Starting phenix.real_space_refine
on Fri Aug 22 15:20:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u1p_41822/08_2025/8u1p_41822.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u1p_41822/08_2025/8u1p_41822.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u1p_41822/08_2025/8u1p_41822.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u1p_41822/08_2025/8u1p_41822.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u1p_41822/08_2025/8u1p_41822.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u1p_41822/08_2025/8u1p_41822.cif"
  }
  resolution = 3.3
  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=   0.005 sd=   0.205
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      26      5.16       5
     C    3110      2.51       5
     N     807      2.21       5
     O     911      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4854
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1639
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1639
          Classifications: {'peptide': 212}
          Incomplete info: {'truncation_to_alanine': 36}
          Link IDs: {'PTRANS': 10, 'TRANS': 201}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 128
          Unresolved non-hydrogen angles: 153
          Unresolved non-hydrogen dihedrals: 114
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'PHE:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 4, 'GLU:plan': 4, 'HIS:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 70
    Chain: "H"
      Number of atoms: 812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 812
          Classifications: {'peptide': 121}
          Incomplete info: {'truncation_to_alanine': 46}
          Link IDs: {'PTRANS': 3, 'TRANS': 117}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 136
          Unresolved non-hydrogen angles: 172
          Unresolved non-hydrogen dihedrals: 104
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 5, 'TYR:plan': 1, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 72
    Chain: "L"
      Number of atoms: 749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 749
          Classifications: {'peptide': 106}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 7, 'TRANS': 98}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 64
          Unresolved non-hydrogen angles: 79
          Unresolved non-hydrogen dihedrals: 55
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 46
    Chain: "C"
      Number of atoms: 733
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 733
          Classifications: {'peptide': 105}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 6, 'TRANS': 98}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 73
          Unresolved non-hydrogen angles: 92
          Unresolved non-hydrogen dihedrals: 55
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'ARG:plan': 2, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 40
    Chain: "B"
      Number of atoms: 851
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 851
          Classifications: {'peptide': 121}
          Incomplete info: {'truncation_to_alanine': 33}
          Link IDs: {'PTRANS': 5, 'TRANS': 115}
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 100
          Unresolved non-hydrogen angles: 123
          Unresolved non-hydrogen dihedrals: 80
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 4, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 49
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      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: 1.13, per 1000 atoms: 0.23
  Number of scatterers: 4854
  At special positions: 0
  Unit cell: (63.86, 75.19, 148.32, 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      26     16.00
     O     911      8.00
     N     807      7.00
     C    3110      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 102 " - pdb=" SG  CYS A 156 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 234 " - pdb=" SG  CYS A 273 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  97 " - pdb=" SG  CYS B 100B" distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
    NAG-ASN
      " NAG A 501 " - " ASN A 131 "
      " NAG D   1 " - " ASN A 190 "
      " NAG E   1 " - " ASN A 204 "
  Time building additional restraints: 0.28
  Conformation dependent library (CDL) restraints added in 180.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1230

  Finding SS restraints...
    Secondary structure from input PDB file:
      2 helices and 17 sheets defined
      1.2% alpha, 35.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 119 through 121
      No H-bonds generated for 'chain 'A' and resid 119 through 121'
    Processing helix  chain 'H' and resid 83 through 87
      removed outlier: 4.100A  pdb=" N   THR H  87 " --> pdb=" O   SER H  84 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 49
      removed outlier: 6.876A  pdb=" N   CYS A  49 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   ILE A 142 " --> pdb=" O   ILE A  82 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   LEU A  84 " --> pdb=" O   ARG A 140 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ARG A 140 " --> pdb=" O   LEU A  84 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   GLU A 139 " --> pdb=" O   ASN A 131 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   GLU A 127 " --> pdb=" O   THR A 143 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 75
      removed outlier: 3.841A  pdb=" N   SER A  75 " --> pdb=" O   ARG A 178 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ILE A 152 " --> pdb=" O   VAL A 179 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 107
    Processing sheet with id=AA4, first strand: chain 'A' and resid 186 through 189
    Processing sheet with id=AA5, first strand: chain 'A' and resid 212 through 216
      removed outlier: 6.546A  pdb=" N   LEU A 213 " --> pdb=" O   VAL A 285 " (cutoff:3.500A)
      removed outlier: 7.929A  pdb=" N   LYS A 287 " --> pdb=" O   LEU A 213 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   VAL A 215 " --> pdb=" O   LYS A 287 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ILE A 284 " --> pdb=" O   CYS A 273 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   CYS A 273 " --> pdb=" O   ILE A 284 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 276 through 277
    Processing sheet with id=AA7, first strand: chain 'H' and resid 4 through 6
      removed outlier: 3.895A  pdb=" N   VAL H   5 " --> pdb=" O   ARG H  23 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ARG H  23 " --> pdb=" O   VAL H   5 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 11
      removed outlier: 3.691A  pdb=" N   ALA H  88 " --> pdb=" O   VAL H 109 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   MET H  34 " --> pdb=" O   SER H  50 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   SER H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   TRP H  36 " --> pdb=" O   MET H  48 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   SER H  58 " --> pdb=" O   SER H  50 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 11
      removed outlier: 3.691A  pdb=" N   ALA H  88 " --> pdb=" O   VAL H 109 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   VAL H 102 " --> pdb=" O   ARG H  94 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 9 through 11
      removed outlier: 3.566A  pdb=" N   THR L 105 " --> pdb=" O   VAL L  10 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ALA L  83 " --> pdb=" O   VAL L 104 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   TRP L  34 " --> pdb=" O   VAL L  46 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 9 through 11
      removed outlier: 3.566A  pdb=" N   THR L 105 " --> pdb=" O   VAL L  10 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ALA L  83 " --> pdb=" O   VAL L 104 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 18 through 23
      removed outlier: 3.522A  pdb=" N   ALA L  18 " --> pdb=" O   ILE L  74 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ILE L  20 " --> pdb=" O   LEU L  72 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 12
      removed outlier: 7.138A  pdb=" N   LEU C  11 " --> pdb=" O   GLU C 105 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54
      removed outlier: 6.662A  pdb=" N   TRP C  35 " --> pdb=" O   LEU C  47 " (cutoff:3.500A)
      removed outlier: 5.432A  pdb=" N   LYS C  49 " --> pdb=" O   LEU C  33 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   LEU C  33 " --> pdb=" O   LYS C  49 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ASN C  34 " --> pdb=" O   GLN C  89 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 62 through 67
      removed outlier: 3.981A  pdb=" N   ASP C  70 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 3 through 6
      removed outlier: 3.507A  pdb=" N   THR B  77 " --> pdb=" O   ASP B  72 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 57 through 59
      removed outlier: 6.838A  pdb=" N   TRP B  36 " --> pdb=" O   MET B  48 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   TRP B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   MET B  34 " --> pdb=" O   TRP B  50 " (cutoff:3.500A)

    136 hydrogen bonds defined for protein.
    351 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: 0.60

  Time building geometry restraints manager: 0.39 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 819
        1.32 -     1.45: 1422
        1.45 -     1.57: 2688
        1.57 -     1.70: 1
        1.70 -     1.82: 38
  Bond restraints: 4968
  Sorted by residual:
  bond pdb=" C   VAL A 224 "
       pdb=" N   LEU A 225 "
    ideal  model  delta    sigma   weight residual
    1.331  1.241  0.090 1.34e-02 5.57e+03 4.48e+01
  bond pdb=" C   LEU A 225 "
       pdb=" N   ALA A 226 "
    ideal  model  delta    sigma   weight residual
    1.331  1.246  0.084 1.48e-02 4.57e+03 3.26e+01
  bond pdb=" CA  ASN A 190 "
       pdb=" CB  ASN A 190 "
    ideal  model  delta    sigma   weight residual
    1.526  1.592 -0.066 1.76e-02 3.23e+03 1.42e+01
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.473 -0.067 2.00e-02 2.50e+03 1.13e+01
  bond pdb=" C   LEU A  98 "
       pdb=" N   PRO A  99 "
    ideal  model  delta    sigma   weight residual
    1.335  1.360 -0.025 8.70e-03 1.32e+04 8.26e+00
  ... (remaining 4963 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.64: 6621
        2.64 -     5.28: 130
        5.28 -     7.92: 29
        7.92 -    10.55: 4
       10.55 -    13.19: 3
  Bond angle restraints: 6787
  Sorted by residual:
  angle pdb=" N   THR A 202 "
        pdb=" CA  THR A 202 "
        pdb=" C   THR A 202 "
      ideal   model   delta    sigma   weight residual
     108.34  120.69  -12.35 1.31e+00 5.83e-01 8.89e+01
  angle pdb=" C   ILE L  52 "
        pdb=" N   ARG L  53 "
        pdb=" CA  ARG L  53 "
      ideal   model   delta    sigma   weight residual
     120.94  134.13  -13.19 1.90e+00 2.77e-01 4.82e+01
  angle pdb=" C   ASN A 204 "
        pdb=" CA  ASN A 204 "
        pdb=" CB  ASN A 204 "
      ideal   model   delta    sigma   weight residual
     115.79  108.73    7.06 1.19e+00 7.06e-01 3.52e+01
  angle pdb=" C   TYR A 198 "
        pdb=" N   LEU A 199 "
        pdb=" CA  LEU A 199 "
      ideal   model   delta    sigma   weight residual
     123.30  114.96    8.34 1.44e+00 4.82e-01 3.36e+01
  angle pdb=" C   TYR L  49 "
        pdb=" N   ASP L  50 "
        pdb=" CA  ASP L  50 "
      ideal   model   delta    sigma   weight residual
     121.54  131.89  -10.35 1.91e+00 2.74e-01 2.94e+01
  ... (remaining 6782 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.45: 2752
       16.45 -    32.90: 154
       32.90 -    49.34: 31
       49.34 -    65.79: 7
       65.79 -    82.24: 5
  Dihedral angle restraints: 2949
    sinusoidal: 1018
      harmonic: 1931
  Sorted by residual:
  dihedral pdb=" CB  CYS B  97 "
           pdb=" SG  CYS B  97 "
           pdb=" SG  CYS B 100B"
           pdb=" CB  CYS B 100B"
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  167.94  -74.94     1      1.00e+01 1.00e-02 7.11e+01
  dihedral pdb=" CB  CYS C  23 "
           pdb=" SG  CYS C  23 "
           pdb=" SG  CYS C  88 "
           pdb=" CB  CYS C  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  151.90  -58.90     1      1.00e+01 1.00e-02 4.64e+01
  dihedral pdb=" CA  LYS A 201 "
           pdb=" C   LYS A 201 "
           pdb=" N   THR A 202 "
           pdb=" CA  THR A 202 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.23  -20.77     0      5.00e+00 4.00e-02 1.73e+01
  ... (remaining 2946 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.362: 780
       0.362 -    0.724: 1
       0.724 -    1.085: 0
       1.085 -    1.447: 0
       1.447 -    1.809: 1
  Chirality restraints: 782
  Sorted by residual:
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN A 204 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.59   -1.81 2.00e-01 2.50e+01 8.18e+01
  chirality pdb=" CB  ILE L  74 "
            pdb=" CA  ILE L  74 "
            pdb=" CG1 ILE L  74 "
            pdb=" CG2 ILE L  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.17    0.47 2.00e-01 2.50e+01 5.55e+00
  chirality pdb=" C1  NAG A 501 "
            pdb=" ND2 ASN A 131 "
            pdb=" C2  NAG A 501 "
            pdb=" O5  NAG A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.06   -0.34 2.00e-01 2.50e+01 2.92e+00
  ... (remaining 779 not shown)

  Planarity restraints: 868
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 204 "    0.014 2.00e-02 2.50e+03   5.89e-02 4.34e+01
        pdb=" CG  ASN A 204 "   -0.074 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 204 "    0.068 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 204 "   -0.064 2.00e-02 2.50e+03
        pdb=" C1  NAG E   1 "    0.056 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR L  49 "   -0.044 2.00e-02 2.50e+03   2.87e-02 1.64e+01
        pdb=" CG  TYR L  49 "    0.066 2.00e-02 2.50e+03
        pdb=" CD1 TYR L  49 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR L  49 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR L  49 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR L  49 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR L  49 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR L  49 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 204 "    0.018 2.00e-02 2.50e+03   3.55e-02 1.26e+01
        pdb=" CG  ASN A 204 "   -0.061 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 204 "    0.023 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 204 "    0.020 2.00e-02 2.50e+03
  ... (remaining 865 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1028
        2.79 -     3.32: 4197
        3.32 -     3.85: 7622
        3.85 -     4.37: 8658
        4.37 -     4.90: 15463
  Nonbonded interactions: 36968
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 182 "
            pdb=" O   GLY A 220 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" OG  SER H  98 "
            pdb=" O   ALA H 100 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" NH2 ARG L  53 "
            pdb=" O   GLU L  59 "
     model   vdw
     2.314 3.120
  nonbonded pdb=" OE2 GLU B  46 "
            pdb=" NH1 ARG B  62 "
     model   vdw
     2.354 3.120
  nonbonded pdb=" O   SER C  50 "
            pdb=" OG  SER C  50 "
     model   vdw
     2.360 3.040
  ... (remaining 36963 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
Found NCS groups:
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     5.300
  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:1.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.090   4980  Z= 0.268
  Angle     :  1.098  20.826   6816  Z= 0.561
  Chirality :  0.088   1.809    782
  Planarity :  0.007   0.077    865
  Dihedral  : 11.479  82.240   1698
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.82 (0.33), residues: 651
  helix: -5.79 (0.11), residues: 6
  sheet:  0.55 (0.36), residues: 213
  loop : -1.10 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.002   ARG B  62 
 TYR   0.066   0.002   TYR L  49 
 PHE   0.033   0.003   PHE A 235 
 TRP   0.016   0.002   TRP B 103 
 HIS   0.005   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 4968)
  covalent geometry    : angle       0.95254 ( 6787)
  SS BOND              : bond        0.00329 (    7)
  SS BOND              : angle       1.10878 (   14)
  hydrogen bonds       : bond        0.29259 (  129)
  hydrogen bonds       : angle      11.23736 (  351)
  link_BETA1-4         : bond        0.01629 (    2)
  link_BETA1-4         : angle       6.49458 (    6)
  link_NAG-ASN         : bond        0.04042 (    3)
  link_NAG-ASN         : angle      14.07829 (    9)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 ILE cc_start: 0.8955 (mp) cc_final: 0.8686 (mt)
REVERT: L   41 GLN cc_start: 0.7919 (mp10) cc_final: 0.7649 (mp10)
REVERT: L   61 PHE cc_start: 0.7535 (m-80) cc_final: 0.7001 (m-80)
REVERT: C   35 TRP cc_start: 0.6972 (m100) cc_final: 0.6264 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.0746
  time to fit residues: 11.1578
Evaluate side-chains
  92 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.1980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 64 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 281 ASN
** L  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  34 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.092261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.086154 restraints weight = 15406.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 2.63
r_work: 0.3509 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.2422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   4980  Z= 0.222
  Angle     :  0.852  15.959   6816  Z= 0.419
  Chirality :  0.057   0.691    782
  Planarity :  0.006   0.059    865
  Dihedral  :  6.926  49.928    822
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  :  9.67 %
    Favored  : 86.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.75 (0.32), residues: 651
  helix: -5.78 (0.11), residues: 6
  sheet:  0.74 (0.33), residues: 219
  loop : -1.16 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  18 
 TYR   0.033   0.002   TYR L  49 
 PHE   0.028   0.003   PHE A 235 
 TRP   0.018   0.003   TRP B  47 
 HIS   0.006   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 ( 4968)
  covalent geometry    : angle       0.75838 ( 6787)
  SS BOND              : bond        0.01206 (    7)
  SS BOND              : angle       1.53961 (   14)
  hydrogen bonds       : bond        0.04654 (  129)
  hydrogen bonds       : angle       7.76271 (  351)
  link_BETA1-4         : bond        0.00635 (    2)
  link_BETA1-4         : angle       4.70375 (    6)
  link_NAG-ASN         : bond        0.02016 (    3)
  link_NAG-ASN         : angle       9.90398 (    9)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
REVERT: L   60 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.7172 (ptp90)
REVERT: C   35 TRP cc_start: 0.7794 (m100) cc_final: 0.6666 (m100)
REVERT: C   78 LEU cc_start: 0.7811 (tp) cc_final: 0.7593 (tp)
REVERT: B   34 MET cc_start: 0.7381 (mmm) cc_final: 0.6551 (mmm)
  outliers start: 15
  outliers final: 9
  residues processed: 103
  average time/residue: 0.0617
  time to fit residues: 8.1698
Evaluate side-chains
  101 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 TYR
Chi-restraints excluded: chain A residue  266 SER
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain L residue   17 THR
Chi-restraints excluded: chain L residue   44 VAL
Chi-restraints excluded: chain L residue   60 ARG
Chi-restraints excluded: chain L residue   74 ILE
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   83 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 62 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 55 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 4 optimal weight:    0.7980
   chunk 11 optimal weight:    0.4980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
L  36 GLN
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  34 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.087302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.081424 restraints weight = 15503.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 2.54
r_work: 0.3412 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3311 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.3457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   4980  Z= 0.228
  Angle     :  0.812  14.443   6816  Z= 0.403
  Chirality :  0.056   0.610    782
  Planarity :  0.006   0.057    865
  Dihedral  :  7.157  51.849    822
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 16.04 %
    Favored  : 79.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.91 (0.33), residues: 651
  helix: -5.78 (0.12), residues: 6
  sheet:  0.57 (0.33), residues: 222
  loop : -1.25 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  93 
 TYR   0.026   0.002   TYR L  49 
 PHE   0.019   0.003   PHE A 235 
 TRP   0.025   0.003   TRP B  47 
 HIS   0.005   0.002   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 ( 4968)
  covalent geometry    : angle       0.73191 ( 6787)
  SS BOND              : bond        0.00693 (    7)
  SS BOND              : angle       1.42695 (   14)
  hydrogen bonds       : bond        0.04215 (  129)
  hydrogen bonds       : angle       7.02525 (  351)
  link_BETA1-4         : bond        0.00317 (    2)
  link_BETA1-4         : angle       4.53502 (    6)
  link_NAG-ASN         : bond        0.01888 (    3)
  link_NAG-ASN         : angle       8.88123 (    9)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
REVERT: C   35 TRP cc_start: 0.8153 (m100) cc_final: 0.6700 (m100)
  outliers start: 19
  outliers final: 13
  residues processed: 105
  average time/residue: 0.0621
  time to fit residues: 8.2418
Evaluate side-chains
  103 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  198 TYR
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  266 SER
Chi-restraints excluded: chain L residue    2 TYR
Chi-restraints excluded: chain L residue   17 THR
Chi-restraints excluded: chain L residue   26 ASP
Chi-restraints excluded: chain L residue   74 ILE
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   83 PHE
Chi-restraints excluded: chain B residue   92 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0970
   chunk 0 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 22 optimal weight:   10.0000
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.7382

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.085172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.079191 restraints weight = 15558.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3433 rms_B_bonded: 2.55
r_work: 0.3356 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3254 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.4182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   4980  Z= 0.236
  Angle     :  0.815  14.091   6816  Z= 0.403
  Chirality :  0.056   0.574    782
  Planarity :  0.006   0.061    865
  Dihedral  :  7.527  56.861    822
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 13.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  5.42 %
    Allowed  : 16.98 %
    Favored  : 77.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.07 (0.33), residues: 651
  helix: -5.79 (0.11), residues: 6
  sheet:  0.52 (0.34), residues: 224
  loop : -1.41 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  53 
 TYR   0.023   0.002   TYR L  49 
 PHE   0.018   0.002   PHE B  63 
 TRP   0.019   0.003   TRP B  47 
 HIS   0.005   0.002   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 ( 4968)
  covalent geometry    : angle       0.74502 ( 6787)
  SS BOND              : bond        0.00567 (    7)
  SS BOND              : angle       1.43461 (   14)
  hydrogen bonds       : bond        0.03623 (  129)
  hydrogen bonds       : angle       6.85274 (  351)
  link_BETA1-4         : bond        0.00369 (    2)
  link_BETA1-4         : angle       4.50262 (    6)
  link_NAG-ASN         : bond        0.01702 (    3)
  link_NAG-ASN         : angle       8.26085 (    9)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 92
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
REVERT: A  268 ASP cc_start: 0.8315 (t0) cc_final: 0.7979 (t0)
REVERT: A  270 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8692 (t0)
REVERT: L   60 ARG cc_start: 0.7916 (ptp90) cc_final: 0.7649 (ptp90)
  outliers start: 23
  outliers final: 15
  residues processed: 101
  average time/residue: 0.0763
  time to fit residues: 9.6722
Evaluate side-chains
  103 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  156 CYS
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  198 TYR
Chi-restraints excluded: chain A residue  266 SER
Chi-restraints excluded: chain A residue  270 ASN
Chi-restraints excluded: chain H residue   20 VAL
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain L residue    2 TYR
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain L residue   17 THR
Chi-restraints excluded: chain L residue   26 ASP
Chi-restraints excluded: chain L residue   74 ILE
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   83 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0170
   chunk 52 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.6018

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.085062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.078966 restraints weight = 15881.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 2.59
r_work: 0.3352 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.4442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   4980  Z= 0.204
  Angle     :  0.760  13.470   6816  Z= 0.378
  Chirality :  0.054   0.549    782
  Planarity :  0.005   0.063    865
  Dihedral  :  7.560  58.345    822
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 18.40 %
    Favored  : 76.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.16 (0.33), residues: 651
  helix: -5.79 (0.11), residues: 6
  sheet:  0.36 (0.34), residues: 222
  loop : -1.40 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  93 
 TYR   0.021   0.002   TYR H  33 
 PHE   0.019   0.002   PHE B  63 
 TRP   0.020   0.003   TRP B  47 
 HIS   0.003   0.001   HIS A 184 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 4968)
  covalent geometry    : angle       0.69390 ( 6787)
  SS BOND              : bond        0.00581 (    7)
  SS BOND              : angle       1.22450 (   14)
  hydrogen bonds       : bond        0.03349 (  129)
  hydrogen bonds       : angle       6.65386 (  351)
  link_BETA1-4         : bond        0.00468 (    2)
  link_BETA1-4         : angle       4.18047 (    6)
  link_NAG-ASN         : bond        0.01676 (    3)
  link_NAG-ASN         : angle       7.80080 (    9)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
REVERT: A  268 ASP cc_start: 0.8069 (t0) cc_final: 0.7754 (t0)
REVERT: L   49 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.7428 (t80)
REVERT: C   93 ARG cc_start: 0.6173 (mtm180) cc_final: 0.5909 (mtm-85)
  outliers start: 21
  outliers final: 15
  residues processed: 98
  average time/residue: 0.0663
  time to fit residues: 8.1123
Evaluate side-chains
  98 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  156 CYS
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  266 SER
Chi-restraints excluded: chain H residue   20 VAL
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain L residue    2 TYR
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain L residue   17 THR
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   26 ASP
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain L residue   74 ILE
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   83 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 55 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 41 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.082709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.076617 restraints weight = 16025.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 2.59
r_work: 0.3311 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.4813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   4980  Z= 0.234
  Angle     :  0.793  13.259   6816  Z= 0.395
  Chirality :  0.055   0.551    782
  Planarity :  0.006   0.061    865
  Dihedral  :  7.778  59.136    822
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.14 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  5.42 %
    Allowed  : 19.81 %
    Favored  : 74.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.29 (0.33), residues: 651
  helix: -5.78 (0.11), residues: 6
  sheet:  0.39 (0.34), residues: 217
  loop : -1.55 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  93 
 TYR   0.021   0.002   TYR A 198 
 PHE   0.017   0.002   PHE L  98 
 TRP   0.018   0.003   TRP B  47 
 HIS   0.004   0.002   HIS B  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00525 ( 4968)
  covalent geometry    : angle       0.73334 ( 6787)
  SS BOND              : bond        0.00685 (    7)
  SS BOND              : angle       1.31848 (   14)
  hydrogen bonds       : bond        0.03271 (  129)
  hydrogen bonds       : angle       6.73807 (  351)
  link_BETA1-4         : bond        0.00543 (    2)
  link_BETA1-4         : angle       4.14812 (    6)
  link_NAG-ASN         : bond        0.01539 (    3)
  link_NAG-ASN         : angle       7.48668 (    9)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   71 MET cc_start: 0.6751 (ptt) cc_final: 0.6373 (ptp)
REVERT: L   49 TYR cc_start: 0.8874 (OUTLIER) cc_final: 0.7673 (t80)
  outliers start: 23
  outliers final: 16
  residues processed: 105
  average time/residue: 0.0800
  time to fit residues: 10.3115
Evaluate side-chains
  104 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  156 CYS
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  266 SER
Chi-restraints excluded: chain H residue   20 VAL
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain L residue    2 TYR
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain L residue   17 THR
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain L residue  105 THR
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   83 PHE
Chi-restraints excluded: chain B residue  100 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 52 optimal weight:    0.0010
   chunk 29 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   chunk 1 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.5386

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

Flipped N/Q/H residues before XYZ refinement:
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  34 ASN ** 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 = 0.3494 r_free = 0.3494 target = 0.076032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.070307 restraints weight = 16046.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 2.53
r_work: 0.3326 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.4968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   4980  Z= 0.190
  Angle     :  0.762  12.849   6816  Z= 0.380
  Chirality :  0.054   0.532    782
  Planarity :  0.006   0.064    865
  Dihedral  :  7.670  59.556    822
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 21.70 %
    Favored  : 73.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.23 (0.33), residues: 651
  helix: -5.79 (0.11), residues: 6
  sheet:  0.49 (0.34), residues: 219
  loop : -1.56 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  93 
 TYR   0.021   0.002   TYR A 198 
 PHE   0.012   0.002   PHE L  98 
 TRP   0.020   0.003   TRP B  50 
 HIS   0.003   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 4968)
  covalent geometry    : angle       0.70306 ( 6787)
  SS BOND              : bond        0.00465 (    7)
  SS BOND              : angle       1.38384 (   14)
  hydrogen bonds       : bond        0.03283 (  129)
  hydrogen bonds       : angle       6.53493 (  351)
  link_BETA1-4         : bond        0.00380 (    2)
  link_BETA1-4         : angle       4.04575 (    6)
  link_NAG-ASN         : bond        0.01520 (    3)
  link_NAG-ASN         : angle       7.25941 (    9)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8490 (t)
REVERT: H   71 MET cc_start: 0.6845 (ptt) cc_final: 0.6433 (ptp)
REVERT: H  100 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7877 (p90)
REVERT: L   49 TYR cc_start: 0.8935 (OUTLIER) cc_final: 0.7779 (t80)
REVERT: L   81 ASP cc_start: 0.8078 (t0) cc_final: 0.7654 (t0)
REVERT: B   69 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.6181 (mtm)
  outliers start: 22
  outliers final: 13
  residues processed: 104
  average time/residue: 0.0821
  time to fit residues: 10.5568
Evaluate side-chains
  106 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  156 CYS
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain A residue  266 SER
Chi-restraints excluded: chain H residue   20 VAL
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain H residue  100 TYR
Chi-restraints excluded: chain L residue    2 TYR
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain L residue   17 THR
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   52 SER
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   83 PHE
Chi-restraints excluded: chain B residue   69 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 35 optimal weight:    0.0050
   chunk 63 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0000
   chunk 24 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0670
   chunk 51 optimal weight:    0.6980
   chunk 30 optimal weight:    0.5980
   chunk 16 optimal weight:    0.1980
   chunk 22 optimal weight:    9.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.1736

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

Flipped N/Q/H residues before XYZ refinement:
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  34 ASN ** 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 = 0.3547 r_free = 0.3547 target = 0.078664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.072816 restraints weight = 16292.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 2.58
r_work: 0.3385 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.4915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4980  Z= 0.124
  Angle     :  0.716  12.088   6816  Z= 0.354
  Chirality :  0.052   0.507    782
  Planarity :  0.005   0.058    865
  Dihedral  :  7.276  56.493    822
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 23.58 %
    Favored  : 73.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.14 (0.33), residues: 651
  helix: -5.78 (0.11), residues: 6
  sheet:  0.49 (0.34), residues: 220
  loop : -1.45 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  93 
 TYR   0.017   0.001   TYR H  33 
 PHE   0.014   0.002   PHE A 235 
 TRP   0.020   0.002   TRP B  50 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 4968)
  covalent geometry    : angle       0.66186 ( 6787)
  SS BOND              : bond        0.00268 (    7)
  SS BOND              : angle       1.13009 (   14)
  hydrogen bonds       : bond        0.03099 (  129)
  hydrogen bonds       : angle       6.16272 (  351)
  link_BETA1-4         : bond        0.00592 (    2)
  link_BETA1-4         : angle       3.74556 (    6)
  link_NAG-ASN         : bond        0.01427 (    3)
  link_NAG-ASN         : angle       6.81807 (    9)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  235 PHE cc_start: 0.7007 (m-10) cc_final: 0.6792 (m-10)
REVERT: H   71 MET cc_start: 0.6657 (ptt) cc_final: 0.6339 (ptp)
REVERT: H  100 TYR cc_start: 0.8129 (OUTLIER) cc_final: 0.7538 (p90)
REVERT: L   49 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.7540 (t80)
REVERT: L   60 ARG cc_start: 0.7427 (ptp90) cc_final: 0.7215 (ptp90)
REVERT: L   81 ASP cc_start: 0.7880 (t0) cc_final: 0.7408 (t0)
REVERT: C   24 ARG cc_start: 0.8687 (mtp-110) cc_final: 0.8469 (ttm110)
  outliers start: 14
  outliers final: 10
  residues processed: 102
  average time/residue: 0.0770
  time to fit residues: 9.7479
Evaluate side-chains
  101 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  156 CYS
Chi-restraints excluded: chain H residue   20 VAL
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain H residue  100 TYR
Chi-restraints excluded: chain L residue    2 TYR
Chi-restraints excluded: chain L residue   17 THR
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   26 ASP
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   83 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 51 optimal weight:    0.4980
   chunk 30 optimal weight:    0.7980
   chunk 50 optimal weight:    0.7980
   chunk 6 optimal weight:    0.5980
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
L  88 GLN
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.075869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.070201 restraints weight = 16195.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 2.46
r_work: 0.3324 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.5188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   4980  Z= 0.219
  Angle     :  0.780  12.588   6816  Z= 0.390
  Chirality :  0.054   0.539    782
  Planarity :  0.006   0.062    865
  Dihedral  :  7.529  59.589    822
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 14.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.14 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 23.58 %
    Favored  : 72.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.14 (0.33), residues: 651
  helix: -5.79 (0.11), residues: 6
  sheet:  0.64 (0.34), residues: 217
  loop : -1.54 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  60 
 TYR   0.021   0.002   TYR L  49 
 PHE   0.016   0.002   PHE L  98 
 TRP   0.020   0.003   TRP B  47 
 HIS   0.004   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 ( 4968)
  covalent geometry    : angle       0.72681 ( 6787)
  SS BOND              : bond        0.00526 (    7)
  SS BOND              : angle       1.33985 (   14)
  hydrogen bonds       : bond        0.03177 (  129)
  hydrogen bonds       : angle       6.45134 (  351)
  link_BETA1-4         : bond        0.00415 (    2)
  link_BETA1-4         : angle       4.02796 (    6)
  link_NAG-ASN         : bond        0.01381 (    3)
  link_NAG-ASN         : angle       6.94330 (    9)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 PHE cc_start: 0.7399 (m-10) cc_final: 0.7144 (m-10)
REVERT: H   71 MET cc_start: 0.6939 (ptt) cc_final: 0.6558 (ptp)
REVERT: H  100 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.7892 (p90)
REVERT: L   49 TYR cc_start: 0.8898 (OUTLIER) cc_final: 0.7885 (t80)
REVERT: L   60 ARG cc_start: 0.7712 (ptp90) cc_final: 0.7510 (ptp90)
  outliers start: 16
  outliers final: 11
  residues processed: 101
  average time/residue: 0.0812
  time to fit residues: 10.0605
Evaluate side-chains
  102 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  156 CYS
Chi-restraints excluded: chain H residue   20 VAL
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain H residue  100 TYR
Chi-restraints excluded: chain L residue    2 TYR
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain L residue   17 THR
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain L residue  105 THR
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   83 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 51 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0970
   chunk 38 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   chunk 46 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  27 GLN
** C  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.076112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.070450 restraints weight = 16530.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 2.49
r_work: 0.3334 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3235 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.5308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   4980  Z= 0.188
  Angle     :  0.768  12.334   6816  Z= 0.382
  Chirality :  0.054   0.525    782
  Planarity :  0.005   0.060    865
  Dihedral  :  7.532  59.733    822
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 15.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.83 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 24.29 %
    Favored  : 71.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.22 (0.33), residues: 651
  helix: -5.79 (0.11), residues: 6
  sheet:  0.48 (0.34), residues: 217
  loop : -1.53 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  60 
 TYR   0.017   0.002   TYR H  33 
 PHE   0.013   0.002   PHE L  98 
 TRP   0.019   0.003   TRP B  47 
 HIS   0.005   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 4968)
  covalent geometry    : angle       0.71582 ( 6787)
  SS BOND              : bond        0.00524 (    7)
  SS BOND              : angle       1.34669 (   14)
  hydrogen bonds       : bond        0.03091 (  129)
  hydrogen bonds       : angle       6.42095 (  351)
  link_BETA1-4         : bond        0.00482 (    2)
  link_BETA1-4         : angle       3.91964 (    6)
  link_NAG-ASN         : bond        0.01351 (    3)
  link_NAG-ASN         : angle       6.84277 (    9)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 PHE cc_start: 0.7386 (m-10) cc_final: 0.7124 (m-10)
REVERT: H   71 MET cc_start: 0.6949 (ptt) cc_final: 0.6548 (ptp)
REVERT: H  100 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7748 (p90)
REVERT: L   49 TYR cc_start: 0.8895 (OUTLIER) cc_final: 0.7819 (t80)
  outliers start: 18
  outliers final: 12
  residues processed: 102
  average time/residue: 0.0733
  time to fit residues: 9.2403
Evaluate side-chains
  102 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  156 CYS
Chi-restraints excluded: chain H residue   20 VAL
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain H residue  100 TYR
Chi-restraints excluded: chain L residue    2 TYR
Chi-restraints excluded: chain L residue   17 THR
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   26 ASP
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain L residue  105 THR
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   83 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 7 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 2 optimal weight:    0.1980
   chunk 39 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
C   6 GLN
C  27 GLN
** C  34 ASN ** 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 = 0.3491 r_free = 0.3491 target = 0.075983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.070345 restraints weight = 16588.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.3400 rms_B_bonded: 2.48
r_work: 0.3330 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3232 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.5419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   4980  Z= 0.203
  Angle     :  0.776  12.204   6816  Z= 0.387
  Chirality :  0.054   0.523    782
  Planarity :  0.005   0.071    865
  Dihedral  :  7.602  59.159    822
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 15.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.14 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 24.76 %
    Favored  : 71.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.28 (0.33), residues: 651
  helix: -5.79 (0.11), residues: 6
  sheet:  0.38 (0.35), residues: 212
  loop : -1.51 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  24 
 TYR   0.018   0.002   TYR H  33 
 PHE   0.014   0.002   PHE L  98 
 TRP   0.020   0.003   TRP B  47 
 HIS   0.005   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 ( 4968)
  covalent geometry    : angle       0.72534 ( 6787)
  SS BOND              : bond        0.00559 (    7)
  SS BOND              : angle       1.25550 (   14)
  hydrogen bonds       : bond        0.03140 (  129)
  hydrogen bonds       : angle       6.41199 (  351)
  link_BETA1-4         : bond        0.00533 (    2)
  link_BETA1-4         : angle       3.93698 (    6)
  link_NAG-ASN         : bond        0.01324 (    3)
  link_NAG-ASN         : angle       6.78011 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1151.59 seconds
wall clock time: 20 minutes 24.24 seconds (1224.24 seconds total)