Starting phenix.real_space_refine
on Wed Sep 17 06:18:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jic_22344/09_2025/7jic_22344.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jic_22344/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jic_22344/09_2025/7jic_22344.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jic_22344/09_2025/7jic_22344.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jic_22344/09_2025/7jic_22344.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jic_22344/09_2025/7jic_22344.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 9, 'GLN:plan1': 3, 'ASP:plan': 2, 'ARG:plan': 5, 'TYR:plan': 1, 'PHE:plan': 1, 'HIS:plan': 1}
          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, 'PHE:plan': 11, 'ASN:plan1': 3, 'TRP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 2}
          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: {'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 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: {'ARG:plan': 3, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 19
  Time building chain proxies: 1.40, per 1000 atoms: 0.23
  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: 0.49
  Conformation dependent library (CDL) restraints added in 391.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.25
  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: 0.88

  Time building geometry restraints manager: 0.63 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:             2.690
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.310
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.530
-------------------------------------------------------------------------------
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 : 5.48
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.97 (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
 ARG   0.001   0.000   ARG L  18 
 TYR   0.007   0.001   TYR H 103 
 PHE   0.008   0.001   PHE A  83 
 TRP   0.006   0.001   TRP B  34 
 HIS   0.003   0.001   HIS A 216 

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

*********************** 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  : 0.159 
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: 0.0787
  time to fit residues: 18.0937
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  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    8.9990
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    9.9990
   overall best weight:    2.4584

-------------------------------------------------------------------------------
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 = 0.3920 r_free = 0.3920 target = 0.112386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.079148 restraints weight = 14575.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.081747 restraints weight = 8416.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.083357 restraints weight = 5991.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.084538 restraints weight = 4838.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.085123 restraints weight = 4182.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.084   6121  Z= 0.263
  Angle     :  0.639   7.008   8368  Z= 0.325
  Chirality :  0.043   0.146    961
  Planarity :  0.004   0.054   1076
  Dihedral  :  3.994  16.756    865
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.23 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 13.86 %
    Favored  : 83.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.96 (0.30), residues: 804
  helix:  2.56 (0.36), residues: 187
  sheet: -1.33 (0.31), residues: 280
  loop : -1.86 (0.31), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 237 
 TYR   0.015   0.002   TYR L 139 
 PHE   0.017   0.002   PHE A  94 
 TRP   0.014   0.002   TRP H 109 
 HIS   0.011   0.002   HIS A 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00604 ( 6113)
  covalent geometry    : angle       0.63874 ( 8352)
  SS BOND              : bond        0.00306 (    8)
  SS BOND              : angle       0.80084 (   16)
  hydrogen bonds       : bond        0.02871 (  286)
  hydrogen bonds       : angle       4.16228 (  792)

*********************** 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
  113 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 MET cc_start: 0.8103 (mpp) cc_final: 0.7898 (mtt)
REVERT: A   80 ILE cc_start: 0.9552 (mt) cc_final: 0.9284 (tt)
REVERT: A   90 GLN cc_start: 0.8554 (pp30) cc_final: 0.8217 (pp30)
REVERT: A  103 SER cc_start: 0.8817 (m) cc_final: 0.8562 (t)
REVERT: B  117 ASP cc_start: 0.7144 (p0) cc_final: 0.6922 (p0)
REVERT: B  119 ILE cc_start: 0.9204 (mm) cc_final: 0.8811 (tp)
REVERT: B  162 LEU cc_start: 0.9325 (tp) cc_final: 0.8787 (tt)
REVERT: H  200 TYR cc_start: 0.6866 (m-80) cc_final: 0.6640 (m-80)
REVERT: H  214 ASP cc_start: 0.8637 (m-30) cc_final: 0.7792 (t0)
REVERT: L   89 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8152 (tm-30)
REVERT: L  104 GLU cc_start: 0.7963 (pt0) cc_final: 0.7750 (pt0)
REVERT: L  187 LYS cc_start: 0.9301 (mtpt) cc_final: 0.9034 (mtmm)
REVERT: L  198 GLN cc_start: 0.7889 (mp10) cc_final: 0.7532 (pm20)
REVERT: L  206 LYS cc_start: 0.8260 (mmtt) cc_final: 0.7183 (mttt)
  outliers start: 13
  outliers final: 7
  residues processed: 109
  average time/residue: 0.0731
  time to fit residues: 10.5122
Evaluate side-chains
  92 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  232 ASP
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  179 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 36 optimal weight:    6.9990
   chunk 79 optimal weight:    7.9990
   chunk 55 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 28 optimal weight:   10.0000
   chunk 77 optimal weight:    9.9990
   chunk 49 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 32 optimal weight:    9.9990
   chunk 81 optimal weight:    4.9990
   overall best weight:    3.5788

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.108659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.079002 restraints weight = 14840.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.078563 restraints weight = 8500.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.079062 restraints weight = 7134.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.079547 restraints weight = 6905.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.079826 restraints weight = 5843.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.3643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.093   6121  Z= 0.361
  Angle     :  0.725   9.539   8368  Z= 0.368
  Chirality :  0.045   0.160    961
  Planarity :  0.004   0.039   1076
  Dihedral  :  4.730  21.062    865
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.72 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 16.29 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.60 (0.31), residues: 804
  helix:  3.27 (0.36), residues: 184
  sheet: -1.28 (0.31), residues: 286
  loop : -1.70 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L 210 
 TYR   0.018   0.002   TYR H  93 
 PHE   0.018   0.002   PHE A  94 
 TRP   0.017   0.002   TRP H 109 
 HIS   0.013   0.002   HIS A 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00821 ( 6113)
  covalent geometry    : angle       0.72481 ( 8352)
  SS BOND              : bond        0.00454 (    8)
  SS BOND              : angle       0.80533 (   16)
  hydrogen bonds       : bond        0.03321 (  286)
  hydrogen bonds       : angle       4.67105 (  792)

*********************** 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
  112 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   48 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6682 (tp30)
REVERT: B  117 ASP cc_start: 0.7342 (p0) cc_final: 0.7063 (p0)
REVERT: B  119 ILE cc_start: 0.9149 (mm) cc_final: 0.8868 (tp)
REVERT: B  132 GLN cc_start: 0.8391 (pp30) cc_final: 0.8113 (pp30)
REVERT: B  162 LEU cc_start: 0.9388 (tp) cc_final: 0.8837 (tt)
REVERT: H  181 LEU cc_start: 0.8301 (mt) cc_final: 0.7964 (mm)
REVERT: H  198 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7622 (tm-30)
REVERT: H  214 ASP cc_start: 0.8557 (m-30) cc_final: 0.7789 (t0)
REVERT: L   11 MET cc_start: 0.8550 (ppp) cc_final: 0.8180 (ppp)
REVERT: L   77 MET cc_start: 0.6645 (tpt) cc_final: 0.6370 (tpt)
REVERT: L  178 LEU cc_start: 0.8393 (tp) cc_final: 0.8147 (tt)
REVERT: L  187 LYS cc_start: 0.9342 (mtpt) cc_final: 0.9072 (mtmm)
REVERT: L  198 GLN cc_start: 0.7735 (mp10) cc_final: 0.7497 (pm20)
REVERT: L  206 LYS cc_start: 0.8205 (mmtt) cc_final: 0.7062 (mttt)
  outliers start: 23
  outliers final: 17
  residues processed: 109
  average time/residue: 0.0776
  time to fit residues: 11.2242
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  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  187 ASP
Chi-restraints excluded: chain A residue  232 ASP
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  141 ASN
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 H residue  198 GLN
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   95 TYR
Chi-restraints excluded: chain L residue  177 THR
Chi-restraints excluded: chain L residue  179 THR
Chi-restraints excluded: chain L residue  190 VAL
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 55 optimal weight:    9.9990
   chunk 81 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 26 optimal weight:    8.9990
   chunk 37 optimal weight:    3.9990
   chunk 74 optimal weight:   10.0000
   chunk 35 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 73 optimal weight:    5.9990
   chunk 57 optimal weight:    8.9990
   chunk 20 optimal weight:   10.0000
   overall best weight:    1.5782

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

Flipped N/Q/H residues before XYZ refinement:
** L  36 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 = 0.3891 r_free = 0.3891 target = 0.111822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.078131 restraints weight = 14529.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.080873 restraints weight = 7964.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.082621 restraints weight = 5532.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.083765 restraints weight = 4407.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.084363 restraints weight = 3813.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.3624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   6121  Z= 0.181
  Angle     :  0.576   5.867   8368  Z= 0.293
  Chirality :  0.042   0.161    961
  Planarity :  0.004   0.040   1076
  Dihedral  :  4.227  18.849    865
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.86 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 16.81 %
    Favored  : 79.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.28 (0.31), residues: 804
  helix:  3.81 (0.35), residues: 183
  sheet: -1.16 (0.31), residues: 290
  loop : -1.58 (0.32), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  18 
 TYR   0.019   0.001   TYR A  95 
 PHE   0.011   0.001   PHE A  83 
 TRP   0.010   0.001   TRP L 147 
 HIS   0.005   0.001   HIS A 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 6113)
  covalent geometry    : angle       0.57522 ( 8352)
  SS BOND              : bond        0.00215 (    8)
  SS BOND              : angle       0.76654 (   16)
  hydrogen bonds       : bond        0.02676 (  286)
  hydrogen bonds       : angle       4.28632 (  792)

*********************** 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
  110 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  216 HIS cc_start: 0.8952 (OUTLIER) cc_final: 0.8196 (t70)
REVERT: B  117 ASP cc_start: 0.7405 (p0) cc_final: 0.7109 (p0)
REVERT: B  119 ILE cc_start: 0.9195 (mm) cc_final: 0.8969 (tp)
REVERT: B  162 LEU cc_start: 0.9280 (tp) cc_final: 0.8722 (tt)
REVERT: H  181 LEU cc_start: 0.8327 (mt) cc_final: 0.7960 (mm)
REVERT: H  200 TYR cc_start: 0.6419 (m-80) cc_final: 0.6015 (m-80)
REVERT: H  214 ASP cc_start: 0.8538 (m-30) cc_final: 0.7738 (t0)
REVERT: L   11 MET cc_start: 0.8409 (ppp) cc_final: 0.8000 (ppp)
REVERT: L  104 GLU cc_start: 0.8050 (pt0) cc_final: 0.7744 (pt0)
REVERT: L  182 LYS cc_start: 0.8702 (tppt) cc_final: 0.8249 (tppt)
REVERT: L  206 LYS cc_start: 0.8247 (mmtt) cc_final: 0.7145 (mttt)
  outliers start: 19
  outliers final: 11
  residues processed: 109
  average time/residue: 0.0798
  time to fit residues: 11.5174
Evaluate side-chains
  93 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 HIS
Chi-restraints excluded: chain A residue  232 ASP
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  141 ASN
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  195 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   chunk 21 optimal weight:   30.0000
   chunk 25 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 78 optimal weight:    7.9990
   chunk 4 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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  36 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 = 0.3917 r_free = 0.3917 target = 0.111921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.079950 restraints weight = 14671.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.082538 restraints weight = 8300.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.084180 restraints weight = 5857.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.085283 restraints weight = 4682.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.085854 restraints weight = 4064.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.3663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6121  Z= 0.125
  Angle     :  0.531   5.437   8368  Z= 0.270
  Chirality :  0.041   0.149    961
  Planarity :  0.004   0.043   1076
  Dihedral  :  3.881  17.309    865
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.36 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 16.46 %
    Favored  : 79.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.03 (0.31), residues: 804
  helix:  3.99 (0.34), residues: 183
  sheet: -1.00 (0.31), residues: 291
  loop : -1.30 (0.33), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L  90 
 TYR   0.014   0.001   TYR A  95 
 PHE   0.010   0.001   PHE A  83 
 TRP   0.014   0.001   TRP L 147 
 HIS   0.007   0.001   HIS L 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 6113)
  covalent geometry    : angle       0.53091 ( 8352)
  SS BOND              : bond        0.00195 (    8)
  SS BOND              : angle       0.76078 (   16)
  hydrogen bonds       : bond        0.02514 (  286)
  hydrogen bonds       : angle       4.04669 (  792)

*********************** 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
  114 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7450 (mtp)
REVERT: B  117 ASP cc_start: 0.7294 (p0) cc_final: 0.6920 (p0)
REVERT: B  119 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8938 (tp)
REVERT: B  162 LEU cc_start: 0.9265 (tp) cc_final: 0.8692 (tt)
REVERT: H   38 LYS cc_start: 0.8877 (tttt) cc_final: 0.8658 (tttm)
REVERT: H  181 LEU cc_start: 0.8236 (mt) cc_final: 0.7892 (mm)
REVERT: H  205 ASN cc_start: 0.8354 (t0) cc_final: 0.7858 (t0)
REVERT: H  214 ASP cc_start: 0.8549 (m-30) cc_final: 0.7761 (t0)
REVERT: L   11 MET cc_start: 0.8247 (ppp) cc_final: 0.7915 (ppp)
REVERT: L  104 GLU cc_start: 0.7918 (pt0) cc_final: 0.7603 (pt0)
REVERT: L  121 ASP cc_start: 0.8640 (m-30) cc_final: 0.7913 (p0)
REVERT: L  178 LEU cc_start: 0.8526 (tp) cc_final: 0.8298 (tt)
REVERT: L  206 LYS cc_start: 0.8213 (mmtt) cc_final: 0.7117 (mttt)
  outliers start: 21
  outliers final: 12
  residues processed: 110
  average time/residue: 0.0722
  time to fit residues: 10.5594
Evaluate side-chains
  98 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  141 ASN
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain H residue   71 VAL
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   20 THR
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 78 optimal weight:    7.9990
   chunk 72 optimal weight:    0.3980
   chunk 42 optimal weight:    5.9990
   chunk 29 optimal weight:    8.9990
   chunk 71 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 17 optimal weight:    7.9990
   chunk 43 optimal weight:    4.9990
   chunk 27 optimal weight:   10.0000
   chunk 58 optimal weight:    9.9990
   chunk 75 optimal weight:    3.9990
   overall best weight:    2.2184

-------------------------------------------------------------------------------
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 161 ASN
** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 123 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.109177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.076835 restraints weight = 14720.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.079362 restraints weight = 8506.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.081012 restraints weight = 5998.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.081976 restraints weight = 4834.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.082689 restraints weight = 4223.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.3996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071   6121  Z= 0.232
  Angle     :  0.612   5.787   8368  Z= 0.312
  Chirality :  0.042   0.150    961
  Planarity :  0.004   0.042   1076
  Dihedral  :  4.222  19.234    865
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.73 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 17.68 %
    Favored  : 77.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (0.31), residues: 804
  helix:  3.76 (0.35), residues: 190
  sheet: -0.99 (0.31), residues: 291
  loop : -1.38 (0.33), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  90 
 TYR   0.013   0.002   TYR A  95 
 PHE   0.013   0.001   PHE A  83 
 TRP   0.012   0.001   TRP L 147 
 HIS   0.007   0.002   HIS A 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00535 ( 6113)
  covalent geometry    : angle       0.61193 ( 8352)
  SS BOND              : bond        0.00295 (    8)
  SS BOND              : angle       0.75853 (   16)
  hydrogen bonds       : bond        0.02761 (  286)
  hydrogen bonds       : angle       4.25586 (  792)

*********************** 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
  117 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 89
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7555 (mtp)
REVERT: B   48 GLU cc_start: 0.7435 (tp30) cc_final: 0.6845 (mm-30)
REVERT: B  117 ASP cc_start: 0.7390 (p0) cc_final: 0.7003 (p0)
REVERT: B  119 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8941 (tp)
REVERT: B  162 LEU cc_start: 0.9295 (tp) cc_final: 0.8716 (tt)
REVERT: H  181 LEU cc_start: 0.8394 (mt) cc_final: 0.7927 (mm)
REVERT: H  214 ASP cc_start: 0.8442 (m-30) cc_final: 0.7693 (t0)
REVERT: L   11 MET cc_start: 0.8345 (ppp) cc_final: 0.7932 (ppp)
REVERT: L   89 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8106 (tm-30)
REVERT: L  104 GLU cc_start: 0.8001 (pt0) cc_final: 0.7708 (pt0)
REVERT: L  121 ASP cc_start: 0.8650 (m-30) cc_final: 0.7960 (p0)
REVERT: L  182 LYS cc_start: 0.8656 (tppt) cc_final: 0.8133 (tppt)
REVERT: L  187 LYS cc_start: 0.9203 (mtpt) cc_final: 0.8874 (mttp)
REVERT: L  206 LYS cc_start: 0.8191 (mmtt) cc_final: 0.7078 (mttt)
  outliers start: 28
  outliers final: 19
  residues processed: 113
  average time/residue: 0.0703
  time to fit residues: 10.6912
Evaluate side-chains
  103 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 82
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
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  215 THR
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  232 ASP
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  141 ASN
Chi-restraints excluded: chain B residue  194 ILE
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   71 VAL
Chi-restraints excluded: chain H residue   74 SER
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue  178 SER
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   20 THR
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 39 optimal weight:    6.9990
   chunk 22 optimal weight:    9.9990
   chunk 38 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 50 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 62 optimal weight:   10.0000
   chunk 53 optimal weight:    0.6980
   chunk 28 optimal weight:   20.0000
   chunk 48 optimal weight:    0.9990
   chunk 34 optimal weight:    8.9990
   overall best weight:    1.5384

-------------------------------------------------------------------------------
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 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.111821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.078308 restraints weight = 15011.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.081067 restraints weight = 8225.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.082827 restraints weight = 5704.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.083982 restraints weight = 4505.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.084600 restraints weight = 3894.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.4060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   6121  Z= 0.174
  Angle     :  0.573   6.125   8368  Z= 0.292
  Chirality :  0.041   0.149    961
  Planarity :  0.004   0.042   1076
  Dihedral  :  4.089  18.180    865
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.73 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 19.06 %
    Favored  : 77.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.02 (0.31), residues: 804
  helix:  3.93 (0.35), residues: 184
  sheet: -0.96 (0.31), residues: 291
  loop : -1.34 (0.33), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  90 
 TYR   0.011   0.001   TYR A  95 
 PHE   0.012   0.001   PHE A  83 
 TRP   0.016   0.001   TRP L 147 
 HIS   0.005   0.001   HIS A 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 6113)
  covalent geometry    : angle       0.57305 ( 8352)
  SS BOND              : bond        0.00178 (    8)
  SS BOND              : angle       0.73794 (   16)
  hydrogen bonds       : bond        0.02629 (  286)
  hydrogen bonds       : angle       4.19110 (  792)

*********************** 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
  111 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  246 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8066 (tt)
REVERT: B   48 GLU cc_start: 0.7493 (tp30) cc_final: 0.7087 (mm-30)
REVERT: B  117 ASP cc_start: 0.7370 (p0) cc_final: 0.6978 (p0)
REVERT: B  119 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8953 (tp)
REVERT: B  162 LEU cc_start: 0.9279 (tp) cc_final: 0.8703 (tt)
REVERT: H  181 LEU cc_start: 0.8378 (mt) cc_final: 0.7925 (mm)
REVERT: H  205 ASN cc_start: 0.8300 (t0) cc_final: 0.7953 (t0)
REVERT: H  214 ASP cc_start: 0.8522 (m-30) cc_final: 0.7819 (t0)
REVERT: L   11 MET cc_start: 0.8285 (ppp) cc_final: 0.7878 (ppp)
REVERT: L  104 GLU cc_start: 0.8027 (pt0) cc_final: 0.7719 (pt0)
REVERT: L  121 ASP cc_start: 0.8732 (m-30) cc_final: 0.8009 (p0)
REVERT: L  122 GLU cc_start: 0.8270 (pt0) cc_final: 0.8067 (pt0)
REVERT: L  182 LYS cc_start: 0.8745 (tppt) cc_final: 0.8223 (tppt)
REVERT: L  206 LYS cc_start: 0.8231 (mmtt) cc_final: 0.7113 (mttt)
  outliers start: 20
  outliers final: 14
  residues processed: 109
  average time/residue: 0.0708
  time to fit residues: 10.3979
Evaluate side-chains
  101 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  141 ASN
Chi-restraints excluded: chain B residue  194 ILE
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   71 VAL
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue  178 SER
Chi-restraints excluded: chain L residue    5 THR
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 58 optimal weight:    7.9990
   chunk 12 optimal weight:    0.8980
   chunk 31 optimal weight:   20.0000
   chunk 21 optimal weight:   30.0000
   chunk 44 optimal weight:    0.9980
   chunk 41 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 39 optimal weight:    9.9990
   chunk 59 optimal weight:    0.7980
   overall best weight:    1.3182

-------------------------------------------------------------------------------
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 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.112422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.079074 restraints weight = 14927.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.081854 restraints weight = 8171.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.083641 restraints weight = 5647.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.084724 restraints weight = 4459.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.085513 restraints weight = 3857.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.4131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6121  Z= 0.157
  Angle     :  0.577   9.174   8368  Z= 0.291
  Chirality :  0.041   0.148    961
  Planarity :  0.004   0.043   1076
  Dihedral  :  4.013  18.542    865
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 19.93 %
    Favored  : 76.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.16 (0.31), residues: 804
  helix:  4.08 (0.34), residues: 184
  sheet: -0.88 (0.31), residues: 291
  loop : -1.27 (0.33), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  90 
 TYR   0.010   0.001   TYR H 103 
 PHE   0.013   0.001   PHE H 128 
 TRP   0.024   0.001   TRP L 147 
 HIS   0.004   0.001   HIS A 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 6113)
  covalent geometry    : angle       0.57629 ( 8352)
  SS BOND              : bond        0.00177 (    8)
  SS BOND              : angle       0.70286 (   16)
  hydrogen bonds       : bond        0.02489 (  286)
  hydrogen bonds       : angle       4.11161 (  792)

*********************** 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
  111 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 LYS cc_start: 0.7525 (tppt) cc_final: 0.7167 (tppt)
REVERT: A  187 ASP cc_start: 0.8632 (p0) cc_final: 0.8429 (p0)
REVERT: A  215 THR cc_start: 0.9318 (OUTLIER) cc_final: 0.8860 (m)
REVERT: A  246 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8029 (tt)
REVERT: B   48 GLU cc_start: 0.7547 (tp30) cc_final: 0.7191 (mm-30)
REVERT: B  117 ASP cc_start: 0.7338 (p0) cc_final: 0.6918 (p0)
REVERT: B  132 GLN cc_start: 0.8374 (pp30) cc_final: 0.8035 (pp30)
REVERT: B  162 LEU cc_start: 0.9251 (tp) cc_final: 0.8667 (tt)
REVERT: H   28 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8463 (p)
REVERT: H  181 LEU cc_start: 0.8283 (mt) cc_final: 0.7895 (mm)
REVERT: H  214 ASP cc_start: 0.8508 (m-30) cc_final: 0.7802 (t0)
REVERT: L    5 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8454 (p)
REVERT: L   11 MET cc_start: 0.8270 (ppp) cc_final: 0.7853 (ppp)
REVERT: L  104 GLU cc_start: 0.8030 (pt0) cc_final: 0.7704 (pt0)
REVERT: L  121 ASP cc_start: 0.8700 (m-30) cc_final: 0.7914 (p0)
REVERT: L  122 GLU cc_start: 0.8416 (pt0) cc_final: 0.8179 (pt0)
REVERT: L  182 LYS cc_start: 0.8669 (tppt) cc_final: 0.8122 (tppt)
REVERT: L  187 LYS cc_start: 0.9175 (mttp) cc_final: 0.8864 (mttp)
REVERT: L  206 LYS cc_start: 0.8241 (mmtt) cc_final: 0.7147 (mttt)
  outliers start: 23
  outliers final: 16
  residues processed: 109
  average time/residue: 0.0789
  time to fit residues: 11.4586
Evaluate side-chains
  104 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 84
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  141 ASN
Chi-restraints excluded: chain B residue  194 ILE
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   71 VAL
Chi-restraints excluded: chain H residue   74 SER
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue  178 SER
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   29 VAL
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 80 optimal weight:    5.9990
   chunk 64 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0970
   chunk 41 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 69 optimal weight:    5.9990
   chunk 78 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   overall best weight:    1.6186

-------------------------------------------------------------------------------
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 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.110640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.081045 restraints weight = 14853.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.080719 restraints weight = 8712.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.081145 restraints weight = 7138.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.081672 restraints weight = 6425.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.081852 restraints weight = 5813.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.4244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   6121  Z= 0.182
  Angle     :  0.601   7.825   8368  Z= 0.305
  Chirality :  0.042   0.149    961
  Planarity :  0.004   0.042   1076
  Dihedral  :  4.066  18.378    865
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 20.28 %
    Favored  : 75.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.15 (0.31), residues: 804
  helix:  3.94 (0.35), residues: 190
  sheet: -0.92 (0.31), residues: 291
  loop : -1.27 (0.34), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  90 
 TYR   0.009   0.001   TYR H 103 
 PHE   0.014   0.001   PHE H 128 
 TRP   0.010   0.001   TRP L 147 
 HIS   0.005   0.001   HIS A 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 6113)
  covalent geometry    : angle       0.60056 ( 8352)
  SS BOND              : bond        0.00186 (    8)
  SS BOND              : angle       0.72422 (   16)
  hydrogen bonds       : bond        0.02509 (  286)
  hydrogen bonds       : angle       4.19235 (  792)

*********************** 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
  110 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 87
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 LYS cc_start: 0.7669 (tppt) cc_final: 0.7315 (tppt)
REVERT: A  246 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8037 (tt)
REVERT: B   48 GLU cc_start: 0.7659 (tp30) cc_final: 0.7429 (mm-30)
REVERT: B  117 ASP cc_start: 0.7328 (p0) cc_final: 0.6930 (p0)
REVERT: B  132 GLN cc_start: 0.8476 (pp30) cc_final: 0.8155 (pp30)
REVERT: B  162 LEU cc_start: 0.9304 (tp) cc_final: 0.8721 (tt)
REVERT: H   28 THR cc_start: 0.8699 (OUTLIER) cc_final: 0.8480 (p)
REVERT: H  181 LEU cc_start: 0.8260 (mt) cc_final: 0.7903 (mm)
REVERT: H  205 ASN cc_start: 0.8216 (t0) cc_final: 0.7851 (t0)
REVERT: H  214 ASP cc_start: 0.8545 (m-30) cc_final: 0.7830 (t0)
REVERT: L    5 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8459 (p)
REVERT: L   11 MET cc_start: 0.8330 (ppp) cc_final: 0.7886 (ppp)
REVERT: L  104 GLU cc_start: 0.8053 (pt0) cc_final: 0.7726 (pt0)
REVERT: L  121 ASP cc_start: 0.8772 (m-30) cc_final: 0.8148 (p0)
REVERT: L  122 GLU cc_start: 0.8406 (pt0) cc_final: 0.8198 (pt0)
REVERT: L  182 LYS cc_start: 0.8660 (tppt) cc_final: 0.8232 (tppt)
REVERT: L  206 LYS cc_start: 0.8324 (mmtt) cc_final: 0.7257 (mttt)
  outliers start: 23
  outliers final: 19
  residues processed: 110
  average time/residue: 0.0712
  time to fit residues: 10.5143
Evaluate side-chains
  107 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  141 ASN
Chi-restraints excluded: chain B residue  194 ILE
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   71 VAL
Chi-restraints excluded: chain H residue   74 SER
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue  178 SER
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   29 VAL
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 27 optimal weight:    9.9990
   chunk 17 optimal weight:    7.9990
   chunk 4 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 81 optimal weight:    7.9990
   chunk 63 optimal weight:    0.7980
   chunk 77 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 56 optimal weight:    0.8980
   chunk 73 optimal weight:    0.0270
   chunk 2 optimal weight:    3.9990
   overall best weight:    0.6438

-------------------------------------------------------------------------------
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 = 0.3933 r_free = 0.3933 target = 0.113020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.083576 restraints weight = 14700.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.083088 restraints weight = 9333.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.083771 restraints weight = 7260.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.084353 restraints weight = 6311.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.084480 restraints weight = 5846.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.4202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6121  Z= 0.113
  Angle     :  0.577   9.209   8368  Z= 0.291
  Chirality :  0.041   0.148    961
  Planarity :  0.004   0.044   1076
  Dihedral  :  3.790  17.836    865
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 21.49 %
    Favored  : 75.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.31), residues: 804
  helix:  4.19 (0.34), residues: 184
  sheet: -0.80 (0.31), residues: 294
  loop : -1.06 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  90 
 TYR   0.010   0.001   TYR H 103 
 PHE   0.011   0.001   PHE A  83 
 TRP   0.024   0.001   TRP L 147 
 HIS   0.002   0.001   HIS L  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 6113)
  covalent geometry    : angle       0.57690 ( 8352)
  SS BOND              : bond        0.00172 (    8)
  SS BOND              : angle       0.68658 (   16)
  hydrogen bonds       : bond        0.02301 (  286)
  hydrogen bonds       : angle       3.99001 (  792)

********************** 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
  104 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 LYS cc_start: 0.7691 (tppt) cc_final: 0.7403 (tppt)
REVERT: A  246 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.7995 (tt)
REVERT: B   48 GLU cc_start: 0.7700 (tp30) cc_final: 0.7482 (mm-30)
REVERT: B  117 ASP cc_start: 0.7405 (p0) cc_final: 0.6953 (p0)
REVERT: B  119 ILE cc_start: 0.9360 (mp) cc_final: 0.8974 (tp)
REVERT: B  132 GLN cc_start: 0.8487 (pp30) cc_final: 0.8193 (pp30)
REVERT: B  162 LEU cc_start: 0.9238 (tp) cc_final: 0.8638 (tt)
REVERT: H   28 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8535 (p)
REVERT: H  181 LEU cc_start: 0.8233 (mt) cc_final: 0.7844 (mm)
REVERT: H  205 ASN cc_start: 0.8147 (t0) cc_final: 0.7725 (t0)
REVERT: H  214 ASP cc_start: 0.8570 (m-30) cc_final: 0.7825 (t0)
REVERT: L    5 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8417 (p)
REVERT: L  104 GLU cc_start: 0.7992 (pt0) cc_final: 0.7624 (pt0)
REVERT: L  121 ASP cc_start: 0.8768 (m-30) cc_final: 0.8086 (p0)
REVERT: L  206 LYS cc_start: 0.8328 (mmtt) cc_final: 0.7265 (mttt)
  outliers start: 17
  outliers final: 11
  residues processed: 103
  average time/residue: 0.0727
  time to fit residues: 10.2267
Evaluate side-chains
  95 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  141 ASN
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   71 VAL
Chi-restraints excluded: chain H residue   74 SER
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue  178 SER
Chi-restraints excluded: chain L residue    5 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 69 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9990
   chunk 36 optimal weight:    8.9990
   chunk 18 optimal weight:    0.6980
   chunk 73 optimal weight:    9.9990
   chunk 80 optimal weight:    7.9990
   chunk 78 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    2.7388

-------------------------------------------------------------------------------
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 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.114539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.084477 restraints weight = 14741.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.083950 restraints weight = 8483.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.084647 restraints weight = 6980.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.085134 restraints weight = 6577.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.085463 restraints weight = 5553.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.4534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.068   6121  Z= 0.283
  Angle     :  0.681   8.673   8368  Z= 0.348
  Chirality :  0.044   0.170    961
  Planarity :  0.004   0.045   1076
  Dihedral  :  4.436  19.750    865
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 20.97 %
    Favored  : 75.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.31), residues: 804
  helix:  3.96 (0.34), residues: 190
  sheet: -0.92 (0.31), residues: 291
  loop : -1.30 (0.34), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L 210 
 TYR   0.012   0.002   TYR L  85 
 PHE   0.019   0.002   PHE H 128 
 TRP   0.013   0.002   TRP L 147 
 HIS   0.009   0.001   HIS A 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00649 ( 6113)
  covalent geometry    : angle       0.68080 ( 8352)
  SS BOND              : bond        0.00267 (    8)
  SS BOND              : angle       0.80207 (   16)
  hydrogen bonds       : bond        0.02855 (  286)
  hydrogen bonds       : angle       4.43709 (  792)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1162.58 seconds
wall clock time: 20 minutes 47.18 seconds (1247.18 seconds total)