Starting phenix.real_space_refine
on Wed Feb  4 07:21:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ldx_63009/02_2026/9ldx_63009.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ldx_63009/02_2026/9ldx_63009.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.83
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ldx_63009/02_2026/9ldx_63009.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ldx_63009/02_2026/9ldx_63009.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ldx_63009/02_2026/9ldx_63009.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ldx_63009/02_2026/9ldx_63009.cif"
  }
  resolution = 2.83
  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=   0.001 sd=   0.027
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      59      5.16       5
     C    5890      2.51       5
     N    1554      2.21       5
     O    1708      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9211
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1919
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1919
          Classifications: {'peptide': 233}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 227}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2601
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "C"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 438
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "R"
      Number of atoms: 2414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 303, 2414
          Classifications: {'peptide': 303}
          Link IDs: {'PTRANS': 14, 'TRANS': 288}
    Chain: "S"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1783
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 56
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 2, 42
          Unusual residues: {'BZQ': 1, 'CLR': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
      Conformer: "B"
        Number of residues, atoms: 2, 42
          Unusual residues: {'BZQ': 1, 'CLR': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          bond proxies already assigned to first conformer: 31
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" O  ABZQ R 402 " occ=0.55
      ... (26 atoms not shown)
      pdb=" C9 BBZQ R 402 " occ=0.45
  Time building chain proxies: 2.29, per 1000 atoms: 0.25
  Number of scatterers: 9211
  At special positions: 0
  Unit cell: (90.24, 128.64, 127.68, 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      59     16.00
     O    1708      8.00
     N    1554      7.00
     C    5890      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  95 " - pdb=" SG  CYS R 177 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 167 " - pdb=" SG  CYS R 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.04

  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: 0.76
  Conformation dependent library (CDL) restraints added in 312.7 milliseconds
  

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2184

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 14 sheets defined
      38.2% alpha, 23.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.955A  pdb=" N   ALA A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 57
    Processing helix  chain 'A' and resid 117 through 130
    Processing helix  chain 'A' and resid 145 through 156
      removed outlier: 3.573A  pdb=" N   LEU A 149 " --> pdb=" O   LYS A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 164
      removed outlier: 4.060A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 170
    Processing helix  chain 'A' and resid 183 through 204
      removed outlier: 4.384A  pdb=" N   ILE A 200 " --> pdb=" O   LEU A 196 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   SER A 201 " --> pdb=" O   PHE A 197 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   THR A 204 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 243
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 280 through 282
      No H-bonds generated for 'chain 'B' and resid 280 through 282'
    Processing helix  chain 'C' and resid 8 through 23
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 45 through 48
      removed outlier: 3.834A  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 'R' and resid 18 through 50
      removed outlier: 4.619A  pdb=" N   VAL R  23 " --> pdb=" O   PRO R  19 " (cutoff:3.500A)
      removed outlier: 4.559A  pdb=" N   LEU R  24 " --> pdb=" O   GLU R  20 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 55 through 72
    Processing helix  chain 'R' and resid 75 through 85
    Processing helix  chain 'R' and resid 92 through 126
    Processing helix  chain 'R' and resid 129 through 134
    Processing helix  chain 'R' and resid 135 through 163
      Proline residue:  R 156  - end of helix
      removed outlier: 4.054A  pdb=" N   GLN R 163 " --> pdb=" O   ILE R 159 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 178 through 184
    Processing helix  chain 'R' and resid 190 through 225
    Processing helix  chain 'R' and resid 229 through 258
    Processing helix  chain 'R' and resid 267 through 274
      removed outlier: 4.006A  pdb=" N   GLY R 271 " --> pdb=" O   ASN R 267 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 278 through 289
      Proline residue:  R 285  - end of helix
    Processing helix  chain 'R' and resid 292 through 306
    Processing helix  chain 'S' and resid 28 through 32
      removed outlier: 3.725A  pdb=" N   SER S  31 " --> pdb=" O   ALA S  28 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.628A  pdb=" N   ASP S  90 " --> pdb=" O   ARG S  87 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 87 through 91'
    Processing helix  chain 'S' and resid 208 through 212
      removed outlier: 4.197A  pdb=" N   VAL S 212 " --> pdb=" O   ALA S 209 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 76
      removed outlier: 6.513A  pdb=" N   HIS A  34 " --> pdb=" O   HIS A  82 " (cutoff:3.500A)
      removed outlier: 8.026A  pdb=" N   PHE A  84 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   ALA A 105 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   ILE A 106 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 7.370A  pdb=" N   PHE A 142 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   TYR A 108 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   ASN A 144 " --> pdb=" O   TYR A 108 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   ALA A 110 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.861A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.080A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.178A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.639A  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: 6.664A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.176A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.388A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.148A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.967A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.307A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.894A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.773A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.049A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.340A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.540A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.723A  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: 6.852A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.074A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.990A  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: 3.735A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LEU B 285 " --> pdb=" O   TRP B 297 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 89 through 91
      removed outlier: 8.442A  pdb=" N   ILE R 172 " --> pdb=" O   GLU R   9 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   ILE R  11 " --> pdb=" O   ILE R 172 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.610A  pdb=" N   SER S  71 " --> pdb=" O   PHE S  80 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 11
      removed outlier: 5.979A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ALA S  49 " --> pdb=" O   TRP S  36 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.299A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 11
      removed outlier: 5.979A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129
      removed outlier: 4.043A  pdb=" N   THR S 129 " --> pdb=" O   ARG S 148 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 174 through 177
      removed outlier: 6.708A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)

    451 hydrogen bonds defined for protein.
    1287 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: 1.49

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1480
        1.31 -     1.44: 2587
        1.44 -     1.57: 5255
        1.57 -     1.70: 0
        1.70 -     1.83: 85
  Bond restraints: 9407
  Sorted by residual:
  bond pdb=" N   LEU R 155 "
       pdb=" CA  LEU R 155 "
    ideal  model  delta    sigma   weight residual
    1.462  1.489 -0.027 7.70e-03 1.69e+04 1.26e+01
  bond pdb=" N   ASP S  74 "
       pdb=" CA  ASP S  74 "
    ideal  model  delta    sigma   weight residual
    1.462  1.492 -0.030 8.50e-03 1.38e+04 1.23e+01
  bond pdb=" N   LYS S  76 "
       pdb=" CA  LYS S  76 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 1.26e-02 6.30e+03 6.19e+00
  bond pdb=" N   LEU R 158 "
       pdb=" CA  LEU R 158 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.028 1.16e-02 7.43e+03 5.64e+00
  bond pdb=" C   LEU R 155 "
       pdb=" N   PRO R 156 "
    ideal  model  delta    sigma   weight residual
    1.329  1.354 -0.025 1.18e-02 7.18e+03 4.44e+00
  ... (remaining 9402 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.77: 12505
        1.77 -     3.54: 211
        3.54 -     5.30: 32
        5.30 -     7.07: 5
        7.07 -     8.84: 4
  Bond angle restraints: 12757
  Sorted by residual:
  angle pdb=" N   PRO R 156 "
        pdb=" CA  PRO R 156 "
        pdb=" C   PRO R 156 "
      ideal   model   delta    sigma   weight residual
     110.70  115.61   -4.91 1.22e+00 6.72e-01 1.62e+01
  angle pdb=" CA  TYR S 178 "
        pdb=" CB  TYR S 178 "
        pdb=" CG  TYR S 178 "
      ideal   model   delta    sigma   weight residual
     113.90  120.68   -6.78 1.80e+00 3.09e-01 1.42e+01
  angle pdb=" N   ILE A  97 "
        pdb=" CA  ILE A  97 "
        pdb=" C   ILE A  97 "
      ideal   model   delta    sigma   weight residual
     113.07  108.50    4.57 1.36e+00 5.41e-01 1.13e+01
  angle pdb=" CB  LYS A  17 "
        pdb=" CG  LYS A  17 "
        pdb=" CD  LYS A  17 "
      ideal   model   delta    sigma   weight residual
     111.30  118.83   -7.53 2.30e+00 1.89e-01 1.07e+01
  angle pdb=" CA  PRO R 156 "
        pdb=" C   PRO R 156 "
        pdb=" N   PRO R 157 "
      ideal   model   delta    sigma   weight residual
     117.93  121.60   -3.67 1.20e+00 6.94e-01 9.35e+00
  ... (remaining 12752 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.75: 4997
       17.75 -    35.49: 452
       35.49 -    53.24: 139
       53.24 -    70.98: 52
       70.98 -    88.73: 4
  Dihedral angle restraints: 5644
    sinusoidal: 2259
      harmonic: 3385
  Sorted by residual:
  dihedral pdb=" CB  CYS R 167 "
           pdb=" SG  CYS R 167 "
           pdb=" SG  CYS R 187 "
           pdb=" CB  CYS R 187 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -147.91   61.91     1      1.00e+01 1.00e-02 5.08e+01
  dihedral pdb=" CB  CYS R  95 "
           pdb=" SG  CYS R  95 "
           pdb=" SG  CYS R 177 "
           pdb=" CB  CYS R 177 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -123.78   37.78     1      1.00e+01 1.00e-02 2.01e+01
  dihedral pdb=" CA  MET R 256 "
           pdb=" C   MET R 256 "
           pdb=" N   TYR R 257 "
           pdb=" CA  TYR R 257 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.75  -18.25     0      5.00e+00 4.00e-02 1.33e+01
  ... (remaining 5641 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 1001
       0.038 -    0.076: 332
       0.076 -    0.114: 100
       0.114 -    0.152: 25
       0.152 -    0.190: 4
  Chirality restraints: 1462
  Sorted by residual:
  chirality pdb=" CA  TYR S 178 "
            pdb=" N   TYR S 178 "
            pdb=" C   TYR S 178 "
            pdb=" CB  TYR S 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.02e-01
  chirality pdb=" CA  PRO R 156 "
            pdb=" N   PRO R 156 "
            pdb=" C   PRO R 156 "
            pdb=" CB  PRO R 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.17 2.00e-01 2.50e+01 7.52e-01
  chirality pdb=" CA  LEU R  34 "
            pdb=" N   LEU R  34 "
            pdb=" C   LEU R  34 "
            pdb=" CB  LEU R  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.26e-01
  ... (remaining 1459 not shown)

  Planarity restraints: 1607
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR S 223 "   -0.039 5.00e-02 4.00e+02   5.93e-02 5.63e+00
        pdb=" N   PRO S 224 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO S 224 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO S 224 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR S 178 "   -0.020 2.00e-02 2.50e+03   1.46e-02 4.29e+00
        pdb=" CG  TYR S 178 "    0.036 2.00e-02 2.50e+03
        pdb=" CD1 TYR S 178 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR S 178 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR S 178 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR S 178 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR S 178 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR S 178 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR R  55 "   -0.030 5.00e-02 4.00e+02   4.58e-02 3.36e+00
        pdb=" N   PRO R  56 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO R  56 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO R  56 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1604 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 599
        2.73 -     3.27: 8524
        3.27 -     3.82: 14218
        3.82 -     4.36: 16326
        4.36 -     4.90: 30210
  Nonbonded interactions: 69877
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 153 "
            pdb=" N   ASP B 154 "
     model   vdw
     2.191 3.120
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.193 3.040
  nonbonded pdb=" O   ASN R 170 "
            pdb=" ND2 ASN R 170 "
     model   vdw
     2.199 3.120
  nonbonded pdb=" O   GLY B 162 "
            pdb=" OD1 ASP B 186 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" CD  ARG A  94 "
            pdb=" CD1 ILE A  97 "
     model   vdw
     2.217 3.860
  ... (remaining 69872 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.45 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.900
  Find NCS groups from input model:        0.040
  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:8.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   9410  Z= 0.238
  Angle     :  0.606   8.838  12763  Z= 0.332
  Chirality :  0.044   0.190   1462
  Planarity :  0.004   0.059   1607
  Dihedral  : 15.975  88.730   3451
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 20.12 %
    Favored  : 79.68 %
  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 are not related in a simple way.
  whole:  1.00 (0.25), residues: 1149
  helix:  2.39 (0.25), residues: 408
  sheet:  1.04 (0.32), residues: 284
  loop : -1.25 (0.26), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 135 
 TYR   0.036   0.002   TYR S 178 
 PHE   0.014   0.002   PHE A  74 
 TRP   0.023   0.002   TRP A 133 
 HIS   0.006   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 ( 9407)
  covalent geometry    : angle       0.60585 (12757)
  SS BOND              : bond        0.00656 (    3)
  SS BOND              : angle       1.05928 (    6)
  hydrogen bonds       : bond        0.14332 (  447)
  hydrogen bonds       : angle       4.98685 ( 1287)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 179
  time to evaluate  : 0.381 
Fit side-chains
  outliers start: 2
  outliers final: 0
  residues processed: 180
  average time/residue: 0.4687
  time to fit residues: 91.5334
Evaluate side-chains
  168 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    1.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 130 ASN
B 239 ASN
B 259 GLN
R 170 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.120302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.101960 restraints weight = 13646.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 2.04
r_work: 0.3204 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3056 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3055
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3055 r_free = 0.3055    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3055 r_free = 0.3055    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3055
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.0665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   9410  Z= 0.193
  Angle     :  0.568   7.818  12763  Z= 0.304
  Chirality :  0.044   0.203   1462
  Planarity :  0.004   0.057   1607
  Dihedral  :  5.220  79.027   1336
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 16.45 %
    Favored  : 78.39 %
  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 are not related in a simple way.
  whole:  1.14 (0.24), residues: 1149
  helix:  2.63 (0.25), residues: 409
  sheet:  1.13 (0.32), residues: 274
  loop : -1.28 (0.26), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 132 
 TYR   0.031   0.002   TYR S 178 
 PHE   0.015   0.002   PHE S  29 
 TRP   0.011   0.002   TRP A 133 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 9407)
  covalent geometry    : angle       0.56752 (12757)
  SS BOND              : bond        0.00515 (    3)
  SS BOND              : angle       1.37924 (    6)
  hydrogen bonds       : bond        0.07506 (  447)
  hydrogen bonds       : angle       4.35668 ( 1287)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 172
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7760 (mppt)
REVERT: R   34 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8266 (mm)
REVERT: S  223 TYR cc_start: 0.7089 (OUTLIER) cc_final: 0.6799 (t80)
  outliers start: 52
  outliers final: 28
  residues processed: 197
  average time/residue: 0.4070
  time to fit residues: 87.0874
Evaluate side-chains
  197 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 166
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LYS
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain C residue   19 LEU
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain R residue    7 VAL
Chi-restraints excluded: chain R residue   34 LEU
Chi-restraints excluded: chain R residue   85 THR
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  162 SER
Chi-restraints excluded: chain R residue  188 THR
Chi-restraints excluded: chain R residue  210 LEU
Chi-restraints excluded: chain R residue  222 THR
Chi-restraints excluded: chain R residue  223 ILE
Chi-restraints excluded: chain R residue  247 SER
Chi-restraints excluded: chain R residue  266 VAL
Chi-restraints excluded: chain S residue   17 SER
Chi-restraints excluded: chain S residue   79 LEU
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  159 ASN
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  212 VAL
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain S residue  233 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 105 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 40 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 78 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 46 optimal weight:    0.6980
   chunk 82 optimal weight:    0.9990
   chunk 54 optimal weight:    0.6980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
R 170 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.121392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.102978 restraints weight = 13770.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 2.05
r_work: 0.3219 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3068
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3068 r_free = 0.3068    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3068 r_free = 0.3068    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3068
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.0863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9410  Z= 0.150
  Angle     :  0.519   6.900  12763  Z= 0.279
  Chirality :  0.042   0.206   1462
  Planarity :  0.004   0.058   1607
  Dihedral  :  5.017  73.186   1336
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 17.64 %
    Favored  : 78.00 %
  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 are not related in a simple way.
  whole:  1.20 (0.25), residues: 1149
  helix:  2.79 (0.25), residues: 409
  sheet:  1.02 (0.32), residues: 278
  loop : -1.29 (0.26), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 117 
 TYR   0.029   0.001   TYR S 178 
 PHE   0.013   0.002   PHE A  74 
 TRP   0.009   0.001   TRP B  63 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 9407)
  covalent geometry    : angle       0.51902 (12757)
  SS BOND              : bond        0.00462 (    3)
  SS BOND              : angle       1.11463 (    6)
  hydrogen bonds       : bond        0.06701 (  447)
  hydrogen bonds       : angle       4.20813 ( 1287)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 177
  time to evaluate  : 0.366 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7708 (mppt)
REVERT: A  160 ILE cc_start: 0.8146 (mm) cc_final: 0.7941 (mp)
REVERT: R   34 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8183 (mm)
REVERT: R  119 ASP cc_start: 0.8596 (t70) cc_final: 0.8383 (t0)
REVERT: S  223 TYR cc_start: 0.6975 (OUTLIER) cc_final: 0.6697 (t80)
  outliers start: 44
  outliers final: 27
  residues processed: 201
  average time/residue: 0.4782
  time to fit residues: 103.9418
Evaluate side-chains
  204 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 174
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LYS
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain R residue   23 VAL
Chi-restraints excluded: chain R residue   34 LEU
Chi-restraints excluded: chain R residue   85 THR
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  159 ILE
Chi-restraints excluded: chain R residue  162 SER
Chi-restraints excluded: chain R residue  188 THR
Chi-restraints excluded: chain R residue  210 LEU
Chi-restraints excluded: chain R residue  222 THR
Chi-restraints excluded: chain R residue  223 ILE
Chi-restraints excluded: chain R residue  247 SER
Chi-restraints excluded: chain R residue  266 VAL
Chi-restraints excluded: chain S residue   17 SER
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  159 ASN
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain S residue  233 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 101 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 110 optimal weight:    0.0030
   chunk 92 optimal weight:    0.6980
   chunk 98 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.6592

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
R 170 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.122092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.103615 restraints weight = 13878.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 2.07
r_work: 0.3230 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3082
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3082 r_free = 0.3082    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3082 r_free = 0.3082    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3082
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.1021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9410  Z= 0.136
  Angle     :  0.503   6.571  12763  Z= 0.269
  Chirality :  0.041   0.192   1462
  Planarity :  0.004   0.059   1607
  Dihedral  :  4.860  67.736   1336
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 17.44 %
    Favored  : 77.90 %
  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 are not related in a simple way.
  whole:  1.29 (0.25), residues: 1149
  helix:  2.90 (0.25), residues: 409
  sheet:  1.09 (0.31), residues: 277
  loop : -1.29 (0.26), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 117 
 TYR   0.028   0.001   TYR S 178 
 PHE   0.013   0.001   PHE A  74 
 TRP   0.008   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 9407)
  covalent geometry    : angle       0.50222 (12757)
  SS BOND              : bond        0.00440 (    3)
  SS BOND              : angle       1.01224 (    6)
  hydrogen bonds       : bond        0.06246 (  447)
  hydrogen bonds       : angle       4.09589 ( 1287)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 177
  time to evaluate  : 0.352 
Fit side-chains
REVERT: A   73 ARG cc_start: 0.8089 (mtp-110) cc_final: 0.7841 (mtp-110)
REVERT: A  148 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7312 (mpt)
REVERT: A  160 ILE cc_start: 0.8163 (mm) cc_final: 0.7942 (mp)
REVERT: B   25 CYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7381 (t)
REVERT: R  119 ASP cc_start: 0.8628 (t70) cc_final: 0.8419 (t0)
REVERT: S  223 TYR cc_start: 0.6917 (OUTLIER) cc_final: 0.6645 (t80)
  outliers start: 47
  outliers final: 29
  residues processed: 199
  average time/residue: 0.4617
  time to fit residues: 99.2649
Evaluate side-chains
  207 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 175
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain C residue   19 LEU
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain R residue   23 VAL
Chi-restraints excluded: chain R residue   85 THR
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  159 ILE
Chi-restraints excluded: chain R residue  188 THR
Chi-restraints excluded: chain R residue  210 LEU
Chi-restraints excluded: chain R residue  222 THR
Chi-restraints excluded: chain R residue  223 ILE
Chi-restraints excluded: chain R residue  247 SER
Chi-restraints excluded: chain R residue  266 VAL
Chi-restraints excluded: chain S residue   17 SER
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  159 ASN
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain S residue  233 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 44 optimal weight:    0.0870
   chunk 38 optimal weight:    0.4980
   chunk 18 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 110 optimal weight:    0.8980
   chunk 71 optimal weight:    0.5980
   chunk 96 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   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 209 HIS
B 259 GLN
R 170 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.123156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.104727 restraints weight = 13823.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 2.07
r_work: 0.3248 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3101 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3098
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3098 r_free = 0.3098    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3098 r_free = 0.3098    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3098
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.1152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9410  Z= 0.119
  Angle     :  0.482   6.450  12763  Z= 0.257
  Chirality :  0.041   0.198   1462
  Planarity :  0.004   0.059   1607
  Dihedral  :  4.686  64.215   1336
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 18.43 %
    Favored  : 77.30 %
  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 are not related in a simple way.
  whole:  1.42 (0.25), residues: 1149
  helix:  3.07 (0.25), residues: 409
  sheet:  1.11 (0.31), residues: 277
  loop : -1.23 (0.26), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 232 
 TYR   0.025   0.001   TYR S 178 
 PHE   0.012   0.001   PHE A  74 
 TRP   0.008   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 9407)
  covalent geometry    : angle       0.48187 (12757)
  SS BOND              : bond        0.00393 (    3)
  SS BOND              : angle       0.90633 (    6)
  hydrogen bonds       : bond        0.05683 (  447)
  hydrogen bonds       : angle       3.97511 ( 1287)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 182
  time to evaluate  : 0.363 
Fit side-chains
REVERT: A  160 ILE cc_start: 0.8159 (mm) cc_final: 0.7936 (mp)
REVERT: R   34 LEU cc_start: 0.8469 (mm) cc_final: 0.8154 (mm)
REVERT: R  119 ASP cc_start: 0.8622 (t70) cc_final: 0.8421 (t0)
REVERT: S  223 TYR cc_start: 0.6757 (OUTLIER) cc_final: 0.6513 (t80)
  outliers start: 43
  outliers final: 24
  residues processed: 202
  average time/residue: 0.4453
  time to fit residues: 97.3197
Evaluate side-chains
  204 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 179
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain C residue   19 LEU
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain R residue    7 VAL
Chi-restraints excluded: chain R residue   23 VAL
Chi-restraints excluded: chain R residue   85 THR
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  188 THR
Chi-restraints excluded: chain R residue  210 LEU
Chi-restraints excluded: chain R residue  223 ILE
Chi-restraints excluded: chain R residue  266 VAL
Chi-restraints excluded: chain S residue   17 SER
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue  159 ASN
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain S residue  233 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0980
   chunk 71 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
R 170 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.122150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.103620 restraints weight = 13862.230|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 2.08
r_work: 0.3229 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3082 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3081
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3081 r_free = 0.3081    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3081 r_free = 0.3081    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3081
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.1126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9410  Z= 0.141
  Angle     :  0.507   6.822  12763  Z= 0.270
  Chirality :  0.041   0.216   1462
  Planarity :  0.004   0.060   1607
  Dihedral  :  4.717  61.976   1336
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 19.13 %
    Favored  : 76.71 %
  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 are not related in a simple way.
  whole:  1.38 (0.25), residues: 1149
  helix:  3.01 (0.25), residues: 409
  sheet:  1.10 (0.31), residues: 279
  loop : -1.25 (0.26), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG S  98 
 TYR   0.029   0.001   TYR S 178 
 PHE   0.013   0.002   PHE A  74 
 TRP   0.008   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 9407)
  covalent geometry    : angle       0.50661 (12757)
  SS BOND              : bond        0.00470 (    3)
  SS BOND              : angle       0.98997 (    6)
  hydrogen bonds       : bond        0.06156 (  447)
  hydrogen bonds       : angle       4.01519 ( 1287)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 177
  time to evaluate  : 0.363 
Fit side-chains
REVERT: A  148 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7602 (mmm)
REVERT: A  160 ILE cc_start: 0.8126 (mm) cc_final: 0.7903 (mp)
REVERT: B   25 CYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7339 (t)
REVERT: R   34 LEU cc_start: 0.8456 (mm) cc_final: 0.8188 (mm)
REVERT: S  223 TYR cc_start: 0.6818 (OUTLIER) cc_final: 0.6549 (t80)
  outliers start: 42
  outliers final: 30
  residues processed: 200
  average time/residue: 0.4979
  time to fit residues: 107.4922
Evaluate side-chains
  208 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 175
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain C residue   19 LEU
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain R residue    7 VAL
Chi-restraints excluded: chain R residue   23 VAL
Chi-restraints excluded: chain R residue   85 THR
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  159 ILE
Chi-restraints excluded: chain R residue  162 SER
Chi-restraints excluded: chain R residue  188 THR
Chi-restraints excluded: chain R residue  210 LEU
Chi-restraints excluded: chain R residue  222 THR
Chi-restraints excluded: chain R residue  223 ILE
Chi-restraints excluded: chain R residue  247 SER
Chi-restraints excluded: chain R residue  266 VAL
Chi-restraints excluded: chain S residue   17 SER
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  159 ASN
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain S residue  233 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 82 optimal weight:    0.5980
   chunk 58 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 79 optimal weight:    0.1980
   chunk 37 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 104 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
R 170 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.123405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.104772 restraints weight = 14097.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 2.10
r_work: 0.3242 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3095 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3093
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3093 r_free = 0.3093    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3093 r_free = 0.3093    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3093
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.1235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9410  Z= 0.125
  Angle     :  0.494   6.386  12763  Z= 0.264
  Chirality :  0.041   0.236   1462
  Planarity :  0.004   0.059   1607
  Dihedral  :  4.610  59.143   1336
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 19.92 %
    Favored  : 76.71 %
  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 are not related in a simple way.
  whole:  1.44 (0.25), residues: 1149
  helix:  3.07 (0.25), residues: 409
  sheet:  1.12 (0.31), residues: 279
  loop : -1.22 (0.26), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 194 
 TYR   0.027   0.001   TYR S 178 
 PHE   0.012   0.001   PHE A  74 
 TRP   0.008   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 9407)
  covalent geometry    : angle       0.49410 (12757)
  SS BOND              : bond        0.00407 (    3)
  SS BOND              : angle       0.90995 (    6)
  hydrogen bonds       : bond        0.05770 (  447)
  hydrogen bonds       : angle       3.95811 ( 1287)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 178
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A  148 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7567 (mmm)
REVERT: A  160 ILE cc_start: 0.8117 (mm) cc_final: 0.7889 (mp)
REVERT: B   25 CYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7334 (t)
REVERT: R   34 LEU cc_start: 0.8396 (mm) cc_final: 0.8136 (mm)
REVERT: S  223 TYR cc_start: 0.6732 (OUTLIER) cc_final: 0.6480 (t80)
  outliers start: 34
  outliers final: 26
  residues processed: 193
  average time/residue: 0.4778
  time to fit residues: 99.5933
Evaluate side-chains
  205 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 176
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain C residue   19 LEU
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain R residue    7 VAL
Chi-restraints excluded: chain R residue   23 VAL
Chi-restraints excluded: chain R residue   85 THR
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  188 THR
Chi-restraints excluded: chain R residue  210 LEU
Chi-restraints excluded: chain R residue  223 ILE
Chi-restraints excluded: chain R residue  247 SER
Chi-restraints excluded: chain R residue  266 VAL
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue  159 ASN
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain S residue  233 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 108 optimal weight:    0.6980
   chunk 96 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9980
   chunk 92 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
** R 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.121176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.102714 restraints weight = 13934.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 2.06
r_work: 0.3216 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3069
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3069 r_free = 0.3069    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3069 r_free = 0.3069    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3069
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.1121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9410  Z= 0.165
  Angle     :  0.530   6.958  12763  Z= 0.284
  Chirality :  0.042   0.210   1462
  Planarity :  0.004   0.059   1607
  Dihedral  :  4.734  57.615   1336
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 19.03 %
    Favored  : 76.81 %
  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 are not related in a simple way.
  whole:  1.33 (0.25), residues: 1149
  helix:  2.94 (0.25), residues: 409
  sheet:  1.10 (0.31), residues: 277
  loop : -1.27 (0.26), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG S  98 
 TYR   0.032   0.002   TYR S 178 
 PHE   0.014   0.002   PHE A  74 
 TRP   0.008   0.001   TRP B  82 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 9407)
  covalent geometry    : angle       0.52933 (12757)
  SS BOND              : bond        0.00517 (    3)
  SS BOND              : angle       1.03672 (    6)
  hydrogen bonds       : bond        0.06613 (  447)
  hydrogen bonds       : angle       4.08039 ( 1287)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 176
  time to evaluate  : 0.321 
Fit side-chains
REVERT: A  115 TYR cc_start: 0.8559 (m-10) cc_final: 0.8251 (m-80)
REVERT: A  148 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7753 (mpt)
REVERT: A  151 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7920 (mt-10)
REVERT: B   25 CYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7391 (t)
REVERT: B   55 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7892 (mt)
REVERT: R   34 LEU cc_start: 0.8376 (mm) cc_final: 0.8113 (mm)
REVERT: S   11 LEU cc_start: 0.8440 (mm) cc_final: 0.8193 (tt)
REVERT: S  223 TYR cc_start: 0.6867 (OUTLIER) cc_final: 0.6608 (t80)
  outliers start: 42
  outliers final: 30
  residues processed: 197
  average time/residue: 0.4488
  time to fit residues: 95.6535
Evaluate side-chains
  209 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 175
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain A residue  159 LYS
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain C residue   19 LEU
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain R residue    7 VAL
Chi-restraints excluded: chain R residue   23 VAL
Chi-restraints excluded: chain R residue   85 THR
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  159 ILE
Chi-restraints excluded: chain R residue  162 SER
Chi-restraints excluded: chain R residue  188 THR
Chi-restraints excluded: chain R residue  210 LEU
Chi-restraints excluded: chain R residue  222 THR
Chi-restraints excluded: chain R residue  223 ILE
Chi-restraints excluded: chain R residue  247 SER
Chi-restraints excluded: chain R residue  266 VAL
Chi-restraints excluded: chain S residue   17 SER
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue  159 ASN
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain S residue  233 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9980
   chunk 90 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 111 optimal weight:    5.9990
   chunk 68 optimal weight:    0.0470
   chunk 106 optimal weight:    0.0570
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
R 170 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.123528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.104876 restraints weight = 14162.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 2.11
r_work: 0.3244 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3097 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3095
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3095 r_free = 0.3095    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3095 r_free = 0.3095    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3095
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.1277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9410  Z= 0.120
  Angle     :  0.496   6.577  12763  Z= 0.264
  Chirality :  0.041   0.279   1462
  Planarity :  0.004   0.057   1607
  Dihedral  :  4.549  55.607   1336
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 19.33 %
    Favored  : 76.81 %
  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 are not related in a simple way.
  whole:  1.45 (0.25), residues: 1149
  helix:  3.08 (0.25), residues: 409
  sheet:  1.11 (0.31), residues: 279
  loop : -1.21 (0.26), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 194 
 TYR   0.025   0.001   TYR S 178 
 PHE   0.012   0.001   PHE A  74 
 TRP   0.009   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 9407)
  covalent geometry    : angle       0.49555 (12757)
  SS BOND              : bond        0.00397 (    3)
  SS BOND              : angle       0.89393 (    6)
  hydrogen bonds       : bond        0.05688 (  447)
  hydrogen bonds       : angle       3.94972 ( 1287)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 182
  time to evaluate  : 0.382 
Fit side-chains
REVERT: A  115 TYR cc_start: 0.8553 (m-10) cc_final: 0.8254 (m-80)
REVERT: A  148 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7604 (mmt)
REVERT: A  151 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7923 (mt-10)
REVERT: B   25 CYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7322 (t)
REVERT: B   55 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7830 (mt)
REVERT: R   34 LEU cc_start: 0.8361 (mm) cc_final: 0.8126 (mm)
REVERT: R   88 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7913 (mtmt)
REVERT: S   11 LEU cc_start: 0.8429 (mm) cc_final: 0.8188 (tt)
REVERT: S  223 TYR cc_start: 0.6697 (OUTLIER) cc_final: 0.6449 (t80)
  outliers start: 39
  outliers final: 29
  residues processed: 203
  average time/residue: 0.4617
  time to fit residues: 101.2435
Evaluate side-chains
  212 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 178
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain A residue  159 LYS
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain C residue   19 LEU
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain R residue    7 VAL
Chi-restraints excluded: chain R residue   23 VAL
Chi-restraints excluded: chain R residue   85 THR
Chi-restraints excluded: chain R residue   88 LYS
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  159 ILE
Chi-restraints excluded: chain R residue  188 THR
Chi-restraints excluded: chain R residue  210 LEU
Chi-restraints excluded: chain R residue  222 THR
Chi-restraints excluded: chain R residue  223 ILE
Chi-restraints excluded: chain R residue  247 SER
Chi-restraints excluded: chain R residue  266 VAL
Chi-restraints excluded: chain S residue   17 SER
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue  159 ASN
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain S residue  233 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 49 optimal weight:    0.1980
   chunk 22 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0000
   chunk 98 optimal weight:    0.8980
   chunk 74 optimal weight:    0.7980
   chunk 92 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 87 optimal weight:    0.7980
   chunk 62 optimal weight:    0.0070
   overall best weight:    0.3602

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
R  40 ASN
R 170 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.124366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.105576 restraints weight = 14331.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 2.14
r_work: 0.3271 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3122 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3120
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3120
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.1503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9410  Z= 0.108
  Angle     :  0.487  10.464  12763  Z= 0.257
  Chirality :  0.041   0.308   1462
  Planarity :  0.004   0.060   1607
  Dihedral  :  4.362  52.207   1336
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 20.32 %
    Favored  : 76.81 %
  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 are not related in a simple way.
  whole:  1.53 (0.25), residues: 1149
  helix:  3.14 (0.25), residues: 411
  sheet:  1.15 (0.31), residues: 279
  loop : -1.17 (0.27), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 194 
 TYR   0.022   0.001   TYR S 178 
 PHE   0.012   0.001   PHE A  74 
 TRP   0.009   0.001   TRP A 129 
 HIS   0.003   0.000   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 9407)
  covalent geometry    : angle       0.48646 (12757)
  SS BOND              : bond        0.00341 (    3)
  SS BOND              : angle       0.80857 (    6)
  hydrogen bonds       : bond        0.05044 (  447)
  hydrogen bonds       : angle       3.83916 ( 1287)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 188
  time to evaluate  : 0.329 
Fit side-chains
REVERT: A  147 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7569 (p0)
REVERT: A  148 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7528 (mpt)
REVERT: A  151 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7916 (mt-10)
REVERT: A  160 ILE cc_start: 0.8138 (mm) cc_final: 0.7908 (mp)
REVERT: B   25 CYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7231 (t)
REVERT: B   55 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7783 (mt)
REVERT: R   34 LEU cc_start: 0.8370 (mm) cc_final: 0.8131 (mm)
REVERT: R   88 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7934 (mttt)
REVERT: S   11 LEU cc_start: 0.8406 (mm) cc_final: 0.8202 (tt)
REVERT: S  223 TYR cc_start: 0.6627 (OUTLIER) cc_final: 0.6391 (t80)
  outliers start: 29
  outliers final: 20
  residues processed: 204
  average time/residue: 0.4663
  time to fit residues: 102.9110
Evaluate side-chains
  211 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 185
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  148 MET
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain C residue   19 LEU
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain R residue    7 VAL
Chi-restraints excluded: chain R residue   85 THR
Chi-restraints excluded: chain R residue   88 LYS
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  188 THR
Chi-restraints excluded: chain R residue  223 ILE
Chi-restraints excluded: chain R residue  247 SER
Chi-restraints excluded: chain R residue  266 VAL
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain S residue  233 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 42 optimal weight:    0.0980
   chunk 45 optimal weight:    4.9990
   chunk 103 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9980
   chunk 56 optimal weight:    5.9990
   chunk 78 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
R  52 HIS
** R 170 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 = 0.3623 r_free = 0.3623 target = 0.122103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.103213 restraints weight = 14268.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 2.13
r_work: 0.3229 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3082 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3079
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3079
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.1348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9410  Z= 0.136
  Angle     :  0.519  10.897  12763  Z= 0.275
  Chirality :  0.042   0.300   1462
  Planarity :  0.004   0.060   1607
  Dihedral  :  4.445  54.262   1336
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 20.42 %
    Favored  : 76.91 %
  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 are not related in a simple way.
  whole:  1.47 (0.25), residues: 1149
  helix:  3.09 (0.25), residues: 409
  sheet:  1.12 (0.31), residues: 279
  loop : -1.18 (0.27), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 194 
 TYR   0.029   0.001   TYR S 178 
 PHE   0.013   0.001   PHE A  74 
 TRP   0.009   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 9407)
  covalent geometry    : angle       0.51883 (12757)
  SS BOND              : bond        0.00443 (    3)
  SS BOND              : angle       0.94031 (    6)
  hydrogen bonds       : bond        0.05876 (  447)
  hydrogen bonds       : angle       3.92545 ( 1287)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3860.54 seconds
wall clock time: 66 minutes 21.66 seconds (3981.66 seconds total)