Starting phenix.real_space_refine
on Tue Feb  3 16:25:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9pv3_71881/02_2026/9pv3_71881.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9pv3_71881/02_2026/9pv3_71881.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9pv3_71881/02_2026/9pv3_71881.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9pv3_71881/02_2026/9pv3_71881.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9pv3_71881/02_2026/9pv3_71881.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9pv3_71881/02_2026/9pv3_71881.cif"
  }
  resolution = 3.95
  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=   0.026
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      19      5.16       5
     C    3101      2.51       5
     N     801      2.21       5
     O     941      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4862
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 913
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 913
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 4, 'TRANS': 112}
    Chain: "C"
      Number of atoms: 821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 821
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101}
    Chain: "D"
      Number of atoms: 1256
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 155, 1256
          Classifications: {'peptide': 155}
          Link IDs: {'PTRANS': 8, 'TRANS': 146}
    Chain: "H"
      Number of atoms: 998
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 998
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "L"
      Number of atoms: 860
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 860
          Classifications: {'peptide': 113}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 107}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "D"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.22, per 1000 atoms: 0.25
  Number of scatterers: 4862
  At special positions: 0
  Unit cell: (57.477, 66.64, 126.616, 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      19     16.00
     O     941      8.00
     N     801      7.00
     C    3101      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  88 " distance=2.05
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.05
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  94 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG D 201 " - " ASN D  74 "
  Time building additional restraints: 0.37
  Conformation dependent library (CDL) restraints added in 268.0 milliseconds
  

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1138

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 15 sheets defined
      13.1% alpha, 27.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'B' and resid 63 through 66
    Processing helix  chain 'D' and resid 8 through 21
      Proline residue:  D  16  - end of helix
    Processing helix  chain 'D' and resid 26 through 38
      removed outlier: 3.576A  pdb=" N   LYS D  30 " --> pdb=" O   ASP D  26 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 98 through 113
    Processing helix  chain 'D' and resid 114 through 119
      removed outlier: 3.863A  pdb=" N   MET D 118 " --> pdb=" O   ASP D 114 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 120 through 124
      removed outlier: 3.772A  pdb=" N   MET D 124 " --> pdb=" O   LEU D 121 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 125 through 139
    Processing helix  chain 'D' and resid 149 through 151
      No H-bonds generated for 'chain 'D' and resid 149 through 151'
    Processing helix  chain 'H' and resid 63 through 67
    Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 7
    Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 12
      removed outlier: 6.749A  pdb=" N   VAL B  36 " --> pdb=" O   HIS B  52 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   HIS B  52 " --> pdb=" O   VAL B  36 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   TRP B  38 " --> pdb=" O   LEU B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 69 through 70
    Processing sheet with id=AA4, first strand: chain 'C' and resid 4 through 7
    Processing sheet with id=AA5, first strand: chain 'C' and resid 10 through 13
      removed outlier: 7.212A  pdb=" N   LEU C  11 " --> pdb=" O   GLU C 105 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 48 through 50
      removed outlier: 6.565A  pdb=" N   THR C  53 " --> pdb=" O   TYR C  49 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 49 through 50
      removed outlier: 6.491A  pdb=" N   ALA D  50 " --> pdb=" O   PHE D  91 " (cutoff:3.500A)
      removed outlier: 7.340A  pdb=" N   LEU D  93 " --> pdb=" O   ALA D  50 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   VAL D  54 " --> pdb=" O   LEU D  93 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'D' and resid 49 through 50
      removed outlier: 6.491A  pdb=" N   ALA D  50 " --> pdb=" O   PHE D  91 " (cutoff:3.500A)
      removed outlier: 7.340A  pdb=" N   LEU D  93 " --> pdb=" O   ALA D  50 " (cutoff:3.500A)
      removed outlier: 9.958A  pdb=" N   VAL D  73 " --> pdb=" O   PRO D  84 " (cutoff:3.500A)
      removed outlier: 10.011A  pdb=" N   LYS D  71 " --> pdb=" O   PRO D  86 " (cutoff:3.500A)
      removed outlier: 4.883A  pdb=" N   ARG D  88 " --> pdb=" O   LEU D  69 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ARG D 154 " --> pdb=" O   VAL D  66 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'H' and resid 45 through 47
      removed outlier: 7.000A  pdb=" N   GLN H  39 " --> pdb=" O   ILE H  92 " (cutoff:3.500A)
      removed outlier: 5.998A  pdb=" N   ILE H  92 " --> pdb=" O   GLN H  39 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 50 through 52
      removed outlier: 3.750A  pdb=" N   VAL H  50 " --> pdb=" O   ASN H  60 " (cutoff:3.500A)
      removed outlier: 5.553A  pdb=" N   TRP H  52 " --> pdb=" O   ASP H  58 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   ASP H  58 " --> pdb=" O   TRP H  52 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 6
    Processing sheet with id=AB4, first strand: chain 'L' and resid 11 through 12
      removed outlier: 7.012A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 111 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'L' and resid 37 through 39
      removed outlier: 3.724A  pdb=" N   TYR L  38 " --> pdb=" O   GLN L  95 " (cutoff:3.500A)
      removed outlier: 5.279A  pdb=" N   CYS L  94 " --> pdb=" O   GLY L 105 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'L' and resid 53 through 54

    135 hydrogen bonds defined for protein.
    339 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: 0.80

  Time building geometry restraints manager: 0.51 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: 1495
        1.34 -     1.47: 1311
        1.47 -     1.59: 2147
        1.59 -     1.71: 0
        1.71 -     1.84: 30
  Bond restraints: 4983
  Sorted by residual:
  bond pdb=" CG  LEU D 121 "
       pdb=" CD2 LEU D 121 "
    ideal  model  delta    sigma   weight residual
    1.521  1.425  0.096 3.30e-02 9.18e+02 8.50e+00
  bond pdb=" CA  GLN H  39 "
       pdb=" C   GLN H  39 "
    ideal  model  delta    sigma   weight residual
    1.528  1.570 -0.042 1.60e-02 3.91e+03 6.99e+00
  bond pdb=" CB  PHE D  49 "
       pdb=" CG  PHE D  49 "
    ideal  model  delta    sigma   weight residual
    1.502  1.447  0.055 2.30e-02 1.89e+03 5.66e+00
  bond pdb=" N   SER H  40 "
       pdb=" CA  SER H  40 "
    ideal  model  delta    sigma   weight residual
    1.453  1.486 -0.033 1.44e-02 4.82e+03 5.32e+00
  bond pdb=" CG1 ILE D  68 "
       pdb=" CD1 ILE D  68 "
    ideal  model  delta    sigma   weight residual
    1.513  1.433  0.080 3.90e-02 6.57e+02 4.25e+00
  ... (remaining 4978 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.37: 6517
        3.37 -     6.74: 223
        6.74 -    10.11: 21
       10.11 -    13.48: 5
       13.48 -    16.85: 2
  Bond angle restraints: 6768
  Sorted by residual:
  angle pdb=" N   GLY H  42 "
        pdb=" CA  GLY H  42 "
        pdb=" C   GLY H  42 "
      ideal   model   delta    sigma   weight residual
     113.18  130.03  -16.85 2.37e+00 1.78e-01 5.05e+01
  angle pdb=" N   SER L  49 "
        pdb=" CA  SER L  49 "
        pdb=" C   SER L  49 "
      ideal   model   delta    sigma   weight residual
     108.39  122.42  -14.03 2.10e+00 2.27e-01 4.46e+01
  angle pdb=" N   PRO L  50 "
        pdb=" CA  PRO L  50 "
        pdb=" C   PRO L  50 "
      ideal   model   delta    sigma   weight residual
     112.47  100.82   11.65 2.06e+00 2.36e-01 3.20e+01
  angle pdb=" N   TYR H  93 "
        pdb=" CA  TYR H  93 "
        pdb=" C   TYR H  93 "
      ideal   model   delta    sigma   weight residual
     110.80  122.37  -11.57 2.13e+00 2.20e-01 2.95e+01
  angle pdb=" CA  TRP L  41 "
        pdb=" CB  TRP L  41 "
        pdb=" CG  TRP L  41 "
      ideal   model   delta    sigma   weight residual
     113.60  122.43   -8.83 1.90e+00 2.77e-01 2.16e+01
  ... (remaining 6763 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.68: 2723
       17.68 -    35.35: 153
       35.35 -    53.03: 52
       53.03 -    70.71: 10
       70.71 -    88.38: 6
  Dihedral angle restraints: 2944
    sinusoidal: 1159
      harmonic: 1785
  Sorted by residual:
  dihedral pdb=" CA  GLY H  42 "
           pdb=" C   GLY H  42 "
           pdb=" N   LYS H  43 "
           pdb=" CA  LYS H  43 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.95   20.05     0      5.00e+00 4.00e-02 1.61e+01
  dihedral pdb=" CA  TYR L  92 "
           pdb=" C   TYR L  92 "
           pdb=" N   PHE L  93 "
           pdb=" CA  PHE L  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.82   17.18     0      5.00e+00 4.00e-02 1.18e+01
  dihedral pdb=" CB  LYS H   5 "
           pdb=" CG  LYS H   5 "
           pdb=" CD  LYS H   5 "
           pdb=" CE  LYS H   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  121.21   58.79     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 2941 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 569
       0.077 -    0.153: 150
       0.153 -    0.229: 15
       0.229 -    0.306: 5
       0.306 -    0.382: 1
  Chirality restraints: 740
  Sorted by residual:
  chirality pdb=" CA  SER L  49 "
            pdb=" N   SER L  49 "
            pdb=" C   SER L  49 "
            pdb=" CB  SER L  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.65e+00
  chirality pdb=" CA  TYR C  32 "
            pdb=" N   TYR C  32 "
            pdb=" C   TYR C  32 "
            pdb=" CB  TYR C  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.74e+00
  chirality pdb=" CA  TYR H  93 "
            pdb=" N   TYR H  93 "
            pdb=" C   TYR H  93 "
            pdb=" CB  TYR H  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.61e+00
  ... (remaining 737 not shown)

  Planarity restraints: 860
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN D  74 "    0.111 2.00e-02 2.50e+03   1.64e-01 3.35e+02
        pdb=" CG  ASN D  74 "   -0.042 2.00e-02 2.50e+03
        pdb=" OD1 ASN D  74 "    0.038 2.00e-02 2.50e+03
        pdb=" ND2 ASN D  74 "   -0.291 2.00e-02 2.50e+03
        pdb=" C1  NAG D 201 "    0.184 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B  78 "    0.018 2.00e-02 2.50e+03   3.61e-02 1.31e+01
        pdb=" C   ASN B  78 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   ASN B  78 "    0.024 2.00e-02 2.50e+03
        pdb=" N   GLN B  79 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE D  51 "   -0.018 2.00e-02 2.50e+03   3.49e-02 1.22e+01
        pdb=" C   ILE D  51 "    0.060 2.00e-02 2.50e+03
        pdb=" O   ILE D  51 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   PRO D  52 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 857 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.51: 28
        2.51 -     3.11: 3537
        3.11 -     3.70: 7201
        3.70 -     4.30: 10131
        4.30 -     4.90: 16568
  Nonbonded interactions: 37465
  Sorted by model distance:
  nonbonded pdb=" O   ARG D  60 "
            pdb=" OD1 ASP D  61 "
     model   vdw
     1.909 3.040
  nonbonded pdb=" OD1 ASN D  74 "
            pdb=" N   PRO D  86 "
     model   vdw
     1.951 3.120
  nonbonded pdb=" OD1 ASN D  74 "
            pdb=" CA  PRO D  86 "
     model   vdw
     2.097 3.470
  nonbonded pdb=" OD1 ASP B  91 "
            pdb=" OH  TYR B  95 "
     model   vdw
     2.175 3.040
  nonbonded pdb=" OE1 GLU D  35 "
            pdb=" OG  SER D  40 "
     model   vdw
     2.191 3.040
  ... (remaining 37460 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.620
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.950
  Find NCS groups from input model:        0.030
  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:1.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6574
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   0.096   4988  Z= 0.349
  Angle     :  1.455  20.376   6779  Z= 0.800
  Chirality :  0.069   0.382    740
  Planarity :  0.007   0.058    859
  Dihedral  : 13.342  88.383   1794
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  : 12.15 %
    Favored  : 87.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.63 (0.31), residues: 608
  helix: -0.52 (0.59), residues: 57
  sheet:  0.65 (0.40), residues: 163
  loop : -0.90 (0.28), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.002   ARG H  66 
 TYR   0.036   0.005   TYR C  36 
 PHE   0.042   0.005   PHE L 104 
 TRP   0.047   0.005   TRP L  41 
 HIS   0.011   0.002   HIS C  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00778 ( 4983)
  covalent geometry    : angle       1.41297 ( 6768)
  SS BOND              : bond        0.01185 (    4)
  SS BOND              : angle       2.98394 (    8)
  hydrogen bonds       : bond        0.16043 (  135)
  hydrogen bonds       : angle       8.79941 (  339)
  link_NAG-ASN         : bond        0.05961 (    1)
  link_NAG-ASN         : angle      16.04653 (    3)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 128
  average time/residue: 0.0720
  time to fit residues: 11.6435
Evaluate side-chains
  101 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 26 optimal weight:    0.4980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  95 GLN ** 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 = 0.4041 r_free = 0.4041 target = 0.147149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.130719 restraints weight = 8849.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.134116 restraints weight = 5762.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.136577 restraints weight = 4058.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.138298 restraints weight = 3035.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.139579 restraints weight = 2398.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6724
moved from start:          0.2063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   4988  Z= 0.203
  Angle     :  0.836  10.015   6779  Z= 0.451
  Chirality :  0.050   0.223    740
  Planarity :  0.005   0.041    859
  Dihedral  :  5.844  23.152    688
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  7.40 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 15.33 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -0.98 (0.31), residues: 608
  helix:  0.10 (0.61), residues: 57
  sheet:  0.15 (0.36), residues: 181
  loop : -1.23 (0.30), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  11 
 TYR   0.022   0.002   TYR L  38 
 PHE   0.020   0.003   PHE H  27 
 TRP   0.024   0.003   TRP L  41 
 HIS   0.002   0.001   HIS L  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 ( 4983)
  covalent geometry    : angle       0.83207 ( 6768)
  SS BOND              : bond        0.00893 (    4)
  SS BOND              : angle       2.02954 (    8)
  hydrogen bonds       : bond        0.05248 (  135)
  hydrogen bonds       : angle       7.18995 (  339)
  link_NAG-ASN         : bond        0.00242 (    1)
  link_NAG-ASN         : angle       2.47314 (    3)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   24 ASP cc_start: 0.6084 (m-30) cc_final: 0.5423 (m-30)
REVERT: D   77 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6951 (tm-30)
REVERT: H  101 TYR cc_start: 0.6514 (OUTLIER) cc_final: 0.6158 (t80)
REVERT: L   56 PHE cc_start: 0.5550 (m-80) cc_final: 0.5303 (p90)
  outliers start: 17
  outliers final: 11
  residues processed: 128
  average time/residue: 0.0767
  time to fit residues: 12.6256
Evaluate side-chains
  105 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 SER
Chi-restraints excluded: chain B residue   56 ASP
Chi-restraints excluded: chain B residue   58 ASP
Chi-restraints excluded: chain B residue   74 ASP
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain C residue   83 PHE
Chi-restraints excluded: chain D residue   77 GLU
Chi-restraints excluded: chain H residue    5 LYS
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue  101 TYR
Chi-restraints excluded: chain H residue  113 TYR
Chi-restraints excluded: chain H residue  122 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    0.2980
   chunk 11 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 31 optimal weight:    0.2980
   chunk 7 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 3 optimal weight:    0.5980
   chunk 33 optimal weight:    3.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  60 ASN
** L  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.145793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.129366 restraints weight = 8726.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.132575 restraints weight = 5646.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.134806 restraints weight = 4002.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.136616 restraints weight = 3046.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.137924 restraints weight = 2407.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6779
moved from start:          0.2792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4988  Z= 0.171
  Angle     :  0.769   8.938   6779  Z= 0.411
  Chirality :  0.048   0.208    740
  Planarity :  0.005   0.048    859
  Dihedral  :  5.598  24.096    688
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 17.20 %
    Favored  : 79.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -1.23 (0.31), residues: 608
  helix:  0.70 (0.64), residues: 57
  sheet: -0.14 (0.37), residues: 175
  loop : -1.46 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  11 
 TYR   0.017   0.002   TYR L  38 
 PHE   0.032   0.002   PHE H  27 
 TRP   0.014   0.002   TRP H  47 
 HIS   0.002   0.001   HIS L  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 4983)
  covalent geometry    : angle       0.76607 ( 6768)
  SS BOND              : bond        0.00546 (    4)
  SS BOND              : angle       1.96321 (    8)
  hydrogen bonds       : bond        0.04490 (  135)
  hydrogen bonds       : angle       6.77049 (  339)
  link_NAG-ASN         : bond        0.00009 (    1)
  link_NAG-ASN         : angle       1.31251 (    3)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   92 THR cc_start: 0.8792 (m) cc_final: 0.8512 (p)
REVERT: C   88 CYS cc_start: 0.5237 (p) cc_final: 0.4986 (p)
REVERT: H  101 TYR cc_start: 0.6562 (OUTLIER) cc_final: 0.6085 (t80)
REVERT: L   56 PHE cc_start: 0.5791 (m-80) cc_final: 0.5489 (p90)
  outliers start: 18
  outliers final: 11
  residues processed: 110
  average time/residue: 0.0808
  time to fit residues: 11.2807
Evaluate side-chains
  100 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 ASP
Chi-restraints excluded: chain B residue   58 ASP
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain C residue   32 TYR
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain D residue   22 MET
Chi-restraints excluded: chain D residue   49 PHE
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue  101 TYR
Chi-restraints excluded: chain H residue  113 TYR
Chi-restraints excluded: chain H residue  122 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0070
   chunk 30 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 52 optimal weight:    0.2980
   chunk 48 optimal weight:    0.0370
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.4478

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

Flipped N/Q/H residues before XYZ refinement:
** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 147 ASN
** L  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  97 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.144912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.128883 restraints weight = 8637.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.132055 restraints weight = 5573.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.134420 restraints weight = 3920.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.136119 restraints weight = 2938.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.137433 restraints weight = 2310.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6784
moved from start:          0.3282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4988  Z= 0.148
  Angle     :  0.727   8.526   6779  Z= 0.385
  Chirality :  0.047   0.189    740
  Planarity :  0.005   0.053    859
  Dihedral  :  5.498  22.577    688
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 17.94 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -1.25 (0.31), residues: 608
  helix:  0.95 (0.64), residues: 57
  sheet: -0.22 (0.38), residues: 181
  loop : -1.50 (0.29), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  11 
 TYR   0.021   0.002   TYR L  42 
 PHE   0.023   0.002   PHE H  27 
 TRP   0.023   0.002   TRP H  36 
 HIS   0.004   0.001   HIS L  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 4983)
  covalent geometry    : angle       0.72536 ( 6768)
  SS BOND              : bond        0.00683 (    4)
  SS BOND              : angle       1.62369 (    8)
  hydrogen bonds       : bond        0.04000 (  135)
  hydrogen bonds       : angle       6.50401 (  339)
  link_NAG-ASN         : bond        0.00125 (    1)
  link_NAG-ASN         : angle       0.95755 (    3)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   92 THR cc_start: 0.8692 (m) cc_final: 0.8473 (p)
REVERT: C   88 CYS cc_start: 0.5389 (p) cc_final: 0.5078 (p)
REVERT: H  101 TYR cc_start: 0.6587 (OUTLIER) cc_final: 0.6103 (t80)
REVERT: L   56 PHE cc_start: 0.5949 (m-80) cc_final: 0.5260 (p90)
REVERT: L   97 HIS cc_start: 0.6591 (OUTLIER) cc_final: 0.5720 (t70)
  outliers start: 17
  outliers final: 11
  residues processed: 105
  average time/residue: 0.0802
  time to fit residues: 10.7849
Evaluate side-chains
  104 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    3 THR
Chi-restraints excluded: chain B residue   56 ASP
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain C residue   32 TYR
Chi-restraints excluded: chain D residue   49 PHE
Chi-restraints excluded: chain D residue   58 TYR
Chi-restraints excluded: chain H residue    5 LYS
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue  101 TYR
Chi-restraints excluded: chain H residue  113 TYR
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain L residue   97 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  95 GLN ** 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 = 0.3956 r_free = 0.3956 target = 0.140657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.124541 restraints weight = 8909.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.127652 restraints weight = 5829.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.129911 restraints weight = 4145.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.131492 restraints weight = 3136.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.132789 restraints weight = 2507.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6924
moved from start:          0.3646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   4988  Z= 0.195
  Angle     :  0.747   8.709   6779  Z= 0.397
  Chirality :  0.049   0.195    740
  Planarity :  0.005   0.053    859
  Dihedral  :  5.656  22.346    688
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 13.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 18.32 %
    Favored  : 78.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -1.47 (0.31), residues: 608
  helix:  1.30 (0.65), residues: 57
  sheet: -0.27 (0.38), residues: 177
  loop : -1.79 (0.28), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D  11 
 TYR   0.021   0.002   TYR C  49 
 PHE   0.017   0.002   PHE H  27 
 TRP   0.016   0.002   TRP L  41 
 HIS   0.008   0.002   HIS L  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 4983)
  covalent geometry    : angle       0.74432 ( 6768)
  SS BOND              : bond        0.00790 (    4)
  SS BOND              : angle       1.79071 (    8)
  hydrogen bonds       : bond        0.04053 (  135)
  hydrogen bonds       : angle       6.50557 (  339)
  link_NAG-ASN         : bond        0.00057 (    1)
  link_NAG-ASN         : angle       1.05998 (    3)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
REVERT: B   45 LYS cc_start: 0.8375 (mmtp) cc_final: 0.7911 (mmmt)
REVERT: B   92 THR cc_start: 0.8782 (m) cc_final: 0.8484 (p)
REVERT: L   97 HIS cc_start: 0.6337 (OUTLIER) cc_final: 0.5415 (t-90)
  outliers start: 18
  outliers final: 15
  residues processed: 100
  average time/residue: 0.0789
  time to fit residues: 10.1486
Evaluate side-chains
  104 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    3 THR
Chi-restraints excluded: chain B residue   43 SER
Chi-restraints excluded: chain B residue   56 ASP
Chi-restraints excluded: chain B residue   58 ASP
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain C residue   32 TYR
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain D residue   49 PHE
Chi-restraints excluded: chain D residue   58 TYR
Chi-restraints excluded: chain H residue    5 LYS
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue  101 TYR
Chi-restraints excluded: chain H residue  113 TYR
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain L residue   97 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 45 optimal weight:    0.5980
   chunk 57 optimal weight:    0.5980
   chunk 12 optimal weight:    2.9990
   chunk 48 optimal weight:    0.2980
   chunk 5 optimal weight:    0.0970
   chunk 50 optimal weight:    0.8980
   chunk 3 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0970
   chunk 35 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0770
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.2334

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

Flipped N/Q/H residues before XYZ refinement:
** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 147 ASN
** L  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  97 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.144872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.128980 restraints weight = 8890.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.132246 restraints weight = 5710.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.134642 restraints weight = 4004.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.136312 restraints weight = 2984.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.137495 restraints weight = 2339.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6789
moved from start:          0.3820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4988  Z= 0.130
  Angle     :  0.702   8.363   6779  Z= 0.368
  Chirality :  0.047   0.171    740
  Planarity :  0.005   0.055    859
  Dihedral  :  5.331  22.544    688
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 19.63 %
    Favored  : 76.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -1.45 (0.32), residues: 608
  helix:  1.32 (0.64), residues: 57
  sheet: -0.13 (0.40), residues: 163
  loop : -1.80 (0.28), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D  11 
 TYR   0.027   0.002   TYR C  49 
 PHE   0.019   0.002   PHE H  27 
 TRP   0.017   0.002   TRP L  41 
 HIS   0.005   0.001   HIS C  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 4983)
  covalent geometry    : angle       0.69910 ( 6768)
  SS BOND              : bond        0.00561 (    4)
  SS BOND              : angle       1.84501 (    8)
  hydrogen bonds       : bond        0.03691 (  135)
  hydrogen bonds       : angle       6.29298 (  339)
  link_NAG-ASN         : bond        0.00135 (    1)
  link_NAG-ASN         : angle       0.75194 (    3)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   45 LYS cc_start: 0.8278 (mmtp) cc_final: 0.7810 (mmmt)
REVERT: D  150 ARG cc_start: 0.9050 (mtt90) cc_final: 0.8545 (ttm110)
REVERT: H   30 THR cc_start: 0.7641 (OUTLIER) cc_final: 0.7263 (m)
REVERT: L   97 HIS cc_start: 0.6589 (OUTLIER) cc_final: 0.5906 (t70)
  outliers start: 20
  outliers final: 11
  residues processed: 107
  average time/residue: 0.0686
  time to fit residues: 9.5671
Evaluate side-chains
  102 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 SER
Chi-restraints excluded: chain B residue   56 ASP
Chi-restraints excluded: chain B residue   58 ASP
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain C residue   32 TYR
Chi-restraints excluded: chain D residue   58 TYR
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue  101 TYR
Chi-restraints excluded: chain H residue  113 TYR
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain L residue   97 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 14 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 55 optimal weight:    6.9990
   chunk 44 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  97 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.139421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.123952 restraints weight = 9046.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.126946 restraints weight = 5933.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.129122 restraints weight = 4237.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.130666 restraints weight = 3222.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.131819 restraints weight = 2583.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6951
moved from start:          0.4153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4988  Z= 0.192
  Angle     :  0.761   8.317   6779  Z= 0.398
  Chirality :  0.049   0.183    740
  Planarity :  0.005   0.053    859
  Dihedral  :  5.573  23.306    688
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 13.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.88 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 20.00 %
    Favored  : 76.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -1.55 (0.32), residues: 608
  helix:  1.36 (0.65), residues: 58
  sheet: -0.31 (0.39), residues: 170
  loop : -1.86 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D  11 
 TYR   0.018   0.002   TYR B  96 
 PHE   0.016   0.002   PHE H  27 
 TRP   0.025   0.002   TRP H  36 
 HIS   0.005   0.002   HIS B  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 4983)
  covalent geometry    : angle       0.75456 ( 6768)
  SS BOND              : bond        0.00315 (    4)
  SS BOND              : angle       2.84920 (    8)
  hydrogen bonds       : bond        0.03889 (  135)
  hydrogen bonds       : angle       6.34610 (  339)
  link_NAG-ASN         : bond        0.00059 (    1)
  link_NAG-ASN         : angle       0.99629 (    3)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    5 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.7013 (tmtt)
REVERT: B   45 LYS cc_start: 0.8505 (mmtp) cc_final: 0.8065 (mmmt)
REVERT: H   30 THR cc_start: 0.7644 (p) cc_final: 0.7266 (m)
REVERT: H   82 MET cc_start: 0.7795 (ptm) cc_final: 0.7437 (ptm)
REVERT: L   95 GLN cc_start: 0.6452 (mp-120) cc_final: 0.5792 (mp-120)
REVERT: L   97 HIS cc_start: 0.6987 (OUTLIER) cc_final: 0.6105 (t70)
  outliers start: 19
  outliers final: 13
  residues processed: 100
  average time/residue: 0.0701
  time to fit residues: 9.1417
Evaluate side-chains
  105 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    3 THR
Chi-restraints excluded: chain B residue    5 LYS
Chi-restraints excluded: chain B residue   43 SER
Chi-restraints excluded: chain B residue   56 ASP
Chi-restraints excluded: chain B residue   58 ASP
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain C residue   32 TYR
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain D residue   49 PHE
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue  113 TYR
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain L residue   45 LYS
Chi-restraints excluded: chain L residue   97 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0370
   chunk 45 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0000
   chunk 43 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.4662

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

Flipped N/Q/H residues before XYZ refinement:
** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  60 ASN
** L  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.141728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.126075 restraints weight = 9026.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.129214 restraints weight = 5830.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.131496 restraints weight = 4120.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.133142 restraints weight = 3089.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.134301 restraints weight = 2434.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6888
moved from start:          0.4266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4988  Z= 0.149
  Angle     :  0.746   9.267   6779  Z= 0.386
  Chirality :  0.048   0.178    740
  Planarity :  0.005   0.057    859
  Dihedral  :  5.467  23.578    688
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 13.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 21.50 %
    Favored  : 74.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -1.57 (0.32), residues: 608
  helix:  1.37 (0.65), residues: 58
  sheet: -0.16 (0.40), residues: 162
  loop : -1.94 (0.28), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D  11 
 TYR   0.034   0.002   TYR C  49 
 PHE   0.018   0.002   PHE H  27 
 TRP   0.039   0.002   TRP H  52 
 HIS   0.007   0.002   HIS L  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 4983)
  covalent geometry    : angle       0.74112 ( 6768)
  SS BOND              : bond        0.00472 (    4)
  SS BOND              : angle       2.49564 (    8)
  hydrogen bonds       : bond        0.03799 (  135)
  hydrogen bonds       : angle       6.23765 (  339)
  link_NAG-ASN         : bond        0.00130 (    1)
  link_NAG-ASN         : angle       0.81437 (    3)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
REVERT: B    5 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6947 (tmtt)
REVERT: B   45 LYS cc_start: 0.8447 (mmtp) cc_final: 0.8005 (mmmt)
REVERT: D  150 ARG cc_start: 0.9041 (mtt90) cc_final: 0.8593 (ttm110)
REVERT: H   30 THR cc_start: 0.7690 (p) cc_final: 0.7348 (m)
REVERT: H   82 MET cc_start: 0.7542 (ptm) cc_final: 0.7245 (ptm)
  outliers start: 19
  outliers final: 12
  residues processed: 101
  average time/residue: 0.0715
  time to fit residues: 9.3245
Evaluate side-chains
  97 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    3 THR
Chi-restraints excluded: chain B residue    5 LYS
Chi-restraints excluded: chain B residue   43 SER
Chi-restraints excluded: chain B residue   56 ASP
Chi-restraints excluded: chain B residue   58 ASP
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain C residue   32 TYR
Chi-restraints excluded: chain D residue   49 PHE
Chi-restraints excluded: chain D residue   58 TYR
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   60 ASN
Chi-restraints excluded: chain H residue  122 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0370
   chunk 50 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 47 optimal weight:    3.9990
   chunk 18 optimal weight:    0.1980
   chunk 25 optimal weight:    0.6980
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.4458

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

Flipped N/Q/H residues before XYZ refinement:
D 103 ASN
H  60 ASN
** L  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.141645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.126421 restraints weight = 8882.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.129589 restraints weight = 5739.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.131815 restraints weight = 4022.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.133450 restraints weight = 3002.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.134575 restraints weight = 2348.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6880
moved from start:          0.4439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4988  Z= 0.149
  Angle     :  0.756   9.233   6779  Z= 0.389
  Chirality :  0.049   0.178    740
  Planarity :  0.005   0.059    859
  Dihedral  :  5.514  24.130    688
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.55 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 21.87 %
    Favored  : 74.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -1.56 (0.32), residues: 608
  helix:  1.36 (0.65), residues: 58
  sheet: -0.14 (0.41), residues: 156
  loop : -1.91 (0.28), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D  11 
 TYR   0.020   0.002   TYR L  42 
 PHE   0.017   0.002   PHE L  93 
 TRP   0.035   0.002   TRP H  52 
 HIS   0.003   0.001   HIS B  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 4983)
  covalent geometry    : angle       0.75109 ( 6768)
  SS BOND              : bond        0.00481 (    4)
  SS BOND              : angle       2.51618 (    8)
  hydrogen bonds       : bond        0.03729 (  135)
  hydrogen bonds       : angle       6.22147 (  339)
  link_NAG-ASN         : bond        0.00124 (    1)
  link_NAG-ASN         : angle       0.80578 (    3)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
REVERT: B    5 LYS cc_start: 0.7240 (OUTLIER) cc_final: 0.6968 (tmtt)
REVERT: B   45 LYS cc_start: 0.8479 (mmtp) cc_final: 0.8034 (mmmt)
REVERT: D  119 LYS cc_start: 0.7863 (mmmt) cc_final: 0.7608 (tppt)
REVERT: D  150 ARG cc_start: 0.9036 (mtt90) cc_final: 0.8571 (ttm110)
REVERT: H   30 THR cc_start: 0.7626 (p) cc_final: 0.7267 (m)
REVERT: L   95 GLN cc_start: 0.6309 (mp-120) cc_final: 0.5650 (mp-120)
REVERT: L   97 HIS cc_start: 0.6554 (OUTLIER) cc_final: 0.5466 (t-90)
  outliers start: 18
  outliers final: 12
  residues processed: 93
  average time/residue: 0.0801
  time to fit residues: 9.5032
Evaluate side-chains
  96 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    3 THR
Chi-restraints excluded: chain B residue    5 LYS
Chi-restraints excluded: chain B residue   43 SER
Chi-restraints excluded: chain B residue   56 ASP
Chi-restraints excluded: chain B residue   58 ASP
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain C residue   32 TYR
Chi-restraints excluded: chain C residue   89 GLN
Chi-restraints excluded: chain D residue   58 TYR
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain L residue   45 LYS
Chi-restraints excluded: chain L residue   64 VAL
Chi-restraints excluded: chain L residue   97 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 50 optimal weight:    0.0870
   chunk 40 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 0 optimal weight:    0.5980
   chunk 55 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0030
   chunk 24 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.3968

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

Flipped N/Q/H residues before XYZ refinement:
D  53 HIS
** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  60 ASN
** L  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.142882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.127427 restraints weight = 8917.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.130678 restraints weight = 5660.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.133006 restraints weight = 3941.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.134583 restraints weight = 2912.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.135804 restraints weight = 2288.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.3896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6855
moved from start:          0.4590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4988  Z= 0.143
  Angle     :  0.758   9.310   6779  Z= 0.395
  Chirality :  0.049   0.191    740
  Planarity :  0.005   0.061    859
  Dihedral  :  5.448  23.521    688
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.22 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 23.36 %
    Favored  : 73.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -1.58 (0.32), residues: 608
  helix:  1.24 (0.63), residues: 59
  sheet:  0.00 (0.41), residues: 156
  loop : -2.00 (0.28), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG D  11 
 TYR   0.020   0.002   TYR L  42 
 PHE   0.017   0.002   PHE H  27 
 TRP   0.032   0.002   TRP H  52 
 HIS   0.004   0.001   HIS B  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 4983)
  covalent geometry    : angle       0.75417 ( 6768)
  SS BOND              : bond        0.00666 (    4)
  SS BOND              : angle       2.43263 (    8)
  hydrogen bonds       : bond        0.03853 (  135)
  hydrogen bonds       : angle       6.18611 (  339)
  link_NAG-ASN         : bond        0.00121 (    1)
  link_NAG-ASN         : angle       0.78602 (    3)

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

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

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1216 Ramachandran restraints generated.
    608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
REVERT: B    5 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.6941 (tmtt)
REVERT: B   45 LYS cc_start: 0.8437 (mmtp) cc_final: 0.7978 (mmmt)
REVERT: D   57 ASP cc_start: 0.5945 (m-30) cc_final: 0.5610 (p0)
REVERT: D  119 LYS cc_start: 0.7848 (mmmt) cc_final: 0.7610 (tppt)
REVERT: H   30 THR cc_start: 0.7635 (p) cc_final: 0.7255 (m)
REVERT: L   95 GLN cc_start: 0.6234 (mp-120) cc_final: 0.5685 (mp-120)
REVERT: L   97 HIS cc_start: 0.6564 (OUTLIER) cc_final: 0.5372 (t-90)
  outliers start: 16
  outliers final: 12
  residues processed: 92
  average time/residue: 0.0812
  time to fit residues: 9.6237
Evaluate side-chains
  95 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    3 THR
Chi-restraints excluded: chain B residue    5 LYS
Chi-restraints excluded: chain B residue   43 SER
Chi-restraints excluded: chain B residue   56 ASP
Chi-restraints excluded: chain B residue   58 ASP
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain C residue   32 TYR
Chi-restraints excluded: chain C residue   89 GLN
Chi-restraints excluded: chain D residue   49 PHE
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   60 ASN
Chi-restraints excluded: chain L residue   64 VAL
Chi-restraints excluded: chain L residue   97 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0270
   chunk 57 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.7240

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

Flipped N/Q/H residues before XYZ refinement:
H  60 ASN
L  35 GLN
** L  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.139741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.124649 restraints weight = 9112.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.127713 restraints weight = 5903.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.129877 restraints weight = 4163.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.131506 restraints weight = 3134.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.132456 restraints weight = 2460.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6943
moved from start:          0.4757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4988  Z= 0.177
  Angle     :  0.783   9.284   6779  Z= 0.409
  Chirality :  0.049   0.205    740
  Planarity :  0.005   0.062    859
  Dihedral  :  5.560  23.466    688
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 14.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.70 %
    Favored  : 90.30 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 23.18 %
    Favored  : 73.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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: -1.66 (0.32), residues: 608
  helix:  1.21 (0.66), residues: 59
  sheet: -0.07 (0.43), residues: 142
  loop : -1.98 (0.28), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG D  11 
 TYR   0.027   0.002   TYR H  59 
 PHE   0.015   0.002   PHE H  27 
 TRP   0.028   0.002   TRP H  52 
 HIS   0.005   0.001   HIS B  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 4983)
  covalent geometry    : angle       0.77745 ( 6768)
  SS BOND              : bond        0.00655 (    4)
  SS BOND              : angle       2.75848 (    8)
  hydrogen bonds       : bond        0.03932 (  135)
  hydrogen bonds       : angle       6.26280 (  339)
  link_NAG-ASN         : bond        0.00090 (    1)
  link_NAG-ASN         : angle       0.92317 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1019.47 seconds
wall clock time: 18 minutes 24.20 seconds (1104.20 seconds total)