Starting phenix.real_space_refine
on Thu Jun  5 10:56:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jic_22344/06_2025/7jic_22344.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jic_22344/06_2025/7jic_22344.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jic_22344/06_2025/7jic_22344.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jic_22344/06_2025/7jic_22344.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jic_22344/06_2025/7jic_22344.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jic_22344/06_2025/7jic_22344.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.002 sd=   0.034
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      29      5.16       5
     C    3770      2.51       5
     N    1013      2.21       5
     O    1168      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 5980
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1625
          Classifications: {'peptide': 228}
          Incomplete info: {'truncation_to_alanine': 50}
          Link IDs: {'PTRANS': 19, 'TRANS': 208}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 181
          Unresolved non-hydrogen angles: 224
          Unresolved non-hydrogen dihedrals: 145
          Unresolved non-hydrogen chiralities: 17
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 97
    Chain: "B"
      Number of atoms: 1285
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 1285
          Classifications: {'peptide': 204}
          Incomplete info: {'truncation_to_alanine': 80}
          Link IDs: {'PTRANS': 4, 'TRANS': 199}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 303
          Unresolved non-hydrogen angles: 397
          Unresolved non-hydrogen dihedrals: 257
          Unresolved non-hydrogen chiralities: 44
          Planarities with less than four sites: {'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 2, 'PHE:plan': 11, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 132
    Chain: "H"
      Number of atoms: 1601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1601
          Classifications: {'peptide': 216}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 201}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 27
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "L"
      Number of atoms: 1469
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1469
          Classifications: {'peptide': 194}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 183}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 19
  Time building chain proxies: 4.47, per 1000 atoms: 0.75
  Number of scatterers: 5980
  At special positions: 0
  Unit cell: (61.05, 75.075, 170.775, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      29     16.00
     O    1168      8.00
     N    1013      7.00
     C    3770      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  38 " - pdb=" SG  CYS A 261 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  97 " - pdb=" SG  CYS A 200 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 156 " - pdb=" SG  CYS B 190 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 157 " - pdb=" SG  CYS B 175 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 146 " - pdb=" SG  CYS H 202 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 133 " - pdb=" SG  CYS L 193 " 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: 1.29
  Conformation dependent library (CDL) restraints added in 859.8 milliseconds
  

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1554

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 13 sheets defined
      24.2% alpha, 27.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 293 through 313
    Processing helix  chain 'B' and resid 10 through 37
    Processing helix  chain 'B' and resid 38 through 45
    Processing helix  chain 'B' and resid 58 through 82
    Processing helix  chain 'B' and resid 90 through 115
    Processing helix  chain 'B' and resid 118 through 135
      removed outlier: 3.827A  pdb=" N   GLN B 129 " --> pdb=" O   GLN B 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 154
    Processing helix  chain 'B' and resid 160 through 165
      removed outlier: 3.626A  pdb=" N   ALA B 164 " --> pdb=" O   THR B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 224
      removed outlier: 3.747A  pdb=" N   LYS B 201 " --> pdb=" O   LEU B 197 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   MET B 224 " --> pdb=" O   MET B 220 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 61 through 64
      removed outlier: 3.904A  pdb=" N   GLN H  64 " --> pdb=" O   GLN H  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 61 through 64'
    Processing helix  chain 'L' and resid 120 through 125
    Processing helix  chain 'L' and resid 182 through 186
      removed outlier: 3.696A  pdb=" N   GLU L 186 " --> pdb=" O   LYS L 182 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 182 through 186'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27
      removed outlier: 3.863A  pdb=" N   GLU A 273 " --> pdb=" O   VAL A  26 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 36
      removed outlier: 4.008A  pdb=" N   ASP A  32 " --> pdb=" O   ALA A 251 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   ALA A  34 " --> pdb=" O   PRO A 249 " (cutoff:3.500A)
      removed outlier: 7.407A  pdb=" N   LEU A  36 " --> pdb=" O   LEU A 247 " (cutoff:3.500A)
      removed outlier: 5.818A  pdb=" N   LEU A 247 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   MET A 239 " --> pdb=" O   MET A  75 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   HIS A  74 " --> pdb=" O   TRP A  81 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ILE A  84 " --> pdb=" O   LEU A 196 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU A 196 " --> pdb=" O   ILE A  84 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 188 through 190
      removed outlier: 7.754A  pdb=" N   LEU A 188 " --> pdb=" O   GLY A 110 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   THR A 112 " --> pdb=" O   LEU A 188 " (cutoff:3.500A)
      removed outlier: 7.211A  pdb=" N   MET A 190 " --> pdb=" O   THR A 112 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   ASN A 114 " --> pdb=" O   MET A 190 " (cutoff:3.500A)
      removed outlier: 5.161A  pdb=" N   CYS A  97 " --> pdb=" O   PRO A 109 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 123
      removed outlier: 6.066A  pdb=" N   LEU A 121 " --> pdb=" O   TYR A 157 " (cutoff:3.500A)
      removed outlier: 7.186A  pdb=" N   TRP A 159 " --> pdb=" O   LEU A 121 " (cutoff:3.500A)
      removed outlier: 7.597A  pdb=" N   ARG A 123 " --> pdb=" O   TRP A 159 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ALA A 160 " --> pdb=" O   ARG A 163 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 5
    Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.513A  pdb=" N   THR H 116 " --> pdb=" O   GLU H  10 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   VAL H  12 " --> pdb=" O   THR H 116 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'H' and resid 57 through 59
      removed outlier: 5.397A  pdb=" N   TRP H  47 " --> pdb=" O   LYS H  38 " (cutoff:3.500A)
      removed outlier: 6.077A  pdb=" N   LYS H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   TYR H 108 " --> pdb=" O   ARG H  97 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 126 through 130
      removed outlier: 4.020A  pdb=" N   GLY H 145 " --> pdb=" O   LEU H 130 " (cutoff:3.500A)
      removed outlier: 5.874A  pdb=" N   TYR H 182 " --> pdb=" O   ASP H 150 " (cutoff:3.500A)
      removed outlier: 5.289A  pdb=" N   SER H 185 " --> pdb=" O   PRO H 173 " (cutoff:3.500A)
      removed outlier: 7.469A  pdb=" N   VAL H 187 " --> pdb=" O   THR H 171 " (cutoff:3.500A)
      removed outlier: 5.312A  pdb=" N   THR H 171 " --> pdb=" O   VAL H 187 " (cutoff:3.500A)
      removed outlier: 7.619A  pdb=" N   THR H 189 " --> pdb=" O   VAL H 169 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   VAL H 169 " --> pdb=" O   THR H 189 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 157 through 160
      removed outlier: 3.742A  pdb=" N   THR H 157 " --> pdb=" O   ASN H 205 " (cutoff:3.500A)
      removed outlier: 4.936A  pdb=" N   TYR H 200 " --> pdb=" O   VAL H 217 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   VAL H 204 " --> pdb=" O   VAL H 213 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   VAL H 213 " --> pdb=" O   VAL H 204 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 7
      removed outlier: 3.645A  pdb=" N   TYR L  70 " --> pdb=" O   CYS L  23 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.570A  pdb=" N   GLU L 104 " --> pdb=" O   MET L  11 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   TYR L  85 " --> pdb=" O   THR L 101 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   TRP L  34 " --> pdb=" O   TRP L  46 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 128 through 135
    Processing sheet with id=AB4, first strand: chain 'L' and resid 144 through 149
      removed outlier: 3.725A  pdb=" N   ALA L 192 " --> pdb=" O   LYS L 148 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   CYS L 193 " --> pdb=" O   LYS L 206 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   LYS L 206 " --> pdb=" O   CYS L 193 " (cutoff:3.500A)

    286 hydrogen bonds defined for protein.
    792 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: 1.64

  Time building geometry restraints manager: 1.56 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1948
        1.35 -     1.46: 1502
        1.46 -     1.58: 2622
        1.58 -     1.70: 0
        1.70 -     1.81: 41
  Bond restraints: 6113
  Sorted by residual:
  bond pdb=" CA  ILE A 297 "
       pdb=" CB  ILE A 297 "
    ideal  model  delta    sigma   weight residual
    1.540  1.528  0.013 1.25e-02 6.40e+03 1.02e+00
  bond pdb=" CA  ILE A 306 "
       pdb=" CB  ILE A 306 "
    ideal  model  delta    sigma   weight residual
    1.540  1.528  0.012 1.25e-02 6.40e+03 8.84e-01
  bond pdb=" CB  PRO B  55 "
       pdb=" CG  PRO B  55 "
    ideal  model  delta    sigma   weight residual
    1.492  1.538 -0.046 5.00e-02 4.00e+02 8.40e-01
  bond pdb=" CA  VAL A 304 "
       pdb=" CB  VAL A 304 "
    ideal  model  delta    sigma   weight residual
    1.540  1.528  0.012 1.29e-02 6.01e+03 8.24e-01
  bond pdb=" CA  THR A 292 "
       pdb=" CB  THR A 292 "
    ideal  model  delta    sigma   weight residual
    1.540  1.516  0.024 2.70e-02 1.37e+03 7.65e-01
  ... (remaining 6108 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.07: 8099
        1.07 -     2.13: 177
        2.13 -     3.20: 64
        3.20 -     4.27: 8
        4.27 -     5.33: 4
  Bond angle restraints: 8352
  Sorted by residual:
  angle pdb=" C   THR L  50 "
        pdb=" CA  THR L  50 "
        pdb=" CB  THR L  50 "
      ideal   model   delta    sigma   weight residual
     110.42  115.75   -5.33 1.99e+00 2.53e-01 7.18e+00
  angle pdb=" N   ALA H  16 "
        pdb=" CA  ALA H  16 "
        pdb=" C   ALA H  16 "
      ideal   model   delta    sigma   weight residual
     108.34  111.03   -2.69 1.31e+00 5.83e-01 4.22e+00
  angle pdb=" N   PRO A 203 "
        pdb=" CA  PRO A 203 "
        pdb=" C   PRO A 203 "
      ideal   model   delta    sigma   weight residual
     110.70  113.05   -2.35 1.22e+00 6.72e-01 3.70e+00
  angle pdb=" C   SER L   7 "
        pdb=" N   PRO L   8 "
        pdb=" CD  PRO L   8 "
      ideal   model   delta    sigma   weight residual
     120.60  124.78   -4.18 2.20e+00 2.07e-01 3.62e+00
  angle pdb=" CA  THR L  50 "
        pdb=" C   THR L  50 "
        pdb=" N   SER L  51 "
      ideal   model   delta    sigma   weight residual
     116.84  119.94   -3.10 1.71e+00 3.42e-01 3.29e+00
  ... (remaining 8347 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.68: 3244
       10.68 -    21.36: 230
       21.36 -    32.04: 82
       32.04 -    42.72: 30
       42.72 -    53.40: 6
  Dihedral angle restraints: 3592
    sinusoidal: 1184
      harmonic: 2408
  Sorted by residual:
  dihedral pdb=" SG  CYS B 156 "
           pdb=" CB  CYS B 190 "
           pdb=" SG  CYS B 190 "
           pdb=" CA  CYS B 190 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00   26.09   52.91     1      2.00e+01 2.50e-03 9.53e+00
  dihedral pdb=" CA  CYS B 157 "
           pdb=" CB  CYS B 157 "
           pdb=" SG  CYS B 157 "
           pdb=" SG  CYS B 175 "
      ideal   model   delta sinusoidal    sigma   weight residual
     183.00  131.19   51.81     1      2.00e+01 2.50e-03 9.16e+00
  dihedral pdb=" N   LYS L 125 "
           pdb=" CA  LYS L 125 "
           pdb=" CB  LYS L 125 "
           pdb=" CG  LYS L 125 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -103.72   43.72     3      1.50e+01 4.44e-03 7.86e+00
  ... (remaining 3589 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 591
       0.026 -    0.052: 237
       0.052 -    0.079: 67
       0.079 -    0.105: 42
       0.105 -    0.131: 24
  Chirality restraints: 961
  Sorted by residual:
  chirality pdb=" CA  ILE A  84 "
            pdb=" N   ILE A  84 "
            pdb=" C   ILE A  84 "
            pdb=" CB  ILE A  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.29e-01
  chirality pdb=" CA  VAL H  92 "
            pdb=" N   VAL H  92 "
            pdb=" C   VAL H  92 "
            pdb=" CB  VAL H  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.25e-01
  chirality pdb=" CA  VAL A 202 "
            pdb=" N   VAL A 202 "
            pdb=" C   VAL A 202 "
            pdb=" CB  VAL A 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.14e-01
  ... (remaining 958 not shown)

  Planarity restraints: 1076
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 203 "   -0.028 5.00e-02 4.00e+02   4.26e-02 2.91e+00
        pdb=" N   PRO A 204 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 204 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 204 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 154 "   -0.024 5.00e-02 4.00e+02   3.57e-02 2.04e+00
        pdb=" N   PRO H 155 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO H 155 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO H 155 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 202 "    0.023 5.00e-02 4.00e+02   3.46e-02 1.91e+00
        pdb=" N   PRO A 203 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO A 203 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 203 "    0.019 5.00e-02 4.00e+02
  ... (remaining 1073 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1045
        2.77 -     3.30: 5445
        3.30 -     3.84: 9764
        3.84 -     4.37: 10329
        4.37 -     4.90: 18705
  Nonbonded interactions: 45288
  Sorted by model distance:
  nonbonded pdb=" OG  SER A  53 "
            pdb=" O   SER A  56 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" OE1 GLN L   6 "
            pdb=" OG1 THR L 101 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   TYR L 185 "
            pdb=" OH  TYR L 191 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" NE2 GLN A  98 "
            pdb=" O   PRO A 101 "
     model   vdw
     2.307 3.120
  nonbonded pdb=" O   PRO A 203 "
            pdb=" OG  SER A 206 "
     model   vdw
     2.310 3.040
  ... (remaining 45283 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             2.670
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.500
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  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:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
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      :  0.002   0.046   6121  Z= 0.098
  Angle     :  0.447   5.334   8368  Z= 0.237
  Chirality :  0.038   0.131    961
  Planarity :  0.003   0.043   1076
  Dihedral  :  9.260  53.399   2014
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.97 (0.27), residues: 804
  helix:  0.90 (0.34), residues: 196
  sheet: -1.81 (0.28), residues: 285
  loop : -2.13 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  34 
 HIS   0.003   0.001   HIS A 216 
 PHE   0.008   0.001   PHE A  83 
 TYR   0.007   0.001   TYR H 103 
 ARG   0.001   0.000   ARG L  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09976 (  286)
  hydrogen bonds       : angle       4.70739 (  792)
  SS BOND              : bond        0.00137 (    8)
  SS BOND              : angle       0.28590 (   16)
  covalent geometry    : bond        0.00200 ( 6113)
  covalent geometry    : angle       0.44690 ( 8352)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.692 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ILE cc_start: 0.9556 (mt) cc_final: 0.9303 (tt)
REVERT: A  215 THR cc_start: 0.9343 (t) cc_final: 0.8963 (m)
REVERT: B  117 ASP cc_start: 0.7363 (p0) cc_final: 0.7141 (p0)
REVERT: B  119 ILE cc_start: 0.9289 (mm) cc_final: 0.9073 (mp)
REVERT: B  162 LEU cc_start: 0.9325 (tp) cc_final: 0.8914 (tt)
REVERT: H   38 LYS cc_start: 0.8842 (tttt) cc_final: 0.8618 (tttm)
REVERT: H  151 TYR cc_start: 0.7248 (p90) cc_final: 0.7014 (p90)
REVERT: L   43 PRO cc_start: 0.7827 (Cg_endo) cc_final: 0.7596 (Cg_exo)
REVERT: L  187 LYS cc_start: 0.9308 (mtpt) cc_final: 0.9077 (mtpp)
REVERT: L  206 LYS cc_start: 0.8210 (mmtt) cc_final: 0.6756 (pttt)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.1826
  time to fit residues: 41.3638
Evaluate side-chains
  91 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 62 optimal weight:    7.9990
   chunk 34 optimal weight:    3.9990
   chunk 21 optimal weight:   20.0000
   chunk 41 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9980
   chunk 64 optimal weight:    0.0070
   chunk 24 optimal weight:   10.0000
   chunk 39 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 74 optimal weight:    9.9990
   overall best weight:    1.4002

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

Flipped N/Q/H residues before XYZ refinement:
A  98 GLN
L 123 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.115108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.082661 restraints weight = 14157.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.085380 restraints weight = 8172.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.087092 restraints weight = 5777.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.2355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   6121  Z= 0.167
  Angle     :  0.564   6.731   8368  Z= 0.285
  Chirality :  0.041   0.142    961
  Planarity :  0.004   0.059   1076
  Dihedral  :  3.514  15.344    865
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.86 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 12.82 %
    Favored  : 85.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.30), residues: 804
  helix:  2.69 (0.35), residues: 182
  sheet: -1.17 (0.31), residues: 277
  loop : -1.71 (0.31), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP L 147 
 HIS   0.006   0.001   HIS A 218 
 PHE   0.016   0.001   PHE L 208 
 TYR   0.011   0.001   TYR L 139 
 ARG   0.002   0.000   ARG A 237 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02583 (  286)
  hydrogen bonds       : angle       3.91237 (  792)
  SS BOND              : bond        0.00163 (    8)
  SS BOND              : angle       0.80013 (   16)
  covalent geometry    : bond        0.00387 ( 6113)
  covalent geometry    : angle       0.56371 ( 8352)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ILE cc_start: 0.9564 (mt) cc_final: 0.9292 (tt)
REVERT: A   90 GLN cc_start: 0.8393 (pp30) cc_final: 0.8110 (pp30)
REVERT: A  215 THR cc_start: 0.9370 (t) cc_final: 0.8971 (m)
REVERT: B  117 ASP cc_start: 0.7139 (p0) cc_final: 0.6917 (p0)
REVERT: B  119 ILE cc_start: 0.9193 (mm) cc_final: 0.8749 (tp)
REVERT: B  162 LEU cc_start: 0.9289 (tp) cc_final: 0.8765 (tt)
REVERT: H  200 TYR cc_start: 0.6827 (m-80) cc_final: 0.6445 (m-80)
REVERT: H  205 ASN cc_start: 0.8125 (t0) cc_final: 0.7370 (t0)
REVERT: L  187 LYS cc_start: 0.9310 (mtpt) cc_final: 0.9062 (mtmm)
REVERT: L  198 GLN cc_start: 0.7959 (mp10) cc_final: 0.7621 (pm20)
REVERT: L  206 LYS cc_start: 0.8259 (mmtt) cc_final: 0.7220 (mttt)
  outliers start: 11
  outliers final: 7
  residues processed: 113
  average time/residue: 0.1745
  time to fit residues: 25.7537
Evaluate side-chains
  91 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 MET
Chi-restraints excluded: chain A residue  232 ASP
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue  177 THR
Chi-restraints excluded: chain L residue  195 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 69 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0270
   chunk 21 optimal weight:   20.0000
   chunk 11 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.1240

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

Flipped N/Q/H residues before XYZ refinement:
** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.114239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.084672 restraints weight = 14267.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.085008 restraints weight = 8370.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.085744 restraints weight = 6403.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.2679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6121  Z= 0.139
  Angle     :  0.531   7.953   8368  Z= 0.265
  Chirality :  0.040   0.145    961
  Planarity :  0.004   0.047   1076
  Dihedral  :  3.487  15.831    865
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.99 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 14.90 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.31), residues: 804
  helix:  3.28 (0.36), residues: 182
  sheet: -0.95 (0.32), residues: 275
  loop : -1.34 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP L 147 
 HIS   0.005   0.001   HIS A 218 
 PHE   0.010   0.001   PHE A  83 
 TYR   0.010   0.001   TYR A  95 
 ARG   0.003   0.001   ARG L  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02397 (  286)
  hydrogen bonds       : angle       3.84146 (  792)
  SS BOND              : bond        0.00129 (    8)
  SS BOND              : angle       0.63024 (   16)
  covalent geometry    : bond        0.00321 ( 6113)
  covalent geometry    : angle       0.53065 ( 8352)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ILE cc_start: 0.9531 (mt) cc_final: 0.9306 (tt)
REVERT: A  215 THR cc_start: 0.9413 (t) cc_final: 0.9032 (m)
REVERT: B   48 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6587 (tp30)
REVERT: B  117 ASP cc_start: 0.6971 (p0) cc_final: 0.6765 (p0)
REVERT: B  119 ILE cc_start: 0.9163 (mm) cc_final: 0.8766 (tp)
REVERT: B  132 GLN cc_start: 0.8346 (pp30) cc_final: 0.8026 (pp30)
REVERT: B  162 LEU cc_start: 0.9286 (tp) cc_final: 0.8771 (tt)
REVERT: H  200 TYR cc_start: 0.6619 (m-80) cc_final: 0.6298 (m-80)
REVERT: H  205 ASN cc_start: 0.8147 (t0) cc_final: 0.7623 (t0)
REVERT: H  207 LYS cc_start: 0.8527 (mmmt) cc_final: 0.8299 (mmmt)
REVERT: L  122 GLU cc_start: 0.8227 (tt0) cc_final: 0.7985 (pt0)
REVERT: L  198 GLN cc_start: 0.7885 (mp10) cc_final: 0.7649 (pm20)
REVERT: L  206 LYS cc_start: 0.8229 (mmtt) cc_final: 0.7152 (mttt)
  outliers start: 14
  outliers final: 8
  residues processed: 104
  average time/residue: 0.1744
  time to fit residues: 23.8326
Evaluate side-chains
  92 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  141 ASN
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue  178 SER
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue  177 THR
Chi-restraints excluded: chain L residue  179 THR
Chi-restraints excluded: chain L residue  195 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 1 optimal weight:    8.9990
   chunk 49 optimal weight:    0.8980
   chunk 2 optimal weight:    7.9990
   chunk 0 optimal weight:    6.9990
   chunk 44 optimal weight:    0.0470
   chunk 63 optimal weight:    4.9990
   chunk 19 optimal weight:    0.0370
   chunk 68 optimal weight:    0.2980
   chunk 7 optimal weight:    7.9990
   chunk 13 optimal weight:    3.9990
   chunk 30 optimal weight:   40.0000
   overall best weight:    1.0558

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

Flipped N/Q/H residues before XYZ refinement:
L  36 GLN
** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.115192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.082082 restraints weight = 14707.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.085052 restraints weight = 7868.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.086858 restraints weight = 5365.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.2979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6121  Z= 0.132
  Angle     :  0.514   7.810   8368  Z= 0.259
  Chirality :  0.040   0.147    961
  Planarity :  0.004   0.046   1076
  Dihedral  :  3.499  15.631    865
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.11 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 14.90 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.31), residues: 804
  helix:  3.70 (0.35), residues: 182
  sheet: -0.80 (0.32), residues: 277
  loop : -1.20 (0.33), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP L 147 
 HIS   0.005   0.001   HIS A 218 
 PHE   0.010   0.001   PHE A  83 
 TYR   0.016   0.001   TYR A  95 
 ARG   0.002   0.000   ARG L  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02250 (  286)
  hydrogen bonds       : angle       3.74614 (  792)
  SS BOND              : bond        0.00187 (    8)
  SS BOND              : angle       0.64613 (   16)
  covalent geometry    : bond        0.00307 ( 6113)
  covalent geometry    : angle       0.51385 ( 8352)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.669 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ILE cc_start: 0.9526 (mt) cc_final: 0.9307 (tt)
REVERT: A  103 SER cc_start: 0.8901 (m) cc_final: 0.8673 (t)
REVERT: A  215 THR cc_start: 0.9386 (t) cc_final: 0.8987 (m)
REVERT: B   48 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6576 (tp30)
REVERT: B  117 ASP cc_start: 0.7213 (p0) cc_final: 0.6979 (p0)
REVERT: B  119 ILE cc_start: 0.9195 (mm) cc_final: 0.8816 (tp)
REVERT: B  162 LEU cc_start: 0.9240 (tp) cc_final: 0.8721 (tt)
REVERT: H  150 ASP cc_start: 0.8505 (m-30) cc_final: 0.8248 (m-30)
REVERT: H  200 TYR cc_start: 0.6677 (m-80) cc_final: 0.6124 (m-80)
REVERT: H  205 ASN cc_start: 0.8210 (t0) cc_final: 0.7558 (t0)
REVERT: L  104 GLU cc_start: 0.7998 (pt0) cc_final: 0.7742 (pt0)
REVERT: L  187 LYS cc_start: 0.9312 (mtpt) cc_final: 0.8880 (mttp)
REVERT: L  206 LYS cc_start: 0.8294 (mmtt) cc_final: 0.7245 (mttt)
  outliers start: 13
  outliers final: 8
  residues processed: 105
  average time/residue: 0.1722
  time to fit residues: 23.9368
Evaluate side-chains
  90 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  232 ASP
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue  187 VAL
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue  179 THR
Chi-restraints excluded: chain L residue  195 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 55 optimal weight:   10.0000
   chunk 76 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 81 optimal weight:    0.2980
   chunk 50 optimal weight:    4.9990
   chunk 54 optimal weight:    8.9990
   chunk 12 optimal weight:    0.0370
   chunk 66 optimal weight:    2.9990
   chunk 34 optimal weight:    8.9990
   chunk 64 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   overall best weight:    1.0262

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

Flipped N/Q/H residues before XYZ refinement:
L 123 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.113486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.084364 restraints weight = 14281.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.084309 restraints weight = 8373.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.085446 restraints weight = 6428.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.3162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   6121  Z= 0.131
  Angle     :  0.512   5.269   8368  Z= 0.259
  Chirality :  0.040   0.146    961
  Planarity :  0.004   0.045   1076
  Dihedral  :  3.538  15.455    865
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.74 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 15.60 %
    Favored  : 82.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.31), residues: 804
  helix:  3.93 (0.34), residues: 182
  sheet: -0.69 (0.32), residues: 287
  loop : -1.09 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP L 147 
 HIS   0.007   0.001   HIS L 197 
 PHE   0.010   0.001   PHE A  83 
 TYR   0.015   0.001   TYR A  95 
 ARG   0.001   0.000   ARG L  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02235 (  286)
  hydrogen bonds       : angle       3.74734 (  792)
  SS BOND              : bond        0.00132 (    8)
  SS BOND              : angle       0.68197 (   16)
  covalent geometry    : bond        0.00309 ( 6113)
  covalent geometry    : angle       0.51180 ( 8352)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.560 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  215 THR cc_start: 0.9398 (t) cc_final: 0.9011 (m)
REVERT: B  117 ASP cc_start: 0.7106 (p0) cc_final: 0.6861 (p0)
REVERT: B  119 ILE cc_start: 0.9169 (mm) cc_final: 0.8890 (tp)
REVERT: B  132 GLN cc_start: 0.8487 (pp30) cc_final: 0.8226 (pp30)
REVERT: B  162 LEU cc_start: 0.9267 (tp) cc_final: 0.8715 (tt)
REVERT: H  150 ASP cc_start: 0.8485 (m-30) cc_final: 0.8248 (m-30)
REVERT: H  200 TYR cc_start: 0.6662 (m-80) cc_final: 0.6153 (m-80)
REVERT: H  205 ASN cc_start: 0.8181 (t0) cc_final: 0.7766 (t0)
REVERT: H  214 ASP cc_start: 0.8665 (m-30) cc_final: 0.7749 (t0)
REVERT: L   11 MET cc_start: 0.8362 (ppp) cc_final: 0.7674 (ppp)
REVERT: L   32 MET cc_start: 0.7939 (mmt) cc_final: 0.7663 (mtp)
REVERT: L  104 GLU cc_start: 0.7977 (pt0) cc_final: 0.7471 (pt0)
REVERT: L  122 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7906 (pt0)
REVERT: L  206 LYS cc_start: 0.8242 (mmtt) cc_final: 0.7176 (mttt)
  outliers start: 13
  outliers final: 8
  residues processed: 100
  average time/residue: 0.1883
  time to fit residues: 25.9883
Evaluate side-chains
  90 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 81
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  232 ASP
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue  122 GLU
Chi-restraints excluded: chain L residue  190 VAL
Chi-restraints excluded: chain L residue  193 CYS
Chi-restraints excluded: chain L residue  195 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 67 optimal weight:    0.8980
   chunk 1 optimal weight:    9.9990
   chunk 36 optimal weight:   10.0000
   chunk 76 optimal weight:    0.0770
   chunk 62 optimal weight:    9.9990
   chunk 7 optimal weight:    6.9990
   chunk 61 optimal weight:   10.0000
   chunk 44 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 77 optimal weight:    5.9990
   overall best weight:    0.7742

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.114559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.082315 restraints weight = 14425.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.085051 restraints weight = 8193.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.086674 restraints weight = 5765.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.3297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6121  Z= 0.114
  Angle     :  0.525   8.290   8368  Z= 0.263
  Chirality :  0.041   0.290    961
  Planarity :  0.004   0.046   1076
  Dihedral  :  3.453  15.459    865
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.24 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 15.94 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.31), residues: 804
  helix:  3.96 (0.34), residues: 182
  sheet: -0.59 (0.31), residues: 288
  loop : -0.97 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP L 147 
 HIS   0.006   0.001   HIS L 197 
 PHE   0.009   0.001   PHE A  83 
 TYR   0.010   0.001   TYR A  95 
 ARG   0.001   0.000   ARG L  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02181 (  286)
  hydrogen bonds       : angle       3.73038 (  792)
  SS BOND              : bond        0.00226 (    8)
  SS BOND              : angle       0.60561 (   16)
  covalent geometry    : bond        0.00269 ( 6113)
  covalent geometry    : angle       0.52488 ( 8352)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.636 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  215 THR cc_start: 0.9362 (t) cc_final: 0.8979 (m)
REVERT: B  117 ASP cc_start: 0.7239 (p0) cc_final: 0.6961 (p0)
REVERT: B  132 GLN cc_start: 0.8477 (pp30) cc_final: 0.8252 (pp30)
REVERT: B  162 LEU cc_start: 0.9256 (tp) cc_final: 0.8690 (tt)
REVERT: H  150 ASP cc_start: 0.8545 (m-30) cc_final: 0.8321 (m-30)
REVERT: H  200 TYR cc_start: 0.6660 (m-80) cc_final: 0.6107 (m-80)
REVERT: H  205 ASN cc_start: 0.8219 (t0) cc_final: 0.7318 (t0)
REVERT: L  122 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7979 (pt0)
REVERT: L  182 LYS cc_start: 0.8601 (tppt) cc_final: 0.8048 (tppt)
REVERT: L  206 LYS cc_start: 0.8280 (mmtt) cc_final: 0.7224 (mttt)
  outliers start: 16
  outliers final: 10
  residues processed: 95
  average time/residue: 0.1873
  time to fit residues: 23.8009
Evaluate side-chains
  86 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue  178 SER
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue  122 GLU
Chi-restraints excluded: chain L residue  179 THR
Chi-restraints excluded: chain L residue  193 CYS
Chi-restraints excluded: chain L residue  195 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 74 optimal weight:    7.9990
   chunk 18 optimal weight:    5.9990
   chunk 65 optimal weight:    4.9990
   chunk 61 optimal weight:    9.9990
   chunk 3 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9990
   chunk 13 optimal weight:    8.9990
   chunk 9 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 59 optimal weight:    0.6980
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.112301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.079899 restraints weight = 14798.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.082518 restraints weight = 8170.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.084191 restraints weight = 5702.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.3607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   6121  Z= 0.213
  Angle     :  0.597   7.531   8368  Z= 0.300
  Chirality :  0.043   0.299    961
  Planarity :  0.004   0.041   1076
  Dihedral  :  3.853  17.991    865
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.73 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 17.85 %
    Favored  : 79.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.31), residues: 804
  helix:  4.02 (0.34), residues: 184
  sheet: -0.75 (0.31), residues: 291
  loop : -1.11 (0.33), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP L 147 
 HIS   0.007   0.001   HIS A 218 
 PHE   0.013   0.001   PHE A  94 
 TYR   0.011   0.001   TYR A  95 
 ARG   0.002   0.000   ARG L 210 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02501 (  286)
  hydrogen bonds       : angle       4.00742 (  792)
  SS BOND              : bond        0.00198 (    8)
  SS BOND              : angle       0.66126 (   16)
  covalent geometry    : bond        0.00491 ( 6113)
  covalent geometry    : angle       0.59655 ( 8352)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.621 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   48 GLU cc_start: 0.7411 (tp30) cc_final: 0.6842 (mm-30)
REVERT: B  117 ASP cc_start: 0.7361 (p0) cc_final: 0.7077 (p0)
REVERT: B  162 LEU cc_start: 0.9275 (tp) cc_final: 0.8706 (tt)
REVERT: H  150 ASP cc_start: 0.8721 (m-30) cc_final: 0.8496 (m-30)
REVERT: H  200 TYR cc_start: 0.6656 (m-80) cc_final: 0.6074 (m-80)
REVERT: H  205 ASN cc_start: 0.8134 (t0) cc_final: 0.7682 (t0)
REVERT: H  214 ASP cc_start: 0.8569 (m-30) cc_final: 0.7789 (t0)
REVERT: L  104 GLU cc_start: 0.7999 (pt0) cc_final: 0.7756 (pt0)
REVERT: L  121 ASP cc_start: 0.8673 (m-30) cc_final: 0.7938 (p0)
REVERT: L  182 LYS cc_start: 0.8610 (tppt) cc_final: 0.8148 (tppt)
REVERT: L  206 LYS cc_start: 0.8317 (mmtt) cc_final: 0.7219 (mttt)
  outliers start: 17
  outliers final: 14
  residues processed: 99
  average time/residue: 0.1646
  time to fit residues: 21.9067
Evaluate side-chains
  93 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  232 ASP
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue  178 SER
Chi-restraints excluded: chain H residue  187 VAL
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue  177 THR
Chi-restraints excluded: chain L residue  193 CYS
Chi-restraints excluded: chain L residue  195 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 60 optimal weight:    9.9990
   chunk 43 optimal weight:    0.8980
   chunk 28 optimal weight:   20.0000
   chunk 68 optimal weight:    3.9990
   chunk 62 optimal weight:    7.9990
   chunk 17 optimal weight:    7.9990
   chunk 5 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 30 optimal weight:   20.0000
   chunk 61 optimal weight:   20.0000
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 198 GLN
** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.110767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.081702 restraints weight = 14466.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.081823 restraints weight = 8041.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.082151 restraints weight = 6574.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.3808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   6121  Z= 0.207
  Angle     :  0.611   8.457   8368  Z= 0.307
  Chirality :  0.043   0.289    961
  Planarity :  0.004   0.040   1076
  Dihedral  :  3.954  17.892    865
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.73 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 18.20 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.31), residues: 804
  helix:  3.94 (0.34), residues: 184
  sheet: -0.81 (0.31), residues: 290
  loop : -1.15 (0.33), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP L 147 
 HIS   0.007   0.001   HIS A 218 
 PHE   0.012   0.001   PHE A  83 
 TYR   0.009   0.002   TYR A  95 
 ARG   0.002   0.000   ARG L 210 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02600 (  286)
  hydrogen bonds       : angle       4.10855 (  792)
  SS BOND              : bond        0.00198 (    8)
  SS BOND              : angle       0.70812 (   16)
  covalent geometry    : bond        0.00479 ( 6113)
  covalent geometry    : angle       0.61096 ( 8352)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 0.623 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7807 (mtp)
REVERT: B   48 GLU cc_start: 0.7444 (tp30) cc_final: 0.7040 (mm-30)
REVERT: B  117 ASP cc_start: 0.7322 (p0) cc_final: 0.6965 (p0)
REVERT: B  162 LEU cc_start: 0.9323 (tp) cc_final: 0.8737 (tt)
REVERT: H  106 MET cc_start: 0.7204 (mtt) cc_final: 0.6994 (mtt)
REVERT: H  150 ASP cc_start: 0.8635 (m-30) cc_final: 0.8402 (m-30)
REVERT: H  198 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7344 (tm-30)
REVERT: H  205 ASN cc_start: 0.8186 (t0) cc_final: 0.7819 (t0)
REVERT: H  214 ASP cc_start: 0.8444 (m-30) cc_final: 0.7680 (t0)
REVERT: L  121 ASP cc_start: 0.8588 (m-30) cc_final: 0.7881 (p0)
REVERT: L  187 LYS cc_start: 0.9236 (mttp) cc_final: 0.8938 (mttp)
REVERT: L  206 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7092 (mttt)
  outliers start: 19
  outliers final: 13
  residues processed: 99
  average time/residue: 0.1600
  time to fit residues: 21.6774
Evaluate side-chains
  94 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  232 ASP
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue  178 SER
Chi-restraints excluded: chain H residue  187 VAL
Chi-restraints excluded: chain H residue  198 GLN
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue  193 CYS
Chi-restraints excluded: chain L residue  195 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 1 optimal weight:    7.9990
   chunk 29 optimal weight:    8.9990
   chunk 39 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   chunk 77 optimal weight:    9.9990
   chunk 19 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.109474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.079893 restraints weight = 14735.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.079935 restraints weight = 8225.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.080762 restraints weight = 6743.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.4046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.080   6121  Z= 0.265
  Angle     :  0.660   8.770   8368  Z= 0.331
  Chirality :  0.044   0.290    961
  Planarity :  0.004   0.039   1076
  Dihedral  :  4.228  19.731    865
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.35 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 18.37 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.31), residues: 804
  helix:  3.84 (0.35), residues: 190
  sheet: -0.90 (0.31), residues: 290
  loop : -1.26 (0.33), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP L 147 
 HIS   0.009   0.001   HIS A 218 
 PHE   0.014   0.002   PHE A  94 
 TYR   0.026   0.002   TYR A  95 
 ARG   0.004   0.000   ARG L  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02737 (  286)
  hydrogen bonds       : angle       4.28909 (  792)
  SS BOND              : bond        0.00259 (    8)
  SS BOND              : angle       0.71130 (   16)
  covalent geometry    : bond        0.00611 ( 6113)
  covalent geometry    : angle       0.66015 ( 8352)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 0.709 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  246 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8178 (tt)
REVERT: B   48 GLU cc_start: 0.7576 (tp30) cc_final: 0.7324 (mm-30)
REVERT: B  117 ASP cc_start: 0.7415 (p0) cc_final: 0.7026 (p0)
REVERT: B  119 ILE cc_start: 0.9330 (mp) cc_final: 0.8940 (tp)
REVERT: B  132 GLN cc_start: 0.8381 (pp30) cc_final: 0.8064 (pp30)
REVERT: B  162 LEU cc_start: 0.9295 (tp) cc_final: 0.8709 (tt)
REVERT: H  106 MET cc_start: 0.7384 (mtt) cc_final: 0.7159 (mtt)
REVERT: H  150 ASP cc_start: 0.8843 (m-30) cc_final: 0.8635 (m-30)
REVERT: H  200 TYR cc_start: 0.6808 (m-80) cc_final: 0.6232 (m-80)
REVERT: H  205 ASN cc_start: 0.8161 (t0) cc_final: 0.7783 (t0)
REVERT: H  214 ASP cc_start: 0.8477 (m-30) cc_final: 0.7697 (t0)
REVERT: L  121 ASP cc_start: 0.8675 (m-30) cc_final: 0.7999 (p0)
REVERT: L  182 LYS cc_start: 0.8728 (tppt) cc_final: 0.8228 (tppt)
REVERT: L  206 LYS cc_start: 0.8279 (mmtt) cc_final: 0.7133 (mttt)
  outliers start: 18
  outliers final: 17
  residues processed: 99
  average time/residue: 0.1821
  time to fit residues: 24.5152
Evaluate side-chains
  95 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 77
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  232 ASP
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue  146 CYS
Chi-restraints excluded: chain H residue  178 SER
Chi-restraints excluded: chain H residue  187 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   47 ILE
Chi-restraints excluded: chain L residue  193 CYS
Chi-restraints excluded: chain L residue  195 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 43 optimal weight:    8.9990
   chunk 39 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9990
   chunk 30 optimal weight:   30.0000
   chunk 34 optimal weight:    8.9990
   chunk 67 optimal weight:    0.9990
   chunk 29 optimal weight:   40.0000
   chunk 28 optimal weight:    9.9990
   chunk 44 optimal weight:    0.8980
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 198 GLN
** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.111488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.079427 restraints weight = 14558.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.082020 restraints weight = 8318.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.083590 restraints weight = 5868.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.4023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6121  Z= 0.147
  Angle     :  0.594   7.650   8368  Z= 0.299
  Chirality :  0.042   0.289    961
  Planarity :  0.004   0.040   1076
  Dihedral  :  3.877  18.103    865
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.11 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 19.06 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.31), residues: 804
  helix:  4.07 (0.34), residues: 184
  sheet: -0.91 (0.30), residues: 299
  loop : -1.09 (0.34), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP L 147 
 HIS   0.005   0.001   HIS A 216 
 PHE   0.010   0.001   PHE A  83 
 TYR   0.021   0.001   TYR A  95 
 ARG   0.002   0.000   ARG L  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02369 (  286)
  hydrogen bonds       : angle       4.07710 (  792)
  SS BOND              : bond        0.00148 (    8)
  SS BOND              : angle       0.74616 (   16)
  covalent geometry    : bond        0.00348 ( 6113)
  covalent geometry    : angle       0.59373 ( 8352)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.646 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  246 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8041 (tt)
REVERT: B   48 GLU cc_start: 0.7554 (tp30) cc_final: 0.7223 (mm-30)
REVERT: B  117 ASP cc_start: 0.7447 (p0) cc_final: 0.7033 (p0)
REVERT: B  119 ILE cc_start: 0.9326 (mp) cc_final: 0.8988 (tp)
REVERT: B  132 GLN cc_start: 0.8398 (pp30) cc_final: 0.8064 (pp30)
REVERT: B  162 LEU cc_start: 0.9236 (tp) cc_final: 0.8646 (tt)
REVERT: H   10 GLU cc_start: 0.7888 (tp30) cc_final: 0.7670 (mm-30)
REVERT: H  106 MET cc_start: 0.7114 (mtt) cc_final: 0.6882 (mtt)
REVERT: H  150 ASP cc_start: 0.8731 (m-30) cc_final: 0.8490 (m-30)
REVERT: H  160 TRP cc_start: 0.7619 (m100) cc_final: 0.6920 (m100)
REVERT: H  198 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.6884 (tm-30)
REVERT: H  200 TYR cc_start: 0.6722 (m-80) cc_final: 0.5822 (m-80)
REVERT: H  205 ASN cc_start: 0.8104 (t0) cc_final: 0.7739 (t0)
REVERT: H  214 ASP cc_start: 0.8436 (m-30) cc_final: 0.7637 (t0)
REVERT: L   11 MET cc_start: 0.8403 (ppp) cc_final: 0.7296 (ppp)
REVERT: L  121 ASP cc_start: 0.8658 (m-30) cc_final: 0.7913 (p0)
REVERT: L  122 GLU cc_start: 0.8142 (pt0) cc_final: 0.7860 (pt0)
REVERT: L  182 LYS cc_start: 0.8725 (tppt) cc_final: 0.8219 (tppt)
REVERT: L  206 LYS cc_start: 0.8309 (mmtt) cc_final: 0.7183 (mttt)
  outliers start: 15
  outliers final: 12
  residues processed: 99
  average time/residue: 0.1732
  time to fit residues: 23.3926
Evaluate side-chains
  96 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue  146 CYS
Chi-restraints excluded: chain H residue  178 SER
Chi-restraints excluded: chain H residue  187 VAL
Chi-restraints excluded: chain H residue  198 GLN
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue  193 CYS
Chi-restraints excluded: chain L residue  195 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 73 optimal weight:    9.9990
   chunk 22 optimal weight:    7.9990
   chunk 34 optimal weight:   10.0000
   chunk 66 optimal weight:    0.9980
   chunk 63 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 54 optimal weight:    9.9990
   chunk 57 optimal weight:    0.0980
   chunk 10 optimal weight:    5.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 198 GLN
** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.111565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.079402 restraints weight = 14635.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.082018 restraints weight = 8328.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.083638 restraints weight = 5876.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.4034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.092   6121  Z= 0.171
  Angle     :  1.029  59.188   8368  Z= 0.584
  Chirality :  0.045   0.503    961
  Planarity :  0.004   0.040   1076
  Dihedral  :  3.906  18.068    865
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.23 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 19.06 %
    Favored  : 77.82 %
  Cbeta Deviations :  0.13 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.31), residues: 804
  helix:  4.08 (0.34), residues: 184
  sheet: -0.90 (0.30), residues: 299
  loop : -1.09 (0.34), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP L 147 
 HIS   0.004   0.001   HIS A 216 
 PHE   0.010   0.001   PHE A  83 
 TYR   0.017   0.001   TYR A  95 
 ARG   0.002   0.000   ARG L  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02363 (  286)
  hydrogen bonds       : angle       4.10500 (  792)
  SS BOND              : bond        0.00133 (    8)
  SS BOND              : angle       0.72744 (   16)
  covalent geometry    : bond        0.00377 ( 6113)
  covalent geometry    : angle       1.02924 ( 8352)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2329.55 seconds
wall clock time: 41 minutes 41.32 seconds (2501.32 seconds total)