Starting phenix.real_space_refine
on Wed Sep 17 08:38:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9l3w_62793/09_2025/9l3w_62793.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9l3w_62793/09_2025/9l3w_62793.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9l3w_62793/09_2025/9l3w_62793.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9l3w_62793/09_2025/9l3w_62793.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9l3w_62793/09_2025/9l3w_62793.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9l3w_62793/09_2025/9l3w_62793.map"
  }
  resolution = 3.5
  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=   0.016 sd=   0.071
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      60      5.16       5
     C    4651      2.51       5
     N    1229      2.21       5
     O    1322      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  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: 7262
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1572
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 205, 1572
          Classifications: {'peptide': 205}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 1, 'TRANS': 203}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 94
          Unresolved non-hydrogen angles: 107
          Unresolved non-hydrogen dihedrals: 81
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 3, 'ASP:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 45
    Chain: "B"
      Number of atoms: 2487
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2487
          Classifications: {'peptide': 335}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 5, 'TRANS': 329}
          Unresolved non-hydrogen bonds: 89
          Unresolved non-hydrogen angles: 107
          Unresolved non-hydrogen dihedrals: 71
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 7, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 69
    Chain: "C"
      Number of atoms: 353
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 353
          Classifications: {'peptide': 54}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
          Unresolved non-hydrogen bonds: 65
          Unresolved non-hydrogen angles: 78
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 40
    Chain: "L"
      Number of atoms: 732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 732
          Classifications: {'peptide': 108}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 4, 'TRANS': 103}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 148
          Unresolved non-hydrogen angles: 177
          Unresolved non-hydrogen dihedrals: 130
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 3, 'ARG:plan': 10, 'PHE:plan': 2, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 107
    Chain: "R"
      Number of atoms: 2118
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2118
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PTRANS': 10, 'TRANS': 270}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 127
          Unresolved non-hydrogen angles: 159
          Unresolved non-hydrogen dihedrals: 103
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 4, 'PHE:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 61
  Time building chain proxies: 1.82, per 1000 atoms: 0.25
  Number of scatterers: 7262
  At special positions: 0
  Unit cell: (76.041, 100.674, 163.863, 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      60     16.00
     O    1322      8.00
     N    1229      7.00
     C    4651      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  47 " - pdb=" SG  CYS A 224 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  77 " - pdb=" SG  CYS L  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  98 " - pdb=" SG  CYS L 117 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 101 " - pdb=" SG  CYS L 135 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 112 " - pdb=" SG  CYS R 189 " 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: 0.55
  Conformation dependent library (CDL) restraints added in 385.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1866

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 10 sheets defined
      42.4% alpha, 17.9% 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 8 through 31
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.733A  pdb=" N   LYS A 210 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.705A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.717A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 278
      removed outlier: 4.036A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 310
      removed outlier: 3.549A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 7 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 10 through 23
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.575A  pdb=" N   ALA C  33 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 48
      removed outlier: 3.585A  pdb=" N   ASP C  48 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 45 through 48'
    Processing helix  chain 'L' and resid 23 through 35
      removed outlier: 3.523A  pdb=" N   VAL L  32 " --> pdb=" O   ARG L  28 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 4.149A  pdb=" N   LYS L  83 " --> pdb=" O   ARG L  80 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LYS L  84 " --> pdb=" O   ASP L  81 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 80 through 84'
    Processing helix  chain 'L' and resid 132 through 137
      removed outlier: 3.883A  pdb=" N   LEU L 136 " --> pdb=" O   GLU L 132 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   ARG L 137 " --> pdb=" O   THR L 133 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 132 through 137'
    Processing helix  chain 'L' and resid 144 through 148
    Processing helix  chain 'R' and resid 37 through 67
      removed outlier: 3.808A  pdb=" N   VAL R  45 " --> pdb=" O   ILE R  41 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   VAL R  46 " --> pdb=" O   PHE R  42 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 72 through 101
      Proline residue:  R  93  - end of helix
    Processing helix  chain 'R' and resid 111 through 143
      removed outlier: 4.408A  pdb=" N   PHE R 117 " --> pdb=" O   LYS R 113 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 143 through 150
    Processing helix  chain 'R' and resid 152 through 177
      Proline residue:  R 173  - end of helix
      removed outlier: 3.806A  pdb=" N   VAL R 176 " --> pdb=" O   SER R 172 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 220 through 250
      removed outlier: 5.569A  pdb=" N   VAL R 231 " --> pdb=" O   CYS R 227 " (cutoff:3.500A)
      Proline residue:  R 232  - end of helix
      removed outlier: 3.913A  pdb=" N   ASN R 250 " --> pdb=" O   LYS R 246 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 256 through 283
      removed outlier: 3.743A  pdb=" N   LYS R 260 " --> pdb=" O   LYS R 256 " (cutoff:3.500A)
      Proline residue:  R 275  - end of helix
    Processing helix  chain 'R' and resid 290 through 317
      removed outlier: 4.153A  pdb=" N   PHE R 294 " --> pdb=" O   PRO R 290 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   LEU R 298 " --> pdb=" O   PHE R 294 " (cutoff:3.500A)
      Proline residue:  R 299  - end of helix
      removed outlier: 3.666A  pdb=" N   ASN R 308 " --> pdb=" O   LEU R 304 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   SER R 309 " --> pdb=" O   ALA R 305 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   CYS R 310 " --> pdb=" O   ILE R 306 " (cutoff:3.500A)
      Proline residue:  R 313  - end of helix
    Processing helix  chain 'R' and resid 320 through 330
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.258A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.738A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.501A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.347A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 5.724A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.686A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.092A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.948A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.238A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 4.984A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.871A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.639A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 5.983A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 45 through 48
      removed outlier: 5.963A  pdb=" N   ALA L  46 " --> pdb=" O   THR L  75 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   THR L  75 " --> pdb=" O   ALA L  46 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   GLN L  48 " --> pdb=" O   GLN L  73 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   GLN L  73 " --> pdb=" O   GLN L  48 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'R' and resid 179 through 181

    378 hydrogen bonds defined for protein.
    1080 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.16

  Time building geometry restraints manager: 0.87 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: 2337
        1.35 -     1.46: 1820
        1.46 -     1.58: 3167
        1.58 -     1.70: 0
        1.70 -     1.82: 81
  Bond restraints: 7405
  Sorted by residual:
  bond pdb=" CA  VAL L  89 "
       pdb=" CB  VAL L  89 "
    ideal  model  delta    sigma   weight residual
    1.540  1.566 -0.026 2.70e-02 1.37e+03 9.52e-01
  bond pdb=" N   ASN B 119 "
       pdb=" CA  ASN B 119 "
    ideal  model  delta    sigma   weight residual
    1.457  1.470 -0.013 1.29e-02 6.01e+03 9.47e-01
  bond pdb=" CA  ILE B  43 "
       pdb=" CB  ILE B  43 "
    ideal  model  delta    sigma   weight residual
    1.530  1.540 -0.010 1.11e-02 8.12e+03 7.85e-01
  bond pdb=" C   LEU R  92 "
       pdb=" N   PRO R  93 "
    ideal  model  delta    sigma   weight residual
    1.335  1.345 -0.010 1.28e-02 6.10e+03 6.11e-01
  bond pdb=" CB  PRO A 282 "
       pdb=" CG  PRO A 282 "
    ideal  model  delta    sigma   weight residual
    1.492  1.531 -0.039 5.00e-02 4.00e+02 6.09e-01
  ... (remaining 7400 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 9928
        1.69 -     3.38: 117
        3.38 -     5.07: 26
        5.07 -     6.77: 3
        6.77 -     8.46: 1
  Bond angle restraints: 10075
  Sorted by residual:
  angle pdb=" C   PHE R  91 "
        pdb=" N   LEU R  92 "
        pdb=" CA  LEU R  92 "
      ideal   model   delta    sigma   weight residual
     120.09  123.64   -3.55 1.25e+00 6.40e-01 8.04e+00
  angle pdb=" CB  MET B 325 "
        pdb=" CG  MET B 325 "
        pdb=" SD  MET B 325 "
      ideal   model   delta    sigma   weight residual
     112.70  121.16   -8.46 3.00e+00 1.11e-01 7.95e+00
  angle pdb=" C   CYS R  51 "
        pdb=" N   PHE R  52 "
        pdb=" CA  PHE R  52 "
      ideal   model   delta    sigma   weight residual
     120.68  116.29    4.39 1.70e+00 3.46e-01 6.68e+00
  angle pdb=" N   PHE L 154 "
        pdb=" CA  PHE L 154 "
        pdb=" C   PHE L 154 "
      ideal   model   delta    sigma   weight residual
     111.81  108.19    3.62 1.44e+00 4.82e-01 6.32e+00
  angle pdb=" N   PHE R  52 "
        pdb=" CA  PHE R  52 "
        pdb=" CB  PHE R  52 "
      ideal   model   delta    sigma   weight residual
     110.30  114.07   -3.77 1.54e+00 4.22e-01 6.00e+00
  ... (remaining 10070 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.37: 3968
       17.37 -    34.74: 305
       34.74 -    52.12: 64
       52.12 -    69.49: 4
       69.49 -    86.86: 5
  Dihedral angle restraints: 4346
    sinusoidal: 1489
      harmonic: 2857
  Sorted by residual:
  dihedral pdb=" CB  CYS L  77 "
           pdb=" SG  CYS L  77 "
           pdb=" SG  CYS L  87 "
           pdb=" CB  CYS L  87 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00    0.86  -86.86     1      1.00e+01 1.00e-02 9.07e+01
  dihedral pdb=" CB  CYS R 112 "
           pdb=" SG  CYS R 112 "
           pdb=" SG  CYS R 189 "
           pdb=" CB  CYS R 189 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  148.82  -55.82     1      1.00e+01 1.00e-02 4.21e+01
  dihedral pdb=" CA  ASN R 191 "
           pdb=" C   ASN R 191 "
           pdb=" N   ASN R 192 "
           pdb=" CA  ASN R 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.18  -18.82     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 4343 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 687
       0.027 -    0.055: 346
       0.055 -    0.082: 110
       0.082 -    0.110: 49
       0.110 -    0.137: 15
  Chirality restraints: 1207
  Sorted by residual:
  chirality pdb=" CA  VAL B 296 "
            pdb=" N   VAL B 296 "
            pdb=" C   VAL B 296 "
            pdb=" CB  VAL B 296 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.71e-01
  chirality pdb=" CA  ILE B 123 "
            pdb=" N   ILE B 123 "
            pdb=" C   ILE B 123 "
            pdb=" CB  ILE B 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.15e-01
  chirality pdb=" CA  ILE B  93 "
            pdb=" N   ILE B  93 "
            pdb=" C   ILE B  93 "
            pdb=" CB  ILE B  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.09e-01
  ... (remaining 1204 not shown)

  Planarity restraints: 1265
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER R 172 "    0.021 5.00e-02 4.00e+02   3.23e-02 1.66e+00
        pdb=" N   PRO R 173 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO R 173 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO R 173 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN B 175 "    0.006 2.00e-02 2.50e+03   1.28e-02 1.63e+00
        pdb=" CD  GLN B 175 "   -0.022 2.00e-02 2.50e+03
        pdb=" OE1 GLN B 175 "    0.008 2.00e-02 2.50e+03
        pdb=" NE2 GLN B 175 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.021 5.00e-02 4.00e+02   3.16e-02 1.60e+00
        pdb=" N   PRO B 236 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1262 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 97
        2.68 -     3.23: 6900
        3.23 -     3.79: 11223
        3.79 -     4.34: 15098
        4.34 -     4.90: 24807
  Nonbonded interactions: 58125
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.121 3.040
  nonbonded pdb=" OG1 THR B  29 "
            pdb=" OE1 GLN B  32 "
     model   vdw
     2.184 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" O   CYS A 254 "
            pdb=" NZ  LYS A 317 "
     model   vdw
     2.297 3.120
  nonbonded pdb=" ND2 ASN B 230 "
            pdb=" OD1 ASP B 246 "
     model   vdw
     2.304 3.120
  ... (remaining 58120 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.540
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7044
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   0.039   7410  Z= 0.102
  Angle     :  0.515   8.458  10085  Z= 0.288
  Chirality :  0.039   0.137   1207
  Planarity :  0.003   0.032   1265
  Dihedral  : 12.785  70.417   2465
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.28), residues: 953
  helix:  2.09 (0.28), residues: 388
  sheet:  0.09 (0.36), residues: 192
  loop : -1.06 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 224 
 TYR   0.021   0.001   TYR R  47 
 PHE   0.010   0.001   PHE A 196 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.005   0.001   HIS L 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00195 ( 7405)
  covalent geometry    : angle       0.51492 (10075)
  SS BOND              : bond        0.00190 (    5)
  SS BOND              : angle       0.34290 (   10)
  hydrogen bonds       : bond        0.14320 (  378)
  hydrogen bonds       : angle       5.24384 ( 1080)

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.278 
Fit side-chains
REVERT: L   64 ILE cc_start: 0.7541 (mp) cc_final: 0.7133 (tp)
REVERT: R   61 VAL cc_start: 0.9050 (p) cc_final: 0.8841 (t)
REVERT: R  132 ILE cc_start: 0.8021 (tp) cc_final: 0.7749 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.0723
  time to fit residues: 11.7040
Evaluate side-chains
  99 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:   20.0000
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.3980
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    2.2788

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

Flipped N/Q/H residues before XYZ refinement:
B 239 ASN
B 259 GLN
** L 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.099744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.083943 restraints weight = 17884.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.083168 restraints weight = 21744.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.081518 restraints weight = 16177.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.081397 restraints weight = 17542.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.081595 restraints weight = 15152.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7393
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.055   7410  Z= 0.280
  Angle     :  0.716  11.611  10085  Z= 0.373
  Chirality :  0.048   0.183   1207
  Planarity :  0.005   0.041   1265
  Dihedral  :  4.581  29.614   1022
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 10.59 %
    Favored  : 87.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.33 (0.28), residues: 953
  helix:  1.42 (0.27), residues: 390
  sheet:  0.33 (0.35), residues: 197
  loop : -1.16 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  15 
 TYR   0.020   0.003   TYR R  47 
 PHE   0.023   0.003   PHE A 196 
 TRP   0.015   0.003   TRP R 273 
 HIS   0.008   0.002   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00662 ( 7405)
  covalent geometry    : angle       0.71559 (10075)
  SS BOND              : bond        0.00777 (    5)
  SS BOND              : angle       1.06991 (   10)
  hydrogen bonds       : bond        0.05257 (  378)
  hydrogen bonds       : angle       4.73885 ( 1080)

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.287 
Fit side-chains
REVERT: B  256 ARG cc_start: 0.7507 (mtm180) cc_final: 0.6996 (mtm180)
REVERT: B  262 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.6771 (tpp)
REVERT: R   61 VAL cc_start: 0.8775 (p) cc_final: 0.8545 (t)
  outliers start: 15
  outliers final: 10
  residues processed: 108
  average time/residue: 0.0844
  time to fit residues: 12.4429
Evaluate side-chains
  107 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue  148 PHE
Chi-restraints excluded: chain R residue   52 PHE
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   90 VAL
Chi-restraints excluded: chain R residue  219 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 8 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 86 optimal weight:    0.4980
   chunk 52 optimal weight:    0.7980
   chunk 68 optimal weight:    5.9990
   chunk 62 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
L 153 GLN
R 286 HIS
R 308 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.101698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.086590 restraints weight = 17863.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.088287 restraints weight = 31122.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.089272 restraints weight = 18117.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.089445 restraints weight = 12555.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.089684 restraints weight = 12968.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7181
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7410  Z= 0.120
  Angle     :  0.529   7.693  10085  Z= 0.280
  Chirality :  0.041   0.137   1207
  Planarity :  0.003   0.037   1265
  Dihedral  :  4.095  26.221   1022
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 13.89 %
    Favored  : 84.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.42 (0.28), residues: 953
  helix:  1.56 (0.27), residues: 393
  sheet:  0.33 (0.36), residues: 189
  loop : -1.15 (0.33), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  15 
 TYR   0.014   0.001   TYR R  47 
 PHE   0.015   0.001   PHE A 196 
 TRP   0.012   0.001   TRP B 211 
 HIS   0.007   0.001   HIS R 286 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 7405)
  covalent geometry    : angle       0.52950 (10075)
  SS BOND              : bond        0.00419 (    5)
  SS BOND              : angle       0.35865 (   10)
  hydrogen bonds       : bond        0.03874 (  378)
  hydrogen bonds       : angle       4.26346 ( 1080)

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A   15 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.6902 (mtp-110)
REVERT: B  256 ARG cc_start: 0.7564 (mtm180) cc_final: 0.6939 (mtm180)
REVERT: B  262 MET cc_start: 0.7543 (ttm) cc_final: 0.6865 (tpp)
REVERT: R   61 VAL cc_start: 0.8659 (p) cc_final: 0.8406 (t)
  outliers start: 15
  outliers final: 12
  residues processed: 107
  average time/residue: 0.0891
  time to fit residues: 12.6266
Evaluate side-chains
  111 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain L residue  148 PHE
Chi-restraints excluded: chain L residue  153 GLN
Chi-restraints excluded: chain R residue   64 ILE
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   90 VAL
Chi-restraints excluded: chain R residue  243 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 80 optimal weight:    0.7980
   chunk 28 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 55 optimal weight:    0.1980
   chunk 44 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 57 optimal weight:    0.3980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
B 175 GLN
R 286 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.101728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.086524 restraints weight = 18056.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.088831 restraints weight = 29896.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.089445 restraints weight = 16765.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.089580 restraints weight = 12011.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.089819 restraints weight = 12559.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7177
moved from start:          0.2274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7410  Z= 0.114
  Angle     :  0.520   7.059  10085  Z= 0.274
  Chirality :  0.040   0.135   1207
  Planarity :  0.003   0.035   1265
  Dihedral  :  3.964  25.434   1022
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 14.99 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.28), residues: 953
  helix:  1.68 (0.27), residues: 393
  sheet:  0.29 (0.37), residues: 183
  loop : -1.19 (0.33), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  15 
 TYR   0.013   0.001   TYR A 302 
 PHE   0.013   0.001   PHE A 196 
 TRP   0.011   0.001   TRP B 211 
 HIS   0.007   0.001   HIS R 286 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 7405)
  covalent geometry    : angle       0.51964 (10075)
  SS BOND              : bond        0.00393 (    5)
  SS BOND              : angle       0.40839 (   10)
  hydrogen bonds       : bond        0.03629 (  378)
  hydrogen bonds       : angle       4.13227 ( 1080)

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.283 
Fit side-chains
REVERT: A   15 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.6940 (mtp-110)
REVERT: B  256 ARG cc_start: 0.7561 (mtm180) cc_final: 0.6938 (mtm180)
REVERT: B  262 MET cc_start: 0.7516 (ttm) cc_final: 0.6557 (tpp)
REVERT: R   61 VAL cc_start: 0.8677 (p) cc_final: 0.8434 (t)
  outliers start: 19
  outliers final: 16
  residues processed: 110
  average time/residue: 0.0942
  time to fit residues: 13.7457
Evaluate side-chains
  113 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain L residue  148 PHE
Chi-restraints excluded: chain R residue   64 ILE
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   90 VAL
Chi-restraints excluded: chain R residue  106 VAL
Chi-restraints excluded: chain R residue  123 MET
Chi-restraints excluded: chain R residue  233 VAL
Chi-restraints excluded: chain R residue  243 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0570
   chunk 94 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 57 optimal weight:    0.0470
   chunk 29 optimal weight:    0.2980
   chunk 62 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
L 153 GLN
R 286 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.102166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.086631 restraints weight = 17963.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.085608 restraints weight = 22036.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.083791 restraints weight = 16750.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.084037 restraints weight = 17183.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.084141 restraints weight = 15004.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7410  Z= 0.101
  Angle     :  0.493   6.023  10085  Z= 0.260
  Chirality :  0.040   0.134   1207
  Planarity :  0.003   0.034   1265
  Dihedral  :  3.787  23.919   1022
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 15.54 %
    Favored  : 81.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.28), residues: 953
  helix:  1.80 (0.27), residues: 392
  sheet:  0.29 (0.37), residues: 177
  loop : -1.17 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  46 
 TYR   0.012   0.001   TYR A 302 
 PHE   0.014   0.001   PHE R  52 
 TRP   0.009   0.001   TRP R  77 
 HIS   0.007   0.001   HIS R 286 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 7405)
  covalent geometry    : angle       0.49266 (10075)
  SS BOND              : bond        0.00323 (    5)
  SS BOND              : angle       0.38635 (   10)
  hydrogen bonds       : bond        0.03311 (  378)
  hydrogen bonds       : angle       4.00286 ( 1080)

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 0.279 
Fit side-chains
REVERT: A   15 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7200 (mtp-110)
REVERT: B  256 ARG cc_start: 0.7598 (mtm180) cc_final: 0.6941 (mtm180)
REVERT: B  262 MET cc_start: 0.7525 (ttm) cc_final: 0.6463 (tpp)
REVERT: R   61 VAL cc_start: 0.8797 (p) cc_final: 0.8557 (t)
  outliers start: 22
  outliers final: 21
  residues processed: 113
  average time/residue: 0.0917
  time to fit residues: 13.8803
Evaluate side-chains
  119 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain L residue  148 PHE
Chi-restraints excluded: chain L residue  153 GLN
Chi-restraints excluded: chain R residue   52 PHE
Chi-restraints excluded: chain R residue   64 ILE
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   90 VAL
Chi-restraints excluded: chain R residue  106 VAL
Chi-restraints excluded: chain R residue  123 MET
Chi-restraints excluded: chain R residue  233 VAL
Chi-restraints excluded: chain R residue  243 ILE
Chi-restraints excluded: chain R residue  289 MET
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 68 optimal weight:    6.9990
   chunk 66 optimal weight:   10.0000
   chunk 94 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 62 optimal weight:    8.9990
   chunk 13 optimal weight:    0.8980
   chunk 67 optimal weight:    7.9990
   chunk 33 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
R 286 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.098374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.082868 restraints weight = 17875.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.080788 restraints weight = 22671.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.078794 restraints weight = 20537.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.079003 restraints weight = 19123.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.079222 restraints weight = 16317.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.3096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.055   7410  Z= 0.285
  Angle     :  0.705  11.617  10085  Z= 0.365
  Chirality :  0.048   0.198   1207
  Planarity :  0.005   0.053   1265
  Dihedral  :  4.715  33.065   1022
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 15.68 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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:  0.19 (0.28), residues: 953
  helix:  1.29 (0.27), residues: 397
  sheet:  0.51 (0.38), residues: 181
  loop : -1.35 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  46 
 TYR   0.016   0.003   TYR R  47 
 PHE   0.028   0.003   PHE L 156 
 TRP   0.014   0.003   TRP B 169 
 HIS   0.007   0.002   HIS R 286 

Details of bonding type rmsd
  covalent geometry    : bond        0.00684 ( 7405)
  covalent geometry    : angle       0.70471 (10075)
  SS BOND              : bond        0.00838 (    5)
  SS BOND              : angle       1.18269 (   10)
  hydrogen bonds       : bond        0.04981 (  378)
  hydrogen bonds       : angle       4.65249 ( 1080)

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 99
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.6792 (mtp-110)
REVERT: B  256 ARG cc_start: 0.7481 (mtm180) cc_final: 0.7002 (mtm180)
REVERT: B  262 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.6269 (tpp)
  outliers start: 30
  outliers final: 22
  residues processed: 117
  average time/residue: 0.0872
  time to fit residues: 13.6651
Evaluate side-chains
  119 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 95
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain L residue  148 PHE
Chi-restraints excluded: chain R residue   52 PHE
Chi-restraints excluded: chain R residue   64 ILE
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   90 VAL
Chi-restraints excluded: chain R residue  106 VAL
Chi-restraints excluded: chain R residue  123 MET
Chi-restraints excluded: chain R residue  139 ILE
Chi-restraints excluded: chain R residue  219 VAL
Chi-restraints excluded: chain R residue  233 VAL
Chi-restraints excluded: chain R residue  243 ILE
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 7 optimal weight:    0.7980
   chunk 25 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 82 optimal weight:    3.9990
   chunk 95 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 91 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
B 175 GLN
** L 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 286 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.100204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.085212 restraints weight = 18005.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.083229 restraints weight = 23295.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.081933 restraints weight = 20644.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.081858 restraints weight = 22486.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.082096 restraints weight = 17909.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.2941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7410  Z= 0.132
  Angle     :  0.551   7.393  10085  Z= 0.288
  Chirality :  0.041   0.144   1207
  Planarity :  0.004   0.036   1265
  Dihedral  :  4.272  28.105   1022
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 17.47 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.28), residues: 953
  helix:  1.54 (0.27), residues: 397
  sheet:  0.39 (0.38), residues: 183
  loop : -1.26 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  46 
 TYR   0.012   0.001   TYR R  47 
 PHE   0.013   0.001   PHE R 124 
 TRP   0.013   0.002   TRP B 211 
 HIS   0.006   0.001   HIS R 286 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 7405)
  covalent geometry    : angle       0.55115 (10075)
  SS BOND              : bond        0.00523 (    5)
  SS BOND              : angle       0.59831 (   10)
  hydrogen bonds       : bond        0.03836 (  378)
  hydrogen bonds       : angle       4.23873 ( 1080)

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 92
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A   15 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7011 (mtp-110)
REVERT: B  256 ARG cc_start: 0.7480 (mtm180) cc_final: 0.6898 (mtm180)
REVERT: B  262 MET cc_start: 0.7503 (ttm) cc_final: 0.6411 (tpp)
  outliers start: 23
  outliers final: 20
  residues processed: 108
  average time/residue: 0.0926
  time to fit residues: 13.2893
Evaluate side-chains
  112 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   77 CYS
Chi-restraints excluded: chain L residue  148 PHE
Chi-restraints excluded: chain R residue   52 PHE
Chi-restraints excluded: chain R residue   64 ILE
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   90 VAL
Chi-restraints excluded: chain R residue  106 VAL
Chi-restraints excluded: chain R residue  123 MET
Chi-restraints excluded: chain R residue  139 ILE
Chi-restraints excluded: chain R residue  233 VAL
Chi-restraints excluded: chain R residue  243 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 50 optimal weight:    5.9990
   chunk 53 optimal weight:   20.0000
   chunk 29 optimal weight:    0.6980
   chunk 82 optimal weight:    3.9990
   chunk 94 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 81 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 90 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
** L 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.100357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.085004 restraints weight = 18006.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.083015 restraints weight = 23125.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.082227 restraints weight = 18622.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.082000 restraints weight = 22325.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.082235 restraints weight = 18166.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.2948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7410  Z= 0.129
  Angle     :  0.542   7.278  10085  Z= 0.284
  Chirality :  0.041   0.146   1207
  Planarity :  0.003   0.035   1265
  Dihedral  :  4.127  28.061   1022
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 18.16 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.42 (0.28), residues: 953
  helix:  1.63 (0.27), residues: 396
  sheet:  0.32 (0.38), residues: 182
  loop : -1.23 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  15 
 TYR   0.012   0.001   TYR R  47 
 PHE   0.013   0.001   PHE R  52 
 TRP   0.012   0.002   TRP B 211 
 HIS   0.002   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 7405)
  covalent geometry    : angle       0.54236 (10075)
  SS BOND              : bond        0.00437 (    5)
  SS BOND              : angle       0.60046 (   10)
  hydrogen bonds       : bond        0.03694 (  378)
  hydrogen bonds       : angle       4.14994 ( 1080)

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 90
  time to evaluate  : 0.284 
Fit side-chains
REVERT: A   15 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.6721 (mtp-110)
REVERT: B   65 THR cc_start: 0.7997 (OUTLIER) cc_final: 0.7767 (t)
REVERT: B  234 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.7247 (m-80)
REVERT: B  256 ARG cc_start: 0.7449 (mtm180) cc_final: 0.6864 (mtm180)
REVERT: B  262 MET cc_start: 0.7476 (ttm) cc_final: 0.6771 (tpp)
  outliers start: 24
  outliers final: 21
  residues processed: 106
  average time/residue: 0.0866
  time to fit residues: 12.1859
Evaluate side-chains
  114 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 90
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   77 CYS
Chi-restraints excluded: chain L residue  148 PHE
Chi-restraints excluded: chain R residue   52 PHE
Chi-restraints excluded: chain R residue   64 ILE
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   90 VAL
Chi-restraints excluded: chain R residue  106 VAL
Chi-restraints excluded: chain R residue  123 MET
Chi-restraints excluded: chain R residue  139 ILE
Chi-restraints excluded: chain R residue  233 VAL
Chi-restraints excluded: chain R residue  243 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 17 optimal weight:    0.0570
   chunk 42 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   chunk 75 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9980
   chunk 21 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 94 optimal weight:    0.0470
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
** L 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.101036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.085316 restraints weight = 17681.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.084704 restraints weight = 21721.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.083592 restraints weight = 17885.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.083652 restraints weight = 19277.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.084003 restraints weight = 14616.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7314
moved from start:          0.2889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7410  Z= 0.112
  Angle     :  0.520   7.187  10085  Z= 0.272
  Chirality :  0.040   0.145   1207
  Planarity :  0.003   0.035   1265
  Dihedral  :  3.969  25.694   1022
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 18.29 %
    Favored  : 78.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.28), residues: 953
  helix:  1.81 (0.27), residues: 388
  sheet:  0.28 (0.38), residues: 183
  loop : -1.20 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  15 
 TYR   0.011   0.001   TYR R  47 
 PHE   0.013   0.001   PHE R  52 
 TRP   0.013   0.001   TRP B 211 
 HIS   0.002   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 7405)
  covalent geometry    : angle       0.52040 (10075)
  SS BOND              : bond        0.00380 (    5)
  SS BOND              : angle       0.49828 (   10)
  hydrogen bonds       : bond        0.03427 (  378)
  hydrogen bonds       : angle       4.02080 ( 1080)

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 92
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A   15 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7184 (mtp-110)
REVERT: A  302 TYR cc_start: 0.7816 (t80) cc_final: 0.7510 (t80)
REVERT: B  234 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.7208 (m-80)
REVERT: B  256 ARG cc_start: 0.7530 (mtm180) cc_final: 0.6917 (mtm180)
REVERT: B  262 MET cc_start: 0.7430 (ttm) cc_final: 0.6839 (tpp)
REVERT: R  123 MET cc_start: 0.6980 (OUTLIER) cc_final: 0.6402 (ptt)
  outliers start: 24
  outliers final: 20
  residues processed: 110
  average time/residue: 0.0899
  time to fit residues: 13.1616
Evaluate side-chains
  113 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 90
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   77 CYS
Chi-restraints excluded: chain L residue  148 PHE
Chi-restraints excluded: chain R residue   52 PHE
Chi-restraints excluded: chain R residue   64 ILE
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   90 VAL
Chi-restraints excluded: chain R residue  106 VAL
Chi-restraints excluded: chain R residue  123 MET
Chi-restraints excluded: chain R residue  139 ILE
Chi-restraints excluded: chain R residue  233 VAL
Chi-restraints excluded: chain R residue  243 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 83 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0770
   chunk 40 optimal weight:    0.0070
   chunk 37 optimal weight:    0.5980
   chunk 20 optimal weight:    7.9990
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
B 175 GLN
** L 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.101303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.086089 restraints weight = 17885.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.084651 restraints weight = 21833.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.083196 restraints weight = 17455.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.083089 restraints weight = 20510.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.083165 restraints weight = 18039.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
moved from start:          0.2872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7410  Z= 0.106
  Angle     :  0.516   6.983  10085  Z= 0.271
  Chirality :  0.041   0.151   1207
  Planarity :  0.003   0.035   1265
  Dihedral  :  3.880  25.413   1022
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 18.98 %
    Favored  : 77.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.28), residues: 953
  helix:  1.91 (0.27), residues: 389
  sheet:  0.29 (0.38), residues: 182
  loop : -1.23 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  46 
 TYR   0.015   0.001   TYR A 302 
 PHE   0.013   0.001   PHE R  52 
 TRP   0.012   0.001   TRP B 211 
 HIS   0.002   0.001   HIS R 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 7405)
  covalent geometry    : angle       0.51601 (10075)
  SS BOND              : bond        0.00340 (    5)
  SS BOND              : angle       0.48824 (   10)
  hydrogen bonds       : bond        0.03337 (  378)
  hydrogen bonds       : angle       3.97908 ( 1080)

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.318 
Fit side-chains
REVERT: A   15 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7172 (mtp-110)
REVERT: B  234 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.7208 (m-80)
REVERT: B  256 ARG cc_start: 0.7523 (mtm180) cc_final: 0.6901 (mtm180)
REVERT: B  262 MET cc_start: 0.7419 (ttm) cc_final: 0.6816 (tpp)
REVERT: B  335 PHE cc_start: 0.8235 (m-80) cc_final: 0.7867 (m-80)
REVERT: R  123 MET cc_start: 0.6952 (OUTLIER) cc_final: 0.6382 (ptt)
  outliers start: 22
  outliers final: 19
  residues processed: 109
  average time/residue: 0.0910
  time to fit residues: 13.2046
Evaluate side-chains
  114 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   77 CYS
Chi-restraints excluded: chain L residue  148 PHE
Chi-restraints excluded: chain R residue   52 PHE
Chi-restraints excluded: chain R residue   64 ILE
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   90 VAL
Chi-restraints excluded: chain R residue  106 VAL
Chi-restraints excluded: chain R residue  123 MET
Chi-restraints excluded: chain R residue  139 ILE
Chi-restraints excluded: chain R residue  233 VAL
Chi-restraints excluded: chain R residue  243 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 82 optimal weight:    3.9990
   chunk 84 optimal weight:    0.0570
   chunk 89 optimal weight:    0.7980
   chunk 58 optimal weight:    6.9990
   chunk 61 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 93 optimal weight:    0.3980
   chunk 73 optimal weight:    0.9990
   overall best weight:    0.8502

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
B 175 GLN
** L 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.100519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.084886 restraints weight = 17871.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.084031 restraints weight = 21269.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.082347 restraints weight = 17169.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.081878 restraints weight = 20547.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.082055 restraints weight = 18871.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.2991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7410  Z= 0.132
  Angle     :  0.543   7.150  10085  Z= 0.284
  Chirality :  0.041   0.146   1207
  Planarity :  0.003   0.035   1265
  Dihedral  :  4.022  26.177   1022
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 18.84 %
    Favored  : 77.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.28), residues: 953
  helix:  1.85 (0.27), residues: 390
  sheet:  0.26 (0.38), residues: 184
  loop : -1.20 (0.33), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  15 
 TYR   0.014   0.001   TYR A 302 
 PHE   0.014   0.001   PHE A 196 
 TRP   0.012   0.001   TRP B 211 
 HIS   0.002   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 7405)
  covalent geometry    : angle       0.54267 (10075)
  SS BOND              : bond        0.00431 (    5)
  SS BOND              : angle       0.59930 (   10)
  hydrogen bonds       : bond        0.03613 (  378)
  hydrogen bonds       : angle       4.07397 ( 1080)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1414.87 seconds
wall clock time: 25 minutes 10.87 seconds (1510.87 seconds total)