Starting phenix.real_space_refine
on Tue Mar  3 16:15:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zyi_15024/03_2026/7zyi_15024.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zyi_15024/03_2026/7zyi_15024.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zyi_15024/03_2026/7zyi_15024.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zyi_15024/03_2026/7zyi_15024.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zyi_15024/03_2026/7zyi_15024.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zyi_15024/03_2026/7zyi_15024.map"
  }
  resolution = 2.88
  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=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     Na      2      4.78       5
     C    4286      2.51       5
     N    1075      2.21       5
     O    1232      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6641
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2248
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2248
          Classifications: {'peptide': 293}
          Link IDs: {'PTRANS': 14, 'TRANS': 278}
    Chain: "H"
      Number of atoms: 1714
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1714
          Classifications: {'peptide': 227}
          Link IDs: {'PTRANS': 11, 'TRANS': 215}
    Chain: "L"
      Number of atoms: 1626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1626
          Classifications: {'peptide': 212}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 200}
    Chain: "K"
      Number of atoms: 930
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 120, 922
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
      Conformer: "B"
        Number of residues, atoms: 120, 922
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
          bond proxies already assigned to first conformer: 931
    Chain: "A"
      Number of atoms: 123
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 123
          Unusual residues: {' NA': 2, 'CHO': 2, 'CLR': 2}
          Classifications: {'undetermined': 6, 'water': 1}
          Link IDs: {None: 6}
  Time building chain proxies: 1.61, per 1000 atoms: 0.24
  Number of scatterers: 6641
  At special positions: 0
  Unit cell: (118.8, 116.82, 89.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      46     16.00
     Na      2     11.00
     O    1232      8.00
     N    1075      7.00
     C    4286      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 140 " - pdb=" SG  CYS H 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.69
  Conformation dependent library (CDL) restraints added in 243.3 milliseconds
  

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1572

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 15 sheets defined
      35.0% alpha, 31.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 43
    Processing helix  chain 'A' and resid 44 through 46
      No H-bonds generated for 'chain 'A' and resid 44 through 46'
    Processing helix  chain 'A' and resid 47 through 57
    Processing helix  chain 'A' and resid 59 through 70
    Processing helix  chain 'A' and resid 71 through 83
    Processing helix  chain 'A' and resid 86 through 97
    Processing helix  chain 'A' and resid 103 through 112
      removed outlier: 3.743A  pdb=" N   VAL A 107 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 142
      removed outlier: 3.528A  pdb=" N   SER A 119 " --> pdb=" O   ASP A 115 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   LEU A 131 " --> pdb=" O   THR A 127 " (cutoff:3.500A)
      removed outlier: 4.559A  pdb=" N   GLY A 132 " --> pdb=" O   PHE A 128 " (cutoff:3.500A)
      Proline residue:  A 135  - end of helix
    Processing helix  chain 'A' and resid 150 through 154
      removed outlier: 3.742A  pdb=" N   VAL A 154 " --> pdb=" O   LYS A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 180
      Proline residue:  A 169  - end of helix
    Processing helix  chain 'A' and resid 183 through 213
      removed outlier: 3.571A  pdb=" N   LEU A 196 " --> pdb=" O   MET A 192 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ALA A 201 " --> pdb=" O   LEU A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 244
      removed outlier: 3.577A  pdb=" N   ILE A 223 " --> pdb=" O   THR A 219 " (cutoff:3.500A)
      Proline residue:  A 230  - end of helix
      removed outlier: 3.666A  pdb=" N   PHE A 244 " --> pdb=" O   LEU A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 260
    Processing helix  chain 'A' and resid 262 through 274
      removed outlier: 4.308A  pdb=" N   CYS A 266 " --> pdb=" O   ASN A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 283
    Processing helix  chain 'A' and resid 284 through 310
    Processing helix  chain 'H' and resid 83 through 87
      removed outlier: 3.907A  pdb=" N   THR H  87 " --> pdb=" O   ALA H  84 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 156 through 158
      No H-bonds generated for 'chain 'H' and resid 156 through 158'
    Processing helix  chain 'H' and resid 187 through 192
      removed outlier: 4.106A  pdb=" N   GLN H 192 " --> pdb=" O   LEU H 189 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 4.160A  pdb=" N   PHE L  83 " --> pdb=" O   PRO L  80 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 121 through 128
    Processing helix  chain 'L' and resid 183 through 189
    Processing helix  chain 'K' and resid 83 through 87
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12
      removed outlier: 5.874A  pdb=" N   SER H  33 " --> pdb=" O   TYR H  95 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   ILE H  34 " --> pdb=" O   SER H  50 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   SER H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.555A  pdb=" N   CYS H  92 " --> pdb=" O   TRP H 103 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   TRP H 103 " --> pdb=" O   CYS H  92 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ARG H  94 " --> pdb=" O   ASP H 101 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 120 through 124
      removed outlier: 6.319A  pdb=" N   TYR H 176 " --> pdb=" O   ASP H 144 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 120 through 124
      removed outlier: 6.319A  pdb=" N   TYR H 176 " --> pdb=" O   ASP H 144 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 136 through 137
    Processing sheet with id=AA7, first strand: chain 'H' and resid 151 through 154
      removed outlier: 3.599A  pdb=" N   VAL H 198 " --> pdb=" O   VAL H 207 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   VAL H 207 " --> pdb=" O   VAL H 198 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   HIS H 200 " --> pdb=" O   THR H 205 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   THR H 205 " --> pdb=" O   HIS H 200 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 5
    Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.896A  pdb=" N   VAL L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 5.057A  pdb=" N   TYR L  49 " --> pdb=" O   VAL L  33 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.891A  pdb=" N   THR L  97 " --> pdb=" O   GLN L  90 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 114 through 118
      removed outlier: 3.636A  pdb=" N   VAL L 133 " --> pdb=" O   PHE L 118 " (cutoff:3.500A)
      removed outlier: 5.765A  pdb=" N   TYR L 173 " --> pdb=" O   ASN L 138 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 153 through 154
      removed outlier: 3.711A  pdb=" N   TYR L 192 " --> pdb=" O   PHE L 209 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'K' and resid 3 through 7
      removed outlier: 3.902A  pdb=" N   GLN K   3 " --> pdb=" O   SER K  25 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   SER K  25 " --> pdb=" O   GLN K   3 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   GLN K   5 " --> pdb=" O   ALA K  23 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ALA K  23 " --> pdb=" O   GLN K   5 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   VAL K  78 " --> pdb=" O   CYS K  22 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'K' and resid 10 through 12
      removed outlier: 3.659A  pdb=" N   THR K 110 " --> pdb=" O   GLY K  10 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   ALA K  33 " --> pdb=" O   ASP K  95 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   MET K  34 " --> pdb=" O   VAL K  50 " (cutoff:3.500A)
      removed outlier: 5.334A  pdb=" N   VAL K  50 " --> pdb=" O   MET K  34 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   TRP K  36 " --> pdb=" O   VAL K  48 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   VAL K  48 " --> pdb=" O   TRP K  36 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'K' and resid 10 through 12
      removed outlier: 3.659A  pdb=" N   THR K 110 " --> pdb=" O   GLY K  10 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ILE K  94 " --> pdb=" O   TYR K 102 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   TYR K 102 " --> pdb=" O   ILE K  94 " (cutoff:3.500A)

    370 hydrogen bonds defined for protein.
    980 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: 0.70

  Time building geometry restraints manager: 0.77 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1028
        1.31 -     1.43: 1856
        1.43 -     1.56: 3825
        1.56 -     1.69: 19
        1.69 -     1.81: 71
  Bond restraints: 6799
  Sorted by residual:
  bond pdb=" C12 CHO A 702 "
       pdb=" C13 CHO A 702 "
    ideal  model  delta    sigma   weight residual
    1.529  1.198  0.331 2.00e-02 2.50e+03 2.73e+02
  bond pdb=" C12 CHO A 703 "
       pdb=" C13 CHO A 703 "
    ideal  model  delta    sigma   weight residual
    1.529  1.202  0.327 2.00e-02 2.50e+03 2.67e+02
  bond pdb=" C13 CHO A 702 "
       pdb=" C17 CHO A 702 "
    ideal  model  delta    sigma   weight residual
    1.549  1.234  0.315 2.00e-02 2.50e+03 2.49e+02
  bond pdb=" C13 CHO A 703 "
       pdb=" C17 CHO A 703 "
    ideal  model  delta    sigma   weight residual
    1.549  1.242  0.307 2.00e-02 2.50e+03 2.36e+02
  bond pdb=" C11 CHO A 702 "
       pdb=" C12 CHO A 702 "
    ideal  model  delta    sigma   weight residual
    1.529  1.812 -0.283 2.00e-02 2.50e+03 2.00e+02
  ... (remaining 6794 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.71: 9113
        2.71 -     5.42: 105
        5.42 -     8.13: 28
        8.13 -    10.84: 3
       10.84 -    13.55: 2
  Bond angle restraints: 9251
  Sorted by residual:
  angle pdb=" CA  PRO A  58 "
        pdb=" N   PRO A  58 "
        pdb=" CD  PRO A  58 "
      ideal   model   delta    sigma   weight residual
     112.00  103.01    8.99 1.40e+00 5.10e-01 4.12e+01
  angle pdb=" N   MET A 229 "
        pdb=" CA  MET A 229 "
        pdb=" CB  MET A 229 "
      ideal   model   delta    sigma   weight residual
     110.42  104.69    5.73 1.18e+00 7.18e-01 2.36e+01
  angle pdb=" CA  GLU H  46 "
        pdb=" CB  GLU H  46 "
        pdb=" CG  GLU H  46 "
      ideal   model   delta    sigma   weight residual
     114.10  123.54   -9.44 2.00e+00 2.50e-01 2.23e+01
  angle pdb=" CB  MET A 229 "
        pdb=" CG  MET A 229 "
        pdb=" SD  MET A 229 "
      ideal   model   delta    sigma   weight residual
     112.70  126.25  -13.55 3.00e+00 1.11e-01 2.04e+01
  angle pdb=" CA  LYS A 151 "
        pdb=" C   LYS A 151 "
        pdb=" O   LYS A 151 "
      ideal   model   delta    sigma   weight residual
     120.90  116.14    4.76 1.07e+00 8.73e-01 1.98e+01
  ... (remaining 9246 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.81: 3935
       25.81 -    51.63: 255
       51.63 -    77.44: 39
       77.44 -   103.25: 7
      103.25 -   129.07: 12
  Dihedral angle restraints: 4248
    sinusoidal: 1782
      harmonic: 2466
  Sorted by residual:
  dihedral pdb=" CA  TYR A 183 "
           pdb=" C   TYR A 183 "
           pdb=" N   MET A 184 "
           pdb=" CA  MET A 184 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.87  -21.13     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" C5  CHO A 703 "
           pdb=" C6  CHO A 703 "
           pdb=" C7  CHO A 703 "
           pdb=" O7  CHO A 703 "
      ideal   model   delta sinusoidal    sigma   weight residual
     287.57  158.50  129.07     1      3.00e+01 1.11e-03 1.74e+01
  dihedral pdb=" C5  CHO A 702 "
           pdb=" C6  CHO A 702 "
           pdb=" C7  CHO A 702 "
           pdb=" O7  CHO A 702 "
      ideal   model   delta sinusoidal    sigma   weight residual
     287.57  163.57  124.00     1      3.00e+01 1.11e-03 1.66e+01
  ... (remaining 4245 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.331: 1065
       0.331 -    0.662: 3
       0.662 -    0.992: 0
       0.992 -    1.323: 0
       1.323 -    1.654: 2
  Chirality restraints: 1070
  Sorted by residual:
  chirality pdb=" C13 CHO A 702 "
            pdb=" C12 CHO A 702 "
            pdb=" C14 CHO A 702 "
            pdb=" C17 CHO A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.94   -1.29   -1.65 2.00e-01 2.50e+01 6.84e+01
  chirality pdb=" C13 CHO A 703 "
            pdb=" C12 CHO A 703 "
            pdb=" C14 CHO A 703 "
            pdb=" C17 CHO A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.94   -1.30   -1.64 2.00e-01 2.50e+01 6.71e+01
  chirality pdb=" C9  CHO A 703 "
            pdb=" C10 CHO A 703 "
            pdb=" C11 CHO A 703 "
            pdb=" C8  CHO A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52   -2.05   -0.47 2.00e-01 2.50e+01 5.48e+00
  ... (remaining 1067 not shown)

  Planarity restraints: 1133
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS L 107 "   -0.017 2.00e-02 2.50e+03   3.45e-02 1.19e+01
        pdb=" C   LYS L 107 "    0.060 2.00e-02 2.50e+03
        pdb=" O   LYS L 107 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   ARG L 108 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A  57 "    0.059 5.00e-02 4.00e+02   8.38e-02 1.12e+01
        pdb=" N   PRO A  58 "   -0.145 5.00e-02 4.00e+02
        pdb=" CA  PRO A  58 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A  58 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 150 "    0.012 2.00e-02 2.50e+03   2.48e-02 6.13e+00
        pdb=" C   LEU A 150 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   LEU A 150 "    0.016 2.00e-02 2.50e+03
        pdb=" N   LYS A 151 "    0.015 2.00e-02 2.50e+03
  ... (remaining 1130 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 140
        2.70 -     3.25: 6091
        3.25 -     3.80: 10069
        3.80 -     4.35: 12979
        4.35 -     4.90: 22646
  Nonbonded interactions: 51925
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP K  97 "
            pdb=" OG  SER K 100A"
     model   vdw
     2.152 3.040
  nonbonded pdb=" OG  SER L 182 "
            pdb=" OD2 ASP L 185 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" O   TYR L 186 "
            pdb=" OH  TYR L 192 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" OG  SER K  17 "
            pdb=" OD1 ASN K  82A"
     model   vdw
     2.311 3.040
  nonbonded pdb=" NH1 ARG L  66 "
            pdb=" O   GLY L  68 "
     model   vdw
     2.324 3.120
  ... (remaining 51920 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.48 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.220
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
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      :  0.013   0.331   6802  Z= 0.653
  Angle     :  0.753  13.548   9257  Z= 0.364
  Chirality :  0.087   1.654   1070
  Planarity :  0.005   0.084   1133
  Dihedral  : 18.278 129.069   2667
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 14.42 %
    Favored  : 84.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  1.17 (0.29), residues: 846
  helix:  1.90 (0.33), residues: 260
  sheet:  1.43 (0.35), residues: 211
  loop : -0.41 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L 108 
 TYR   0.024   0.001   TYR L 140 
 PHE   0.006   0.001   PHE A  37 
 TRP   0.005   0.001   TRP L  93 
 HIS   0.024   0.003   HIS H 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.01309 ( 6799)
  covalent geometry    : angle       0.75360 ( 9251)
  SS BOND              : bond        0.00202 (    3)
  SS BOND              : angle       0.18228 (    6)
  hydrogen bonds       : bond        0.19631 (  343)
  hydrogen bonds       : angle       7.46331 (  980)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 90
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  108 ARG cc_start: 0.7510 (ttp80) cc_final: 0.7020 (ptm-80)
REVERT: L  142 ARG cc_start: 0.7657 (ttt180) cc_final: 0.7071 (ttt-90)
  outliers start: 5
  outliers final: 5
  residues processed: 94
  average time/residue: 0.5235
  time to fit residues: 51.8710
Evaluate side-chains
  91 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 86
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue   97 LYS
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue  172 THR
Chi-restraints excluded: chain K residue   70 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.1980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:   10.0000
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A  54 HIS
A 103 ASN
A 293 GLN
H 100EGLN
H 105 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.189988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.149102 restraints weight = 15575.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 6.63
r_work: 0.3000 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2975
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2975 r_free = 0.2975    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2975 r_free = 0.2975    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2975
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.1056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   6802  Z= 0.127
  Angle     :  0.595   7.672   9257  Z= 0.291
  Chirality :  0.044   0.273   1070
  Planarity :  0.004   0.033   1133
  Dihedral  :  9.414  77.025   1206
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 14.29 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  1.29 (0.29), residues: 846
  helix:  2.22 (0.32), residues: 261
  sheet:  1.34 (0.33), residues: 238
  loop : -0.57 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  66 
 TYR   0.013   0.001   TYR A 238 
 PHE   0.008   0.001   PHE A  37 
 TRP   0.006   0.001   TRP L  93 
 HIS   0.001   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 6799)
  covalent geometry    : angle       0.59461 ( 9251)
  SS BOND              : bond        0.00486 (    3)
  SS BOND              : angle       0.58743 (    6)
  hydrogen bonds       : bond        0.04222 (  343)
  hydrogen bonds       : angle       5.25355 (  980)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
REVERT: L   11 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8147 (tt)
REVERT: L  108 ARG cc_start: 0.7768 (ttp80) cc_final: 0.7118 (ptm-80)
REVERT: K   34 MET cc_start: 0.7380 (ttt) cc_final: 0.6514 (mmm)
  outliers start: 18
  outliers final: 8
  residues processed: 100
  average time/residue: 0.5617
  time to fit residues: 59.0282
Evaluate side-chains
  94 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain H residue   97 LYS
Chi-restraints excluded: chain H residue  100 GLN
Chi-restraints excluded: chain H residue  105 GLN
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue  170 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 69 optimal weight:   10.0000
   chunk 4 optimal weight:    0.6980
   chunk 25 optimal weight:    0.3980
   chunk 36 optimal weight:    2.9990
   chunk 71 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 49 optimal weight:    7.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
H  99 GLN
H 100EGLN
H 105 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.191581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.135378 restraints weight = 15376.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 3.76
r_work: 0.3086 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3073
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3073 r_free = 0.3073    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3073 r_free = 0.3073    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3073
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.1315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   6802  Z= 0.106
  Angle     :  0.536   7.877   9257  Z= 0.264
  Chirality :  0.042   0.245   1070
  Planarity :  0.004   0.032   1133
  Dihedral  :  7.336  57.656   1200
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.07 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  1.44 (0.29), residues: 846
  helix:  2.49 (0.32), residues: 261
  sheet:  1.42 (0.33), residues: 239
  loop : -0.62 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  66 
 TYR   0.010   0.001   TYR A 238 
 PHE   0.007   0.001   PHE A  37 
 TRP   0.006   0.001   TRP H 100H
 HIS   0.001   0.000   HIS H 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 6799)
  covalent geometry    : angle       0.53610 ( 9251)
  SS BOND              : bond        0.00430 (    3)
  SS BOND              : angle       0.43967 (    6)
  hydrogen bonds       : bond        0.03605 (  343)
  hydrogen bonds       : angle       4.82444 (  980)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A  113 LYS cc_start: 0.7986 (mtmm) cc_final: 0.7709 (mtmm)
REVERT: A  215 MET cc_start: 0.8124 (mmm) cc_final: 0.7651 (mmp)
REVERT: H   46 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8269 (tm-30)
REVERT: H  105 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7433 (pp30)
REVERT: L   11 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8156 (tt)
REVERT: L  105 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7172 (pt0)
REVERT: L  108 ARG cc_start: 0.7609 (ttp80) cc_final: 0.6922 (ptm-80)
REVERT: L  142 ARG cc_start: 0.7320 (tmt90) cc_final: 0.6975 (ttt-90)
REVERT: K   34 MET cc_start: 0.7340 (ttt) cc_final: 0.6614 (mmm)
  outliers start: 17
  outliers final: 6
  residues processed: 102
  average time/residue: 0.5193
  time to fit residues: 55.8906
Evaluate side-chains
  96 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain H residue   97 LYS
Chi-restraints excluded: chain H residue  105 GLN
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue  105 GLU
Chi-restraints excluded: chain L residue  135 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0870
   chunk 22 optimal weight:    0.4980
   chunk 66 optimal weight:    8.9990
   chunk 80 optimal weight:    7.9990
   chunk 38 optimal weight:    1.9990
   chunk 79 optimal weight:    8.9990
   chunk 74 optimal weight:   10.0000
   chunk 81 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.0962

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

Flipped N/Q/H residues before XYZ refinement:
A 117 ASN
A 293 GLN
H 100EGLN
H 105 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.190599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.136471 restraints weight = 21229.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 5.26
r_work: 0.3059 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3047
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3047 r_free = 0.3047    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3047 r_free = 0.3047    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3047
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.1522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6802  Z= 0.123
  Angle     :  0.537   7.534   9257  Z= 0.267
  Chirality :  0.042   0.241   1070
  Planarity :  0.004   0.032   1133
  Dihedral  :  6.872  52.999   1200
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 16.48 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  1.46 (0.29), residues: 846
  helix:  2.49 (0.32), residues: 261
  sheet:  1.64 (0.34), residues: 220
  loop : -0.64 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  66 
 TYR   0.008   0.001   TYR A 238 
 PHE   0.009   0.001   PHE A 128 
 TRP   0.006   0.001   TRP H 100H
 HIS   0.001   0.000   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6799)
  covalent geometry    : angle       0.53689 ( 9251)
  SS BOND              : bond        0.00418 (    3)
  SS BOND              : angle       0.41818 (    6)
  hydrogen bonds       : bond        0.03645 (  343)
  hydrogen bonds       : angle       4.64117 (  980)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 90
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 MET cc_start: 0.8590 (mmm) cc_final: 0.8334 (mmm)
REVERT: A  215 MET cc_start: 0.8128 (mmm) cc_final: 0.7579 (mmp)
REVERT: H   97 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7220 (mptp)
REVERT: H   99 GLN cc_start: 0.7381 (mm-40) cc_final: 0.7167 (mm110)
REVERT: L   11 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8157 (tt)
REVERT: L  105 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7176 (pt0)
REVERT: L  108 ARG cc_start: 0.7526 (ttp80) cc_final: 0.6795 (ptm-80)
REVERT: L  142 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6802 (ttt-90)
REVERT: K   34 MET cc_start: 0.7263 (ttt) cc_final: 0.6529 (mmm)
  outliers start: 29
  outliers final: 12
  residues processed: 104
  average time/residue: 0.5084
  time to fit residues: 55.9143
Evaluate side-chains
  105 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  229 MET
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  290 MET
Chi-restraints excluded: chain H residue   97 LYS
Chi-restraints excluded: chain H residue  100 GLN
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue  105 GLU
Chi-restraints excluded: chain L residue  142 ARG
Chi-restraints excluded: chain L residue  170 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 12 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   chunk 48 optimal weight:    7.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
H 100EGLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.190679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.138339 restraints weight = 23882.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 5.73
r_work: 0.3041 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3027
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3027 r_free = 0.3027    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3027 r_free = 0.3027    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3027
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.1630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6802  Z= 0.113
  Angle     :  0.516   7.067   9257  Z= 0.258
  Chirality :  0.041   0.239   1070
  Planarity :  0.004   0.033   1133
  Dihedral  :  6.669  51.446   1200
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 17.03 %
    Favored  : 78.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  1.50 (0.29), residues: 846
  helix:  2.61 (0.32), residues: 261
  sheet:  1.60 (0.34), residues: 220
  loop : -0.65 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  66 
 TYR   0.009   0.001   TYR A 238 
 PHE   0.008   0.001   PHE A  37 
 TRP   0.008   0.001   TRP H 100H
 HIS   0.001   0.000   HIS H 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 6799)
  covalent geometry    : angle       0.51649 ( 9251)
  SS BOND              : bond        0.00436 (    3)
  SS BOND              : angle       0.45188 (    6)
  hydrogen bonds       : bond        0.03449 (  343)
  hydrogen bonds       : angle       4.50842 (  980)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 88
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 MET cc_start: 0.8644 (mmm) cc_final: 0.8308 (mmm)
REVERT: A  215 MET cc_start: 0.8135 (mmm) cc_final: 0.7595 (mmp)
REVERT: H  105 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.6934 (pp30)
REVERT: L   11 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8138 (tt)
REVERT: L   42 LYS cc_start: 0.8539 (mppt) cc_final: 0.7937 (mmtt)
REVERT: L  105 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7215 (pt0)
REVERT: L  108 ARG cc_start: 0.7455 (ttp80) cc_final: 0.6714 (ptm-80)
REVERT: L  142 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.6956 (ttt-90)
REVERT: K   34 MET cc_start: 0.7236 (ttt) cc_final: 0.6517 (mmm)
  outliers start: 28
  outliers final: 12
  residues processed: 102
  average time/residue: 0.4823
  time to fit residues: 52.2063
Evaluate side-chains
  103 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  229 MET
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  290 MET
Chi-restraints excluded: chain H residue  100 GLN
Chi-restraints excluded: chain H residue  105 GLN
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue  105 GLU
Chi-restraints excluded: chain L residue  135 LEU
Chi-restraints excluded: chain L residue  142 ARG
Chi-restraints excluded: chain L residue  170 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   chunk 57 optimal weight:    0.0010
   chunk 40 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0670
   chunk 46 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9990
   chunk 80 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 83 optimal weight:    6.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.5528

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

Flipped N/Q/H residues before XYZ refinement:
H 100EGLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.191960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.136262 restraints weight = 15702.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 4.01
r_work: 0.3097 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3080
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3080
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6802  Z= 0.100
  Angle     :  0.512   8.137   9257  Z= 0.252
  Chirality :  0.040   0.235   1070
  Planarity :  0.004   0.033   1133
  Dihedral  :  6.217  49.999   1196
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 17.58 %
    Favored  : 79.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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 (0.29), residues: 846
  helix:  2.69 (0.32), residues: 262
  sheet:  1.63 (0.34), residues: 220
  loop : -0.60 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 100F
 TYR   0.012   0.001   TYR H 100D
 PHE   0.024   0.001   PHE K  67 
 TRP   0.007   0.001   TRP H 100H
 HIS   0.001   0.000   HIS L 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 6799)
  covalent geometry    : angle       0.51178 ( 9251)
  SS BOND              : bond        0.00677 (    3)
  SS BOND              : angle       0.75196 (    6)
  hydrogen bonds       : bond        0.03123 (  343)
  hydrogen bonds       : angle       4.35661 (  980)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 90
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 MET cc_start: 0.8596 (mmm) cc_final: 0.8228 (mmm)
REVERT: A  215 MET cc_start: 0.8088 (mmm) cc_final: 0.7565 (mmp)
REVERT: H   46 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7712 (tm-30)
REVERT: L   11 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8151 (tt)
REVERT: L   42 LYS cc_start: 0.8501 (mppt) cc_final: 0.7916 (mmtt)
REVERT: L  108 ARG cc_start: 0.7345 (ttp80) cc_final: 0.6632 (ptm-80)
REVERT: L  142 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6974 (ttt-90)
REVERT: K   34 MET cc_start: 0.7263 (ttt) cc_final: 0.6601 (mmm)
  outliers start: 23
  outliers final: 11
  residues processed: 101
  average time/residue: 0.5148
  time to fit residues: 54.8547
Evaluate side-chains
  102 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  290 MET
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   97 LYS
Chi-restraints excluded: chain H residue  100 GLN
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue  135 LEU
Chi-restraints excluded: chain L residue  142 ARG
Chi-restraints excluded: chain L residue  169 LYS
Chi-restraints excluded: chain L residue  170 ASP
Chi-restraints excluded: chain K residue   63 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 77 optimal weight:    0.7980
   chunk 83 optimal weight:   10.0000
   chunk 47 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
H 100EGLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.190156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.134776 restraints weight = 23847.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 6.09
r_work: 0.2999 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2992
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2992 r_free = 0.2992    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2992 r_free = 0.2992    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2992
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.1874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6802  Z= 0.150
  Angle     :  0.548   7.149   9257  Z= 0.274
  Chirality :  0.042   0.236   1070
  Planarity :  0.004   0.033   1133
  Dihedral  :  6.495  52.646   1196
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 16.48 %
    Favored  : 79.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  1.44 (0.29), residues: 846
  helix:  2.56 (0.32), residues: 262
  sheet:  1.55 (0.34), residues: 220
  loop : -0.67 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  66 
 TYR   0.014   0.001   TYR H 100D
 PHE   0.020   0.001   PHE K  67 
 TRP   0.009   0.001   TRP H 100H
 HIS   0.002   0.001   HIS H 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 6799)
  covalent geometry    : angle       0.54812 ( 9251)
  SS BOND              : bond        0.00517 (    3)
  SS BOND              : angle       0.60041 (    6)
  hydrogen bonds       : bond        0.03782 (  343)
  hydrogen bonds       : angle       4.43423 (  980)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 90
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 MET cc_start: 0.8659 (mmm) cc_final: 0.8223 (mmm)
REVERT: L   82 ASP cc_start: 0.9060 (m-30) cc_final: 0.8766 (m-30)
REVERT: L  105 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7234 (pt0)
REVERT: L  108 ARG cc_start: 0.7403 (ttp80) cc_final: 0.6671 (ptm-80)
REVERT: L  142 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6980 (ttt-90)
REVERT: K   34 MET cc_start: 0.7213 (ttt) cc_final: 0.6535 (mmm)
  outliers start: 27
  outliers final: 17
  residues processed: 103
  average time/residue: 0.4771
  time to fit residues: 52.0199
Evaluate side-chains
  106 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  290 MET
Chi-restraints excluded: chain H residue   97 LYS
Chi-restraints excluded: chain H residue  100 GLN
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   70 ASP
Chi-restraints excluded: chain L residue  105 GLU
Chi-restraints excluded: chain L residue  135 LEU
Chi-restraints excluded: chain L residue  142 ARG
Chi-restraints excluded: chain L residue  169 LYS
Chi-restraints excluded: chain L residue  170 ASP
Chi-restraints excluded: chain K residue   63 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 65 optimal weight:    7.9990
   chunk 66 optimal weight:    7.9990
   chunk 22 optimal weight:    1.9990
   chunk 69 optimal weight:    6.9990
   chunk 72 optimal weight:    0.4980
   chunk 0 optimal weight:    9.9990
   chunk 2 optimal weight:    0.7980
   chunk 76 optimal weight:    6.9990
   chunk 35 optimal weight:    0.0170
   overall best weight:    0.8020

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

Flipped N/Q/H residues before XYZ refinement:
H 100EGLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.190619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.135484 restraints weight = 24446.054|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 5.84
r_work: 0.3029 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3027
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3027 r_free = 0.3027    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3027 r_free = 0.3027    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3027
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.1918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6802  Z= 0.108
  Angle     :  0.519   8.646   9257  Z= 0.256
  Chirality :  0.041   0.235   1070
  Planarity :  0.004   0.033   1133
  Dihedral  :  6.244  50.979   1196
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 17.17 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  1.48 (0.29), residues: 846
  helix:  2.61 (0.32), residues: 263
  sheet:  1.58 (0.34), residues: 220
  loop : -0.69 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K  52A
 TYR   0.010   0.001   TYR A 238 
 PHE   0.016   0.001   PHE K  67 
 TRP   0.008   0.001   TRP H 100H
 HIS   0.001   0.000   HIS H 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 6799)
  covalent geometry    : angle       0.51875 ( 9251)
  SS BOND              : bond        0.00409 (    3)
  SS BOND              : angle       0.51409 (    6)
  hydrogen bonds       : bond        0.03341 (  343)
  hydrogen bonds       : angle       4.31629 (  980)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 85
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 MET cc_start: 0.8619 (mmm) cc_final: 0.8108 (mmm)
REVERT: A  215 MET cc_start: 0.8125 (mmm) cc_final: 0.7592 (mmp)
REVERT: L   11 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8140 (tt)
REVERT: L  105 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7234 (pt0)
REVERT: L  142 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6964 (ttt-90)
REVERT: K   34 MET cc_start: 0.7234 (ttt) cc_final: 0.6503 (mmm)
  outliers start: 24
  outliers final: 17
  residues processed: 97
  average time/residue: 0.4806
  time to fit residues: 49.4143
Evaluate side-chains
  105 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 85
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  229 MET
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  290 MET
Chi-restraints excluded: chain H residue   97 LYS
Chi-restraints excluded: chain H residue  100 GLN
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue  105 GLU
Chi-restraints excluded: chain L residue  135 LEU
Chi-restraints excluded: chain L residue  142 ARG
Chi-restraints excluded: chain L residue  169 LYS
Chi-restraints excluded: chain L residue  170 ASP
Chi-restraints excluded: chain K residue   63 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 65 optimal weight:    7.9990
   chunk 56 optimal weight:    0.9990
   chunk 62 optimal weight:    7.9990
   chunk 24 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 82 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
H  99 GLN
H 100EGLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.190057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.130699 restraints weight = 16626.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 3.79
r_work: 0.3072 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3069
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3069 r_free = 0.3069    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3069 r_free = 0.3069    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3069
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.1962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6802  Z= 0.111
  Angle     :  0.508   7.036   9257  Z= 0.254
  Chirality :  0.041   0.234   1070
  Planarity :  0.004   0.033   1133
  Dihedral  :  6.161  51.831   1196
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 17.17 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  1.50 (0.29), residues: 846
  helix:  2.68 (0.32), residues: 262
  sheet:  1.56 (0.34), residues: 220
  loop : -0.68 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  66 
 TYR   0.009   0.001   TYR A 238 
 PHE   0.014   0.001   PHE K  67 
 TRP   0.008   0.001   TRP H 100H
 HIS   0.001   0.000   HIS H 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 6799)
  covalent geometry    : angle       0.50821 ( 9251)
  SS BOND              : bond        0.00398 (    3)
  SS BOND              : angle       0.49723 (    6)
  hydrogen bonds       : bond        0.03313 (  343)
  hydrogen bonds       : angle       4.25906 (  980)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 88
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 MET cc_start: 0.8603 (mmm) cc_final: 0.8023 (mmm)
REVERT: A  184 MET cc_start: 0.5545 (OUTLIER) cc_final: 0.5250 (tmm)
REVERT: A  215 MET cc_start: 0.8119 (mmm) cc_final: 0.7590 (mmp)
REVERT: L   11 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8167 (tt)
REVERT: L  105 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7136 (pt0)
REVERT: L  142 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6979 (ttt-90)
REVERT: K   34 MET cc_start: 0.7267 (ttt) cc_final: 0.6533 (mmm)
  outliers start: 24
  outliers final: 17
  residues processed: 100
  average time/residue: 0.4909
  time to fit residues: 51.8669
Evaluate side-chains
  109 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 88
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  184 MET
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  229 MET
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  290 MET
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   97 LYS
Chi-restraints excluded: chain H residue  100 GLN
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue  105 GLU
Chi-restraints excluded: chain L residue  135 LEU
Chi-restraints excluded: chain L residue  142 ARG
Chi-restraints excluded: chain L residue  170 ASP
Chi-restraints excluded: chain K residue   63 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 55 optimal weight:    0.0670
   chunk 2 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 68 optimal weight:    8.9990
   chunk 43 optimal weight:   20.0000
   chunk 5 optimal weight:    0.7980
   chunk 21 optimal weight:    0.4980
   chunk 54 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
H 100EGLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.192094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.136012 restraints weight = 14123.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 3.86
r_work: 0.3130 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3114
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3114 r_free = 0.3114    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3114 r_free = 0.3114    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3114
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.2014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6802  Z= 0.096
  Angle     :  0.503   8.893   9257  Z= 0.248
  Chirality :  0.040   0.231   1070
  Planarity :  0.004   0.033   1133
  Dihedral  :  5.950  51.298   1196
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 18.13 %
    Favored  : 79.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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 (0.29), residues: 846
  helix:  2.74 (0.32), residues: 263
  sheet:  1.59 (0.34), residues: 220
  loop : -0.65 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 100F
 TYR   0.010   0.001   TYR A 238 
 PHE   0.011   0.001   PHE K  67 
 TRP   0.007   0.001   TRP L  93 
 HIS   0.001   0.000   HIS L 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 6799)
  covalent geometry    : angle       0.50324 ( 9251)
  SS BOND              : bond        0.00343 (    3)
  SS BOND              : angle       0.44864 (    6)
  hydrogen bonds       : bond        0.03070 (  343)
  hydrogen bonds       : angle       4.16760 (  980)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 MET cc_start: 0.8556 (mmm) cc_final: 0.7977 (mmm)
REVERT: A  184 MET cc_start: 0.5443 (OUTLIER) cc_final: 0.5154 (tmm)
REVERT: A  215 MET cc_start: 0.8066 (mmm) cc_final: 0.7560 (mmp)
REVERT: L   11 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8147 (tt)
REVERT: L  105 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7049 (pt0)
REVERT: L  142 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6929 (ttt-90)
REVERT: K   34 MET cc_start: 0.7246 (ttt) cc_final: 0.6491 (mmm)
  outliers start: 18
  outliers final: 13
  residues processed: 97
  average time/residue: 0.5114
  time to fit residues: 52.5099
Evaluate side-chains
  105 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  184 MET
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  290 MET
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   97 LYS
Chi-restraints excluded: chain H residue  100 GLN
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue  105 GLU
Chi-restraints excluded: chain L residue  135 LEU
Chi-restraints excluded: chain L residue  142 ARG
Chi-restraints excluded: chain K residue   63 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 46 optimal weight:    0.3980
   chunk 50 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 8 optimal weight:    6.9990
   chunk 68 optimal weight:    3.9990
   chunk 44 optimal weight:    0.8980
   chunk 32 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   chunk 74 optimal weight:    0.8980
   chunk 17 optimal weight:    4.9990
   chunk 83 optimal weight:    7.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
H  99 GLN
H 100EGLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.190973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.137588 restraints weight = 21179.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 5.00
r_work: 0.3055 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3047
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3047 r_free = 0.3047    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3047 r_free = 0.3047    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3047
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.2025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6802  Z= 0.108
  Angle     :  0.502   6.994   9257  Z= 0.251
  Chirality :  0.040   0.231   1070
  Planarity :  0.004   0.033   1133
  Dihedral  :  5.953  52.594   1196
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 18.41 %
    Favored  : 78.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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 (0.29), residues: 846
  helix:  2.77 (0.32), residues: 262
  sheet:  1.59 (0.34), residues: 220
  loop : -0.65 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  66 
 TYR   0.009   0.001   TYR A 238 
 PHE   0.011   0.001   PHE K  67 
 TRP   0.008   0.001   TRP H 100H
 HIS   0.001   0.000   HIS H 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 6799)
  covalent geometry    : angle       0.50209 ( 9251)
  SS BOND              : bond        0.00380 (    3)
  SS BOND              : angle       0.48950 (    6)
  hydrogen bonds       : bond        0.03204 (  343)
  hydrogen bonds       : angle       4.15545 (  980)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2959.78 seconds
wall clock time: 51 minutes 6.25 seconds (3066.25 seconds total)