU C  53 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 19 through 24
      removed outlier: 3.532A  pdb=" N   THR C  78 " --> pdb=" O   SER C  71 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 30 through 31
      removed outlier: 3.811A  pdb=" N   LYS C  36 " --> pdb=" O   TYR C  31 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 120 through 124
      removed outlier: 3.542A  pdb=" N   VAL C 139 " --> pdb=" O   PHE C 124 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   VAL C 138 " --> pdb=" O   LEU C 185 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LEU C 185 " --> pdb=" O   VAL C 138 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 159 through 161
      removed outlier: 4.827A  pdb=" N   TRP C 154 " --> pdb=" O   GLN C 161 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   TYR C 198 " --> pdb=" O   PHE C 215 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 4 through 6
      removed outlier: 3.571A  pdb=" N   VAL B  18 " --> pdb=" O   LEU B  83 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 10 through 12
      removed outlier: 6.459A  pdb=" N   GLU B  10 " --> pdb=" O   THR B 119 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ALA B  33 " --> pdb=" O   GLU B  99 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   GLY B  49 " --> pdb=" O   TRP B  36 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 10 through 12
      removed outlier: 6.459A  pdb=" N   GLU B  10 " --> pdb=" O   THR B 119 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   LEU B 111 " --> pdb=" O   ARG B  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 129 through 133
      removed outlier: 6.332A  pdb=" N   TYR B 185 " --> pdb=" O   ASP B 153 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 129 through 133
      removed outlier: 6.332A  pdb=" N   TYR B 185 " --> pdb=" O   ASP B 153 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 162 through 163

    142 hydrogen bonds defined for protein.
    348 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: 0.66

  Time building geometry restraints manager: 0.39 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: 1349
        1.34 -     1.46: 1038
        1.46 -     1.58: 1904
        1.58 -     1.69: 0
        1.69 -     1.81: 31
  Bond restraints: 4322
  Sorted by residual:
  bond pdb=" CB  PRO C 147 "
       pdb=" CG  PRO C 147 "
    ideal  model  delta    sigma   weight residual
    1.506  1.457  0.049 3.90e-02 6.57e+02 1.56e+00
  bond pdb=" CB  GLN C  96 "
       pdb=" CG  GLN C  96 "
    ideal  model  delta    sigma   weight residual
    1.520  1.483  0.037 3.00e-02 1.11e+03 1.56e+00
  bond pdb=" N   ASN A 112 "
       pdb=" CA  ASN A 112 "
    ideal  model  delta    sigma   weight residual
    1.457  1.472 -0.015 1.29e-02 6.01e+03 1.26e+00
  bond pdb=" C   PHE C 104 "
       pdb=" N   GLY C 105 "
    ideal  model  delta    sigma   weight residual
    1.334  1.321  0.013 1.20e-02 6.94e+03 1.23e+00
  bond pdb=" CB  VAL C  29 "
       pdb=" CG1 VAL C  29 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.22e+00
  ... (remaining 4317 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.16: 5437
        1.16 -     2.33: 351
        2.33 -     3.49: 68
        3.49 -     4.66: 14
        4.66 -     5.82: 5
  Bond angle restraints: 5875
  Sorted by residual:
  angle pdb=" C   GLN C  96 "
        pdb=" N   TYR C  97 "
        pdb=" CA  TYR C  97 "
      ideal   model   delta    sigma   weight residual
     122.65  116.83    5.82 1.66e+00 3.63e-01 1.23e+01
  angle pdb=" N   TYR C 146 "
        pdb=" CA  TYR C 146 "
        pdb=" C   TYR C 146 "
      ideal   model   delta    sigma   weight residual
     108.82  103.55    5.27 1.69e+00 3.50e-01 9.74e+00
  angle pdb=" C   GLU A 111 "
        pdb=" N   ASN A 112 "
        pdb=" CA  ASN A 112 "
      ideal   model   delta    sigma   weight residual
     121.54  127.24   -5.70 1.91e+00 2.74e-01 8.91e+00
  angle pdb=" C   HIS B 209 "
        pdb=" N   LYS B 210 "
        pdb=" CA  LYS B 210 "
      ideal   model   delta    sigma   weight residual
     120.09  123.62   -3.53 1.25e+00 6.40e-01 7.99e+00
  angle pdb=" C   LEU B 133 "
        pdb=" N   ALA B 134 "
        pdb=" CA  ALA B 134 "
      ideal   model   delta    sigma   weight residual
     120.60  124.34   -3.74 1.53e+00 4.27e-01 5.99e+00
  ... (remaining 5870 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.30: 2385
       16.30 -    32.61: 150
       32.61 -    48.91: 40
       48.91 -    65.21: 3
       65.21 -    81.52: 13
  Dihedral angle restraints: 2591
    sinusoidal: 1004
      harmonic: 1587
  Sorted by residual:
  dihedral pdb=" CB  CYS C  23 "
           pdb=" SG  CYS C  23 "
           pdb=" SG  CYS C  94 "
           pdb=" CB  CYS C  94 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  159.24  -66.24     1      1.00e+01 1.00e-02 5.73e+01
  dihedral pdb=" CB  CYS B  22 "
           pdb=" SG  CYS B  22 "
           pdb=" SG  CYS B  96 "
           pdb=" CB  CYS B  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  143.75  -50.75     1      1.00e+01 1.00e-02 3.53e+01
  dihedral pdb=" CA  GLU A 113 "
           pdb=" C   GLU A 113 "
           pdb=" N   ALA A 114 "
           pdb=" CA  ALA A 114 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.99   22.01     0      5.00e+00 4.00e-02 1.94e+01
  ... (remaining 2588 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 348
       0.027 -    0.054: 182
       0.054 -    0.081: 59
       0.081 -    0.107: 43
       0.107 -    0.134: 14
  Chirality restraints: 646
  Sorted by residual:
  chirality pdb=" CA  ILE C  54 "
            pdb=" N   ILE C  54 "
            pdb=" C   ILE C  54 "
            pdb=" CB  ILE C  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.50e-01
  chirality pdb=" CA  TYR C  97 "
            pdb=" N   TYR C  97 "
            pdb=" C   TYR C  97 "
            pdb=" CB  TYR C  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.39e-01
  chirality pdb=" CA  VAL B  93 "
            pdb=" N   VAL B  93 "
            pdb=" C   VAL B  93 "
            pdb=" CB  VAL B  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.82e-01
  ... (remaining 643 not shown)

  Planarity restraints: 753
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C  56 "   -0.015 2.00e-02 2.50e+03   1.72e-02 7.43e+00
        pdb=" CG  TRP C  56 "    0.046 2.00e-02 2.50e+03
        pdb=" CD1 TRP C  56 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD2 TRP C  56 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP C  56 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP C  56 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP C  56 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C  56 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C  56 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP C  56 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 134 "   -0.035 5.00e-02 4.00e+02   5.29e-02 4.47e+00
        pdb=" N   PRO B 135 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO B 135 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 135 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 155 "    0.026 5.00e-02 4.00e+02   3.99e-02 2.55e+00
        pdb=" N   PRO B 156 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B 156 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 156 "    0.021 5.00e-02 4.00e+02
  ... (remaining 750 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 85
        2.67 -     3.23: 3920
        3.23 -     3.79: 6053
        3.79 -     4.34: 8034
        4.34 -     4.90: 13974
  Nonbonded interactions: 32066
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU C 111 "
            pdb=" NE2 GLN C 172 "
     model   vdw
     2.114 3.120
  nonbonded pdb=" OG  SER B 212 "
            pdb=" OG1 THR B 214 "
     model   vdw
     2.171 3.040
  nonbonded pdb=" OG1 THR A  47 "
            pdb=" O   SER A  54 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" O   SER C  83 "
            pdb=" NE2 GLN C  85 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" N   GLY A 141 "
            pdb=" OG  SER B 104 "
     model   vdw
     2.252 3.120
  ... (remaining 32061 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.600
  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:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
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      :  0.005   0.049   4328  Z= 0.235
  Angle     :  0.677   5.819   5887  Z= 0.371
  Chirality :  0.043   0.134    646
  Planarity :  0.005   0.053    753
  Dihedral  : 12.990  81.517   1557
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  0.21 %
    Favored  : 99.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.62 %
    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 are not related in a simple way.
  whole:  0.24 (0.38), residues: 539
  helix:  0.20 (1.48), residues: 13
  sheet:  0.41 (0.37), residues: 234
  loop :  0.05 (0.37), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  67 
 TYR   0.024   0.002   TYR C  97 
 PHE   0.014   0.002   PHE C 145 
 TRP   0.046   0.002   TRP C  56 
 HIS   0.002   0.000   HIS B 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 ( 4322)
  covalent geometry    : angle       0.67697 ( 5875)
  SS BOND              : bond        0.00181 (    6)
  SS BOND              : angle       0.74308 (   12)
  hydrogen bonds       : bond        0.25634 (  123)
  hydrogen bonds       : angle      10.10635 (  348)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.176 
Fit side-chains
REVERT: A   18 MET cc_start: 0.8748 (mmp) cc_final: 0.8530 (mmm)
REVERT: A   26 LEU cc_start: 0.6275 (tt) cc_final: 0.5996 (tt)
REVERT: A   45 LEU cc_start: 0.8311 (tp) cc_final: 0.8090 (tt)
REVERT: A  106 GLU cc_start: 0.8553 (pp20) cc_final: 0.8322 (pp20)
REVERT: A  155 ARG cc_start: 0.8664 (ptm-80) cc_final: 0.8381 (tmt170)
REVERT: A  160 GLN cc_start: 0.8279 (mm110) cc_final: 0.8026 (mm110)
REVERT: C    1 ASP cc_start: 0.8395 (p0) cc_final: 0.8182 (p0)
REVERT: C  128 ASP cc_start: 0.8519 (p0) cc_final: 0.8087 (p0)
REVERT: C  153 GLN cc_start: 0.7248 (mp10) cc_final: 0.6837 (mp10)
REVERT: B   59 ASP cc_start: 0.7667 (t0) cc_final: 0.7417 (t0)
REVERT: B   73 ASP cc_start: 0.8333 (t0) cc_final: 0.8130 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 95
  average time/residue: 0.0850
  time to fit residues: 9.8880
Evaluate side-chains
  83 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 48 optimal weight:    0.0770
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0070
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   chunk 50 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   overall best weight:    1.1560

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

Flipped N/Q/H residues before XYZ refinement:
C  27 GLN
C  34 ASN
** C  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 172 GLN
B  65 GLN
B 206 ASN
** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.127102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.087968 restraints weight = 26449.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 6.75
r_work: 0.3014 rms_B_bonded: 5.89 restraints_weight: 2.0000
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3022
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3022 r_free = 0.3022    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3022 r_free = 0.3022    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3022
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.1403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4328  Z= 0.154
  Angle     :  0.642   6.578   5887  Z= 0.336
  Chirality :  0.044   0.155    646
  Planarity :  0.005   0.042    753
  Dihedral  :  4.741  21.998    589
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  6.13 %
    Favored  : 93.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.62 %
    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 are not related in a simple way.
  whole:  0.52 (0.39), residues: 539
  helix:  0.65 (1.52), residues: 13
  sheet:  0.55 (0.36), residues: 245
  loop :  0.27 (0.39), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 217 
 TYR   0.020   0.002   TYR C  97 
 PHE   0.010   0.001   PHE C  77 
 TRP   0.010   0.001   TRP C  56 
 HIS   0.002   0.000   HIS B 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 4322)
  covalent geometry    : angle       0.64224 ( 5875)
  SS BOND              : bond        0.00143 (    6)
  SS BOND              : angle       0.64543 (   12)
  hydrogen bonds       : bond        0.04310 (  123)
  hydrogen bonds       : angle       6.56166 (  348)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 87
  time to evaluate  : 0.103 
Fit side-chains
REVERT: A    9 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7417 (tm-30)
REVERT: A   18 MET cc_start: 0.9021 (mmp) cc_final: 0.8598 (mmp)
REVERT: A  155 ARG cc_start: 0.9028 (ptm-80) cc_final: 0.8701 (tmt170)
REVERT: A  160 GLN cc_start: 0.8522 (mm110) cc_final: 0.8098 (mm110)
REVERT: C    1 ASP cc_start: 0.8731 (p0) cc_final: 0.8456 (p0)
REVERT: C   17 GLU cc_start: 0.8561 (tm-30) cc_final: 0.7759 (tm-30)
REVERT: C  176 ASP cc_start: 0.8370 (m-30) cc_final: 0.7984 (t70)
REVERT: B   59 ASP cc_start: 0.7756 (t0) cc_final: 0.7492 (t0)
REVERT: B   73 ASP cc_start: 0.8624 (t0) cc_final: 0.8353 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 87
  average time/residue: 0.0699
  time to fit residues: 7.6290
Evaluate side-chains
  80 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   chunk 23 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0000
   chunk 5 optimal weight:    8.9990
   chunk 40 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    1.3992

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

Flipped N/Q/H residues before XYZ refinement:
C  34 ASN
** C  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
B  65 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.127313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.089063 restraints weight = 19375.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 5.80
r_work: 0.3056 rms_B_bonded: 5.29 restraints_weight: 2.0000
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3065
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3065 r_free = 0.3065    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3065 r_free = 0.3065    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3065
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.1772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4328  Z= 0.158
  Angle     :  0.626   6.741   5887  Z= 0.326
  Chirality :  0.043   0.159    646
  Planarity :  0.004   0.035    753
  Dihedral  :  4.588  20.949    589
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  :  9.94 %
    Favored  : 88.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.62 %
    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 are not related in a simple way.
  whole:  0.54 (0.39), residues: 539
  helix:  0.60 (1.52), residues: 13
  sheet:  0.60 (0.36), residues: 242
  loop :  0.25 (0.39), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 217 
 TYR   0.021   0.002   TYR C  97 
 PHE   0.015   0.001   PHE B  64 
 TRP   0.012   0.001   TRP A 110 
 HIS   0.001   0.000   HIS B 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 4322)
  covalent geometry    : angle       0.62594 ( 5875)
  SS BOND              : bond        0.00148 (    6)
  SS BOND              : angle       0.56789 (   12)
  hydrogen bonds       : bond        0.03379 (  123)
  hydrogen bonds       : angle       5.74040 (  348)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 0.169 
Fit side-chains
REVERT: A    9 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7424 (tm-30)
REVERT: A   18 MET cc_start: 0.8963 (mmp) cc_final: 0.8694 (mmt)
REVERT: A  126 MET cc_start: 0.8701 (ppp) cc_final: 0.8379 (ppp)
REVERT: A  157 THR cc_start: 0.8387 (p) cc_final: 0.8110 (p)
REVERT: A  160 GLN cc_start: 0.8477 (mm110) cc_final: 0.8083 (mm110)
REVERT: C    1 ASP cc_start: 0.8707 (p0) cc_final: 0.8437 (p0)
REVERT: C   17 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8003 (tm-30)
REVERT: C   88 ASP cc_start: 0.8407 (m-30) cc_final: 0.7662 (m-30)
REVERT: B   59 ASP cc_start: 0.7744 (t0) cc_final: 0.7490 (t0)
REVERT: B   73 ASP cc_start: 0.8627 (t0) cc_final: 0.8359 (t0)
  outliers start: 5
  outliers final: 3
  residues processed: 84
  average time/residue: 0.0643
  time to fit residues: 6.9088
Evaluate side-chains
  81 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 78
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  142 LEU
Chi-restraints excluded: chain C residue  191 ASP
Chi-restraints excluded: chain B residue   28 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 51 optimal weight:   10.0000
   chunk 20 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 13 optimal weight:    3.9990
   chunk 52 optimal weight:    5.9990
   chunk 8 optimal weight:    9.9990
   chunk 39 optimal weight:    5.9990
   chunk 28 optimal weight:    7.9990
   chunk 24 optimal weight:    0.4980
   chunk 45 optimal weight:   10.0000
   overall best weight:    2.8386

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

Flipped N/Q/H residues before XYZ refinement:
C  34 ASN
** C  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 208 ASN ** 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 = 0.3794 r_free = 0.3794 target = 0.124024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.086066 restraints weight = 22285.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 5.99
r_work: 0.2982 rms_B_bonded: 5.40 restraints_weight: 2.0000
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2989
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2989 r_free = 0.2989    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2989 r_free = 0.2989    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2989
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.1934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060   4328  Z= 0.278
  Angle     :  0.682   8.144   5887  Z= 0.357
  Chirality :  0.045   0.162    646
  Planarity :  0.004   0.037    753
  Dihedral  :  4.825  21.170    589
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 12.68 %
    Favored  : 85.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.62 %
    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 are not related in a simple way.
  whole:  0.31 (0.38), residues: 539
  helix:  0.38 (1.45), residues: 13
  sheet:  0.50 (0.36), residues: 242
  loop :  0.04 (0.39), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 155 
 TYR   0.033   0.002   TYR C  97 
 PHE   0.009   0.002   PHE C  77 
 TRP   0.012   0.002   TRP C 154 
 HIS   0.002   0.001   HIS B 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00643 ( 4322)
  covalent geometry    : angle       0.68226 ( 5875)
  SS BOND              : bond        0.00250 (    6)
  SS BOND              : angle       0.72059 (   12)
  hydrogen bonds       : bond        0.03659 (  123)
  hydrogen bonds       : angle       5.78959 (  348)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 88
  time to evaluate  : 0.144 
Fit side-chains
REVERT: A    9 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7521 (tm-30)
REVERT: A  160 GLN cc_start: 0.8538 (mm110) cc_final: 0.8093 (mm110)
REVERT: C    1 ASP cc_start: 0.8741 (p0) cc_final: 0.8408 (p0)
REVERT: C   17 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8067 (tm-30)
REVERT: C   88 ASP cc_start: 0.8599 (m-30) cc_final: 0.7773 (m-30)
REVERT: C   96 GLN cc_start: 0.7878 (tp-100) cc_final: 0.7594 (tm-30)
REVERT: C  167 GLU cc_start: 0.8054 (pt0) cc_final: 0.7843 (pt0)
REVERT: C  176 ASP cc_start: 0.8443 (m-30) cc_final: 0.8108 (t70)
REVERT: B   59 ASP cc_start: 0.7830 (t0) cc_final: 0.7570 (t0)
REVERT: B   64 PHE cc_start: 0.7438 (m-10) cc_final: 0.7106 (m-10)
REVERT: B   73 ASP cc_start: 0.8623 (t0) cc_final: 0.8339 (t0)
  outliers start: 5
  outliers final: 4
  residues processed: 90
  average time/residue: 0.0783
  time to fit residues: 8.6365
Evaluate side-chains
  87 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  142 LEU
Chi-restraints excluded: chain C residue  191 ASP
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue  191 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 45 optimal weight:    9.9990
   chunk 42 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 3 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0270
   chunk 41 optimal weight:    0.0570
   overall best weight:    0.8160

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

Flipped N/Q/H residues before XYZ refinement:
C   6 GLN
C  34 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.127790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.089242 restraints weight = 22892.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 6.21
r_work: 0.3041 rms_B_bonded: 5.56 restraints_weight: 2.0000
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3050
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3050 r_free = 0.3050    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3050 r_free = 0.3050    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3050
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.2175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4328  Z= 0.124
  Angle     :  0.597   7.722   5887  Z= 0.307
  Chirality :  0.042   0.157    646
  Planarity :  0.004   0.038    753
  Dihedral  :  4.481  22.062    589
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 13.32 %
    Favored  : 85.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.62 %
    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 are not related in a simple way.
  whole:  0.51 (0.38), residues: 539
  helix:  0.62 (1.49), residues: 13
  sheet:  0.76 (0.36), residues: 236
  loop :  0.05 (0.39), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 155 
 TYR   0.012   0.001   TYR C  97 
 PHE   0.011   0.001   PHE B  64 
 TRP   0.009   0.001   TRP C 154 
 HIS   0.001   0.000   HIS A 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 4322)
  covalent geometry    : angle       0.59743 ( 5875)
  SS BOND              : bond        0.00112 (    6)
  SS BOND              : angle       0.49380 (   12)
  hydrogen bonds       : bond        0.02810 (  123)
  hydrogen bonds       : angle       5.20824 (  348)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 87
  time to evaluate  : 0.142 
Fit side-chains
REVERT: A    9 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7572 (tm-30)
REVERT: A   18 MET cc_start: 0.8790 (mmm) cc_final: 0.8521 (mmp)
REVERT: A  160 GLN cc_start: 0.8487 (mm110) cc_final: 0.8051 (mm110)
REVERT: C    1 ASP cc_start: 0.8665 (p0) cc_final: 0.8354 (p0)
REVERT: C   17 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8048 (tm-30)
REVERT: C   88 ASP cc_start: 0.8410 (m-30) cc_final: 0.7601 (m-30)
REVERT: C  176 ASP cc_start: 0.8312 (m-30) cc_final: 0.7932 (t70)
REVERT: B   59 ASP cc_start: 0.7773 (t0) cc_final: 0.7496 (t0)
REVERT: B   73 ASP cc_start: 0.8600 (t0) cc_final: 0.8301 (t0)
  outliers start: 5
  outliers final: 2
  residues processed: 89
  average time/residue: 0.0668
  time to fit residues: 7.4858
Evaluate side-chains
  85 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 83
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  142 LEU
Chi-restraints excluded: chain B residue   28 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   chunk 43 optimal weight:    8.9990
   chunk 33 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 45 optimal weight:    6.9990
   chunk 47 optimal weight:    3.9990
   chunk 39 optimal weight:    8.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
C  34 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.123847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.085134 restraints weight = 32152.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 7.02
r_work: 0.2956 rms_B_bonded: 5.95 restraints_weight: 2.0000
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2960
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2960 r_free = 0.2960    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2960 r_free = 0.2960    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2960
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058   4328  Z= 0.254
  Angle     :  0.649   8.641   5887  Z= 0.337
  Chirality :  0.044   0.150    646
  Planarity :  0.004   0.038    753
  Dihedral  :  4.643  20.417    589
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 13.53 %
    Favored  : 83.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.62 %
    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 are not related in a simple way.
  whole:  0.33 (0.38), residues: 539
  helix:  0.42 (1.45), residues: 13
  sheet:  0.50 (0.36), residues: 243
  loop :  0.07 (0.39), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 217 
 TYR   0.031   0.002   TYR C  97 
 PHE   0.007   0.001   PHE B 155 
 TRP   0.012   0.001   TRP C 154 
 HIS   0.002   0.000   HIS B 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00586 ( 4322)
  covalent geometry    : angle       0.64841 ( 5875)
  SS BOND              : bond        0.00203 (    6)
  SS BOND              : angle       0.73452 (   12)
  hydrogen bonds       : bond        0.03410 (  123)
  hydrogen bonds       : angle       5.44364 (  348)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.169 
Fit side-chains
REVERT: A    9 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7627 (tm-30)
REVERT: A   18 MET cc_start: 0.8835 (mmm) cc_final: 0.8495 (mmt)
REVERT: A  160 GLN cc_start: 0.8536 (mm110) cc_final: 0.8091 (mm110)
REVERT: C    1 ASP cc_start: 0.8730 (p0) cc_final: 0.8390 (p0)
REVERT: C   17 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8035 (tm-30)
REVERT: C   88 ASP cc_start: 0.8639 (m-30) cc_final: 0.7810 (m-30)
REVERT: C  176 ASP cc_start: 0.8416 (m-30) cc_final: 0.8088 (t70)
REVERT: C  217 ARG cc_start: 0.7432 (ttp80) cc_final: 0.7084 (mtm110)
REVERT: B   59 ASP cc_start: 0.7884 (t0) cc_final: 0.7617 (t0)
REVERT: B   64 PHE cc_start: 0.7420 (m-10) cc_final: 0.7110 (m-10)
REVERT: B   73 ASP cc_start: 0.8615 (t0) cc_final: 0.8340 (t0)
REVERT: B  157 GLU cc_start: 0.8480 (pt0) cc_final: 0.8032 (pm20)
  outliers start: 10
  outliers final: 6
  residues processed: 92
  average time/residue: 0.0683
  time to fit residues: 7.8890
Evaluate side-chains
  91 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  142 LEU
Chi-restraints excluded: chain C residue  191 ASP
Chi-restraints excluded: chain C residue  214 SER
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue  191 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 14 optimal weight:    0.5980
   chunk 33 optimal weight:    7.9990
   chunk 16 optimal weight:    0.0970
   chunk 36 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
C  34 ASN
C  96 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.126782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.088873 restraints weight = 18122.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 5.57
r_work: 0.3061 rms_B_bonded: 5.07 restraints_weight: 2.0000
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3062
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3062
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.2421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4328  Z= 0.129
  Angle     :  0.618   8.346   5887  Z= 0.317
  Chirality :  0.043   0.151    646
  Planarity :  0.004   0.034    753
  Dihedral  :  4.435  21.403    589
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 14.38 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.62 %
    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 are not related in a simple way.
  whole:  0.41 (0.38), residues: 539
  helix:  0.62 (1.43), residues: 13
  sheet:  0.65 (0.36), residues: 235
  loop :  0.02 (0.39), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 217 
 TYR   0.016   0.001   TYR C  97 
 PHE   0.011   0.001   PHE A  15 
 TRP   0.012   0.001   TRP C 154 
 HIS   0.002   0.000   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 4322)
  covalent geometry    : angle       0.61802 ( 5875)
  SS BOND              : bond        0.00089 (    6)
  SS BOND              : angle       0.58639 (   12)
  hydrogen bonds       : bond        0.02802 (  123)
  hydrogen bonds       : angle       5.13380 (  348)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.126 
Fit side-chains
REVERT: A    9 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7540 (tm-30)
REVERT: A   18 MET cc_start: 0.8731 (mmm) cc_final: 0.8402 (mmt)
REVERT: A  111 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8868 (mp0)
REVERT: A  160 GLN cc_start: 0.8479 (mm110) cc_final: 0.8046 (mm110)
REVERT: C    1 ASP cc_start: 0.8652 (p0) cc_final: 0.8342 (p0)
REVERT: C   17 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8048 (tm-30)
REVERT: C   88 ASP cc_start: 0.8417 (m-30) cc_final: 0.7596 (m-30)
REVERT: C  176 ASP cc_start: 0.8309 (m-30) cc_final: 0.7997 (t0)
REVERT: C  217 ARG cc_start: 0.7462 (ttp80) cc_final: 0.7175 (mtm110)
REVERT: B   59 ASP cc_start: 0.7824 (t0) cc_final: 0.7576 (t0)
REVERT: B   73 ASP cc_start: 0.8523 (t0) cc_final: 0.8259 (t0)
REVERT: B  157 GLU cc_start: 0.8377 (pt0) cc_final: 0.7922 (pm20)
  outliers start: 8
  outliers final: 4
  residues processed: 92
  average time/residue: 0.0690
  time to fit residues: 7.9854
Evaluate side-chains
  90 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 86
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue  191 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   chunk 28 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 38 optimal weight:    6.9990
   chunk 52 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    2.1184

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

Flipped N/Q/H residues before XYZ refinement:
C  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.124055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.087812 restraints weight = 14424.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 4.90
r_work: 0.3037 rms_B_bonded: 4.63 restraints_weight: 0.5000
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3043
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3043
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.2427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   4328  Z= 0.217
  Angle     :  0.664   9.000   5887  Z= 0.342
  Chirality :  0.044   0.152    646
  Planarity :  0.004   0.036    753
  Dihedral  :  4.547  20.620    589
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 14.80 %
    Favored  : 82.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.62 %
    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 are not related in a simple way.
  whole:  0.33 (0.38), residues: 539
  helix:  0.46 (1.38), residues: 13
  sheet:  0.48 (0.35), residues: 244
  loop :  0.09 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 217 
 TYR   0.024   0.002   TYR C  97 
 PHE   0.006   0.001   PHE C 215 
 TRP   0.015   0.001   TRP C 154 
 HIS   0.001   0.000   HIS B 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00495 ( 4322)
  covalent geometry    : angle       0.66405 ( 5875)
  SS BOND              : bond        0.00176 (    6)
  SS BOND              : angle       0.62977 (   12)
  hydrogen bonds       : bond        0.03107 (  123)
  hydrogen bonds       : angle       5.25648 (  348)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.212 
Fit side-chains
REVERT: A    9 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7531 (tm-30)
REVERT: A   18 MET cc_start: 0.8808 (mmm) cc_final: 0.8428 (mmt)
REVERT: A  111 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8853 (mp0)
REVERT: A  126 MET cc_start: 0.8807 (ppp) cc_final: 0.8351 (ppp)
REVERT: A  144 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7228 (mt-10)
REVERT: A  160 GLN cc_start: 0.8476 (mm110) cc_final: 0.8077 (mm110)
REVERT: C    1 ASP cc_start: 0.8662 (p0) cc_final: 0.8325 (p0)
REVERT: C   17 GLU cc_start: 0.8611 (tm-30) cc_final: 0.7986 (tm-30)
REVERT: C   88 ASP cc_start: 0.8512 (m-30) cc_final: 0.7682 (m-30)
REVERT: C  111 GLU cc_start: 0.8603 (tp30) cc_final: 0.8229 (tt0)
REVERT: C  176 ASP cc_start: 0.8366 (m-30) cc_final: 0.8032 (t0)
REVERT: C  217 ARG cc_start: 0.7522 (ttp80) cc_final: 0.7274 (mtm110)
REVERT: B   59 ASP cc_start: 0.7846 (t0) cc_final: 0.7601 (t0)
REVERT: B   73 ASP cc_start: 0.8518 (t0) cc_final: 0.8250 (t0)
REVERT: B  102 ASP cc_start: 0.8604 (p0) cc_final: 0.8120 (p0)
REVERT: B  157 GLU cc_start: 0.8390 (pt0) cc_final: 0.7965 (pm20)
  outliers start: 11
  outliers final: 10
  residues processed: 96
  average time/residue: 0.0725
  time to fit residues: 8.6098
Evaluate side-chains
  98 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain C residue   35 ASN
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  191 ASP
Chi-restraints excluded: chain C residue  214 SER
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue  103 TYR
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  191 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 29 optimal weight:    6.9990
   chunk 12 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 32 optimal weight:    7.9990
   chunk 20 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   overall best weight:    1.1184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.125943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.088110 restraints weight = 22184.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 5.94
r_work: 0.3026 rms_B_bonded: 5.31 restraints_weight: 2.0000
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3033
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3033 r_free = 0.3033    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3033 r_free = 0.3033    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3033
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.2521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4328  Z= 0.142
  Angle     :  0.638   9.070   5887  Z= 0.325
  Chirality :  0.042   0.151    646
  Planarity :  0.004   0.034    753
  Dihedral  :  4.457  19.730    589
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 15.22 %
    Favored  : 82.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.62 %
    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 are not related in a simple way.
  whole:  0.38 (0.39), residues: 539
  helix:  0.68 (1.40), residues: 13
  sheet:  0.63 (0.36), residues: 235
  loop :  0.01 (0.39), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 217 
 TYR   0.014   0.001   TYR C  97 
 PHE   0.011   0.001   PHE A  15 
 TRP   0.015   0.001   TRP C 154 
 HIS   0.001   0.000   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 4322)
  covalent geometry    : angle       0.63836 ( 5875)
  SS BOND              : bond        0.00097 (    6)
  SS BOND              : angle       0.57960 (   12)
  hydrogen bonds       : bond        0.02773 (  123)
  hydrogen bonds       : angle       5.09274 (  348)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A    9 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7609 (tm-30)
REVERT: A   18 MET cc_start: 0.8777 (mmm) cc_final: 0.8405 (mmt)
REVERT: A  126 MET cc_start: 0.8881 (ppp) cc_final: 0.8497 (ppp)
REVERT: A  144 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7195 (mt-10)
REVERT: A  155 ARG cc_start: 0.8305 (tmt170) cc_final: 0.8087 (ttp80)
REVERT: A  160 GLN cc_start: 0.8485 (mm110) cc_final: 0.8098 (mm110)
REVERT: C    1 ASP cc_start: 0.8641 (p0) cc_final: 0.8322 (p0)
REVERT: C   17 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8063 (tm-30)
REVERT: C   88 ASP cc_start: 0.8489 (m-30) cc_final: 0.7663 (m-30)
REVERT: C  111 GLU cc_start: 0.8639 (tp30) cc_final: 0.8269 (tt0)
REVERT: C  129 GLU cc_start: 0.8738 (mp0) cc_final: 0.8518 (mp0)
REVERT: C  176 ASP cc_start: 0.8335 (m-30) cc_final: 0.8013 (t0)
REVERT: C  217 ARG cc_start: 0.7513 (ttp80) cc_final: 0.7261 (mtm110)
REVERT: B   59 ASP cc_start: 0.7838 (t0) cc_final: 0.7554 (t0)
REVERT: B   73 ASP cc_start: 0.8553 (t0) cc_final: 0.8278 (t0)
REVERT: B  102 ASP cc_start: 0.8548 (p0) cc_final: 0.8088 (p0)
REVERT: B  157 GLU cc_start: 0.8407 (pt0) cc_final: 0.7938 (pm20)
  outliers start: 8
  outliers final: 8
  residues processed: 97
  average time/residue: 0.0654
  time to fit residues: 8.0783
Evaluate side-chains
  95 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain C residue   35 ASN
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  214 SER
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue  103 TYR
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  191 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 45 optimal weight:    9.9990
   chunk 23 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 39 optimal weight:    6.9990
   chunk 2 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 7 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 14 optimal weight:    0.1980
   chunk 21 optimal weight:    1.9990
   overall best weight:    2.0186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.124509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.086443 restraints weight = 22905.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 6.04
r_work: 0.2994 rms_B_bonded: 5.34 restraints_weight: 2.0000
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3000
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3000 r_free = 0.3000    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3000 r_free = 0.3000    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3000
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.2536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   4328  Z= 0.208
  Angle     :  0.669   9.261   5887  Z= 0.342
  Chirality :  0.044   0.150    646
  Planarity :  0.004   0.035    753
  Dihedral  :  4.559  20.871    589
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 15.86 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.62 %
    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 are not related in a simple way.
  whole:  0.28 (0.39), residues: 539
  helix:  0.62 (1.39), residues: 13
  sheet:  0.43 (0.35), residues: 244
  loop :  0.05 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 217 
 TYR   0.022   0.002   TYR C  97 
 PHE   0.011   0.001   PHE A  15 
 TRP   0.013   0.001   TRP C 154 
 HIS   0.001   0.000   HIS B 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 ( 4322)
  covalent geometry    : angle       0.66930 ( 5875)
  SS BOND              : bond        0.00161 (    6)
  SS BOND              : angle       0.62032 (   12)
  hydrogen bonds       : bond        0.03077 (  123)
  hydrogen bonds       : angle       5.23114 (  348)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.150 
Fit side-chains
REVERT: A    9 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7602 (tm-30)
REVERT: A   18 MET cc_start: 0.8827 (mmm) cc_final: 0.8436 (mmt)
REVERT: A  126 MET cc_start: 0.8854 (ppp) cc_final: 0.8472 (ppp)
REVERT: A  144 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7275 (mt-10)
REVERT: A  160 GLN cc_start: 0.8507 (mm110) cc_final: 0.8118 (mm110)
REVERT: C    1 ASP cc_start: 0.8704 (p0) cc_final: 0.8359 (p0)
REVERT: C   17 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8052 (tm-30)
REVERT: C   88 ASP cc_start: 0.8531 (m-30) cc_final: 0.7699 (m-30)
REVERT: C  111 GLU cc_start: 0.8681 (tp30) cc_final: 0.8306 (tt0)
REVERT: C  128 ASP cc_start: 0.9027 (p0) cc_final: 0.8822 (p0)
REVERT: C  217 ARG cc_start: 0.7520 (ttp80) cc_final: 0.7284 (mtm110)
REVERT: B   59 ASP cc_start: 0.7882 (t0) cc_final: 0.7576 (t0)
REVERT: B   73 ASP cc_start: 0.8546 (t0) cc_final: 0.8261 (t0)
REVERT: B  102 ASP cc_start: 0.8578 (p0) cc_final: 0.8122 (p0)
REVERT: B  157 GLU cc_start: 0.8446 (pt0) cc_final: 0.7974 (pm20)
  outliers start: 10
  outliers final: 10
  residues processed: 95
  average time/residue: 0.0748
  time to fit residues: 8.8738
Evaluate side-chains
  99 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain C residue   35 ASN
Chi-restraints excluded: chain C residue   73 SER
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  191 ASP
Chi-restraints excluded: chain C residue  214 SER
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue  103 TYR
Chi-restraints excluded: chain B residue  191 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 28 optimal weight:    8.9990
   chunk 39 optimal weight:    0.0770
   chunk 46 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0670
   chunk 50 optimal weight:    0.0980
   chunk 42 optimal weight:    0.8980
   chunk 26 optimal weight:    8.9990
   overall best weight:    0.4076

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.127706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.090016 restraints weight = 19193.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 5.67
r_work: 0.3068 rms_B_bonded: 5.18 restraints_weight: 2.0000
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3076
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3076 r_free = 0.3076    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3076 r_free = 0.3076    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3076
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.2732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4328  Z= 0.113
  Angle     :  0.636   9.445   5887  Z= 0.322
  Chirality :  0.042   0.148    646
  Planarity :  0.004   0.033    753
  Dihedral  :  4.353  21.283    589
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 16.70 %
    Favored  : 81.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.62 %
    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 are not related in a simple way.
  whole:  0.35 (0.38), residues: 539
  helix:  0.76 (1.39), residues: 13
  sheet:  0.56 (0.36), residues: 237
  loop :  0.02 (0.39), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 217 
 TYR   0.010   0.001   TYR C  55 
 PHE   0.005   0.001   PHE C 215 
 TRP   0.012   0.001   TRP A 156 
 HIS   0.002   0.000   HIS C 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 4322)
  covalent geometry    : angle       0.63618 ( 5875)
  SS BOND              : bond        0.00130 (    6)
  SS BOND              : angle       0.56738 (   12)
  hydrogen bonds       : bond        0.02570 (  123)
  hydrogen bonds       : angle       4.88763 (  348)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1419.46 seconds
wall clock time: 24 minutes 55.11 seconds (1495.11 seconds total)