Starting phenix.real_space_refine
on Wed Mar 12 15:52:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rmi_24572/03_2025/7rmi_24572.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rmi_24572/03_2025/7rmi_24572.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rmi_24572/03_2025/7rmi_24572.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rmi_24572/03_2025/7rmi_24572.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rmi_24572/03_2025/7rmi_24572.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rmi_24572/03_2025/7rmi_24572.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.006 sd=   0.375
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1045 atoms to isotropic.
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      52      5.16       5
     C    4667      2.51       5
     N    1220      2.21       5
     O    1266      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7205
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1517
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1517
          Classifications: {'peptide': 194}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 4, 'TRANS': 189}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 104
          Unresolved non-hydrogen angles: 127
          Unresolved non-hydrogen dihedrals: 81
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 8}
          Unresolved non-hydrogen planarities: 73
    Chain: "R"
      Number of atoms: 2221
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2221
          Classifications: {'peptide': 285}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 13, 'TRANS': 271}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 119
          Unresolved non-hydrogen angles: 146
          Unresolved non-hydrogen dihedrals: 101
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 63
    Chain: "S"
      Number of atoms: 51
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 51
          Classifications: {'peptide': 6}
          Link IDs: {'TRANS': 5}
    Chain: "S"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 2319
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 322, 2319
          Classifications: {'peptide': 322}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PTRANS': 5, 'TRANS': 316}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 149
          Unresolved non-hydrogen angles: 183
          Unresolved non-hydrogen dihedrals: 115
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 7, 'ASN:plan1': 5, 'ASP:plan': 13}
          Unresolved non-hydrogen planarities: 113
    Chain: "G"
      Number of atoms: 245
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 245
          Classifications: {'peptide': 38}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 1, 'TRANS': 36}
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 61
          Unresolved non-hydrogen dihedrals: 45
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 28
    Chain: "N"
      Number of atoms: 851
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 851
          Classifications: {'peptide': 115}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 4, 'TRANS': 110}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 38
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 23
  Time building chain proxies: 5.16, per 1000 atoms: 0.72
  Number of scatterers: 7205
  At special positions: 0
  Unit cell: (67.635, 98.53, 128.59, 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      52     16.00
     O    1266      8.00
     N    1220      7.00
     C    4667      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 105 " - pdb=" SG  CYS R 180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.85
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1822

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 11 sheets defined
      39.8% alpha, 22.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 39
      removed outlier: 3.773A  pdb=" N   GLN A  31 " --> pdb=" O   GLU A  27 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ASP A  33 " --> pdb=" O   GLN A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.729A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 264
      No H-bonds generated for 'chain 'A' and resid 252 through 264'
    Processing helix  chain 'A' and resid 265 through 278
      removed outlier: 3.819A  pdb=" N   ALA A 269 " --> pdb=" O   ARG A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 302
    Processing helix  chain 'A' and resid 332 through 350
      removed outlier: 3.741A  pdb=" N   ARG A 336 " --> pdb=" O   PRO A 332 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.655A  pdb=" N   ARG A 374 " --> pdb=" O   GLU A 370 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 28 through 60
      removed outlier: 3.698A  pdb=" N   HIS R  60 " --> pdb=" O   ILE R  56 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 65 through 67
      No H-bonds generated for 'chain 'R' and resid 65 through 67'
    Processing helix  chain 'R' and resid 68 through 94
    Processing helix  chain 'R' and resid 100 through 135
      removed outlier: 4.284A  pdb=" N   TYR R 104 " --> pdb=" O   TYR R 100 " (cutoff:3.500A)
      Proline residue:  R 112  - end of helix
    Processing helix  chain 'R' and resid 143 through 168
      Proline residue:  R 164  - end of helix
    Processing helix  chain 'R' and resid 190 through 205
      removed outlier: 3.908A  pdb=" N   LYS R 194 " --> pdb=" O   LYS R 190 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 205 through 224
      removed outlier: 3.683A  pdb=" N   LEU R 209 " --> pdb=" O   TYR R 205 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 239 through 270
      removed outlier: 3.654A  pdb=" N   LYS R 243 " --> pdb=" O   GLN R 239 " (cutoff:3.500A)
      Proline residue:  R 263  - end of helix
    Processing helix  chain 'R' and resid 271 through 273
      No H-bonds generated for 'chain 'R' and resid 271 through 273'
    Processing helix  chain 'R' and resid 274 through 278
      removed outlier: 4.001A  pdb=" N   LEU R 277 " --> pdb=" O   ASN R 274 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   TYR R 278 " --> pdb=" O   PRO R 275 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 274 through 278'
    Processing helix  chain 'R' and resid 281 through 296
    Processing helix  chain 'R' and resid 299 through 309
      removed outlier: 3.619A  pdb=" N   ILE R 303 " --> pdb=" O   MET R 299 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 309 through 320
      removed outlier: 3.650A  pdb=" N   ARG R 313 " --> pdb=" O   ASN R 309 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   PHE R 320 " --> pdb=" O   PHE R 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 15 through 25
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.965A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   THR B  34 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 29 through 34'
    Processing helix  chain 'G' and resid 14 through 24
      removed outlier: 3.705A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 43
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.811A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 6.506A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.885A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.013A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'R' and resid 169 through 174
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.300A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.499A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.055A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 7.047A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.816A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.714A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.936A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.041A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.179A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.071A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.857A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.972A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.588A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.886A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.720A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.977A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 5.211A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 7.011A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 7.104A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.983A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.510A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.602A  pdb=" N   GLN N   3 " --> pdb=" O   SER N  25 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 59 through 60
      removed outlier: 3.664A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.785A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)

    360 hydrogen bonds defined for protein.
    1035 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: 2.18

  Time building geometry restraints manager: 2.10 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2259
        1.35 -     1.46: 1946
        1.46 -     1.58: 3096
        1.58 -     1.70: 0
        1.70 -     1.82: 75
  Bond restraints: 7376
  Sorted by residual:
  bond pdb=" CB  ASN B 155 "
       pdb=" CG  ASN B 155 "
    ideal  model  delta    sigma   weight residual
    1.516  1.569 -0.053 2.50e-02 1.60e+03 4.47e+00
  bond pdb=" CG1 ILE R 290 "
       pdb=" CD1 ILE R 290 "
    ideal  model  delta    sigma   weight residual
    1.513  1.449  0.064 3.90e-02 6.57e+02 2.73e+00
  bond pdb=" C   LEU R 262 "
       pdb=" N   PRO R 263 "
    ideal  model  delta    sigma   weight residual
    1.336  1.355 -0.019 1.25e-02 6.40e+03 2.29e+00
  bond pdb=" CB  GLN N  39 "
       pdb=" CG  GLN N  39 "
    ideal  model  delta    sigma   weight residual
    1.520  1.565 -0.045 3.00e-02 1.11e+03 2.22e+00
  bond pdb=" C   PHE R 163 "
       pdb=" N   PRO R 164 "
    ideal  model  delta    sigma   weight residual
    1.335  1.353 -0.018 1.28e-02 6.10e+03 1.97e+00
  ... (remaining 7371 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.50: 9844
        2.50 -     5.01: 189
        5.01 -     7.51: 28
        7.51 -    10.01: 4
       10.01 -    12.52: 2
  Bond angle restraints: 10067
  Sorted by residual:
  angle pdb=" CB  MET G  21 "
        pdb=" CG  MET G  21 "
        pdb=" SD  MET G  21 "
      ideal   model   delta    sigma   weight residual
     112.70  124.23  -11.53 3.00e+00 1.11e-01 1.48e+01
  angle pdb=" C   ASN A 292 "
        pdb=" N   LYS A 293 "
        pdb=" CA  LYS A 293 "
      ideal   model   delta    sigma   weight residual
     122.82  128.27   -5.45 1.42e+00 4.96e-01 1.47e+01
  angle pdb=" CA  LEU B 308 "
        pdb=" CB  LEU B 308 "
        pdb=" CG  LEU B 308 "
      ideal   model   delta    sigma   weight residual
     116.30  128.82  -12.52 3.50e+00 8.16e-02 1.28e+01
  angle pdb=" CA  ASN B 155 "
        pdb=" CB  ASN B 155 "
        pdb=" CG  ASN B 155 "
      ideal   model   delta    sigma   weight residual
     112.60  116.09   -3.49 1.00e+00 1.00e+00 1.21e+01
  angle pdb=" CB  GLN N  39 "
        pdb=" CG  GLN N  39 "
        pdb=" CD  GLN N  39 "
      ideal   model   delta    sigma   weight residual
     112.60  118.41   -5.81 1.70e+00 3.46e-01 1.17e+01
  ... (remaining 10062 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.03: 3906
       17.03 -    34.06: 293
       34.06 -    51.10: 49
       51.10 -    68.13: 4
       68.13 -    85.16: 5
  Dihedral angle restraints: 4257
    sinusoidal: 1445
      harmonic: 2812
  Sorted by residual:
  dihedral pdb=" CA  PHE N 108 "
           pdb=" C   PHE N 108 "
           pdb=" N   ASP N 109 "
           pdb=" CA  ASP N 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.34  -27.66     0      5.00e+00 4.00e-02 3.06e+01
  dihedral pdb=" CA  CYS N  99 "
           pdb=" C   CYS N  99 "
           pdb=" N   PRO N 100 "
           pdb=" CA  PRO N 100 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.61  -26.39     0      5.00e+00 4.00e-02 2.78e+01
  dihedral pdb=" CA  MET R 299 "
           pdb=" C   MET R 299 "
           pdb=" N   TYR R 300 "
           pdb=" CA  TYR R 300 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.03  -21.97     0      5.00e+00 4.00e-02 1.93e+01
  ... (remaining 4254 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 814
       0.048 -    0.095: 268
       0.095 -    0.143: 74
       0.143 -    0.191: 19
       0.191 -    0.239: 2
  Chirality restraints: 1177
  Sorted by residual:
  chirality pdb=" CB  VAL A 241 "
            pdb=" CA  VAL A 241 "
            pdb=" CG1 VAL A 241 "
            pdb=" CG2 VAL A 241 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CG  LEU B 255 "
            pdb=" CB  LEU B 255 "
            pdb=" CD1 LEU B 255 "
            pdb=" CD2 LEU B 255 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 9.19e-01
  chirality pdb=" CB  ILE N  70 "
            pdb=" CA  ILE N  70 "
            pdb=" CG1 ILE N  70 "
            pdb=" CG2 ILE N  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.96e-01
  ... (remaining 1174 not shown)

  Planarity restraints: 1255
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 332 "   -0.043 2.00e-02 2.50e+03   3.80e-02 3.60e+01
        pdb=" CG  TRP B 332 "    0.102 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 332 "   -0.045 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 332 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 332 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 332 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 332 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 332 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 332 "   -0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 332 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.050 5.00e-02 4.00e+02   7.50e-02 8.99e+00
        pdb=" N   PRO B 236 "   -0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA R  82 "    0.013 2.00e-02 2.50e+03   2.55e-02 6.51e+00
        pdb=" C   ALA R  82 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   ALA R  82 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ALA R  83 "    0.015 2.00e-02 2.50e+03
  ... (remaining 1252 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2074
        2.82 -     3.34: 6135
        3.34 -     3.86: 11901
        3.86 -     4.38: 12954
        4.38 -     4.90: 23826
  Nonbonded interactions: 56890
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 163 "
            pdb=" OG1 THR B 165 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   ASP N  90 "
            pdb=" OH  TYR N  94 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" O   VAL R 116 "
            pdb=" OG  SER R 119 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" O   GLN B  75 "
            pdb=" OG  SER B  98 "
     model   vdw
     2.328 3.040
  ... (remaining 56885 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     21.160
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7069
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      :  0.004   0.068   7376  Z= 0.273
  Angle     :  0.842  12.516  10067  Z= 0.456
  Chirality :  0.053   0.239   1177
  Planarity :  0.007   0.075   1255
  Dihedral  : 12.681  85.159   2426
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.03 (0.26), residues: 934
  helix: -0.65 (0.24), residues: 338
  sheet:  0.24 (0.36), residues: 201
  loop : -1.09 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.102   0.003   TRP B 332 
 HIS   0.007   0.001   HIS R 108 
 PHE   0.021   0.002   PHE B 241 
 TYR   0.025   0.002   TYR N  60 
 ARG   0.007   0.001   ARG B 137 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.803 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.2137
  time to fit residues: 46.2279
Evaluate side-chains
  113 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 70 optimal weight:    9.9990
   chunk 39 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 47 optimal weight:    0.2980
   chunk 37 optimal weight:    0.9990
   chunk 72 optimal weight:    0.3980
   chunk 28 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 54 optimal weight:    5.9990
   chunk 84 optimal weight:    4.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
B 220 GLN
B 230 ASN
B 295 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.141584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.123039 restraints weight = 15521.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3727 rms_B_bonded: 3.31
r_work: 0.3618 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.1436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7376  Z= 0.168
  Angle     :  0.534   5.773  10067  Z= 0.286
  Chirality :  0.042   0.140   1177
  Planarity :  0.004   0.054   1255
  Dihedral  :  4.299  23.536   1029
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  8.57 %
    Favored  : 91.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.27), residues: 934
  helix:  1.03 (0.28), residues: 342
  sheet:  0.29 (0.35), residues: 220
  loop : -0.81 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.062   0.002   TRP B 332 
 HIS   0.006   0.001   HIS R 108 
 PHE   0.021   0.001   PHE B 292 
 TYR   0.011   0.001   TYR N  94 
 ARG   0.004   0.000   ARG N  67 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 130
  time to evaluate  : 0.780 
Fit side-chains
REVERT: A  378 ASP cc_start: 0.8478 (m-30) cc_final: 0.8193 (m-30)
REVERT: B  308 LEU cc_start: 0.7157 (mm) cc_final: 0.6499 (tt)
REVERT: B  325 MET cc_start: 0.6905 (ptt) cc_final: 0.6560 (ptt)
REVERT: N   32 TYR cc_start: 0.7771 (m-80) cc_final: 0.7547 (m-80)
REVERT: N   38 ARG cc_start: 0.8218 (mtm180) cc_final: 0.8002 (mtm110)
REVERT: N   53 GLN cc_start: 0.8254 (mp10) cc_final: 0.8007 (mp10)
  outliers start: 3
  outliers final: 2
  residues processed: 130
  average time/residue: 0.1876
  time to fit residues: 33.8676
Evaluate side-chains
  115 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 113
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  153 VAL
Chi-restraints excluded: chain R residue  252 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 70 optimal weight:   10.0000
   chunk 22 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 68 optimal weight:    8.9990
   chunk 44 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 80 optimal weight:    3.9990
   chunk 56 optimal weight:    0.4980
   overall best weight:    2.4988

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
A 267 GLN
R 136 HIS
** R 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 183 HIS
B 295 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.130650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.111795 restraints weight = 15755.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3592 rms_B_bonded: 3.33
r_work: 0.3481 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.2492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   7376  Z= 0.380
  Angle     :  0.644   8.834  10067  Z= 0.345
  Chirality :  0.045   0.148   1177
  Planarity :  0.004   0.050   1255
  Dihedral  :  4.495  23.721   1029
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 11.57 %
    Favored  : 86.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.27), residues: 934
  helix:  1.05 (0.27), residues: 351
  sheet:  0.42 (0.36), residues: 200
  loop : -0.77 (0.32), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.002   TRP B 332 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.014   0.002   PHE R 264 
 TYR   0.017   0.002   TYR N  94 
 ARG   0.003   0.000   ARG R 141 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 121
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
REVERT: A  249 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7801 (t70)
REVERT: A  368 ASP cc_start: 0.8607 (t0) cc_final: 0.8037 (t0)
REVERT: A  378 ASP cc_start: 0.8747 (m-30) cc_final: 0.8367 (m-30)
REVERT: R   54 MET cc_start: 0.7695 (mmt) cc_final: 0.7324 (mmt)
REVERT: R  293 LEU cc_start: 0.9396 (tp) cc_final: 0.9137 (tt)
REVERT: B  308 LEU cc_start: 0.7655 (mm) cc_final: 0.7025 (tt)
REVERT: N   53 GLN cc_start: 0.8455 (mp10) cc_final: 0.8211 (mp10)
  outliers start: 15
  outliers final: 10
  residues processed: 129
  average time/residue: 0.1907
  time to fit residues: 34.2518
Evaluate side-chains
  122 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain R residue   94 VAL
Chi-restraints excluded: chain R residue  153 VAL
Chi-restraints excluded: chain R residue  156 VAL
Chi-restraints excluded: chain R residue  171 THR
Chi-restraints excluded: chain R residue  202 VAL
Chi-restraints excluded: chain R residue  252 VAL
Chi-restraints excluded: chain R residue  253 VAL
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain N residue   99 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 88 optimal weight:    6.9990
   chunk 2 optimal weight:    0.5980
   chunk 82 optimal weight:    7.9990
   chunk 50 optimal weight:    7.9990
   chunk 49 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 27 optimal weight:    0.6980
   chunk 80 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 48 optimal weight:    6.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
** R 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.133534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.114896 restraints weight = 15635.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3634 rms_B_bonded: 3.31
r_work: 0.3523 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7376  Z= 0.194
  Angle     :  0.534   8.283  10067  Z= 0.280
  Chirality :  0.042   0.135   1177
  Planarity :  0.003   0.046   1255
  Dihedral  :  4.160  21.822   1029
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 13.43 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.28), residues: 934
  helix:  1.56 (0.28), residues: 349
  sheet:  0.37 (0.35), residues: 207
  loop : -0.61 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP B 332 
 HIS   0.006   0.001   HIS R 108 
 PHE   0.011   0.001   PHE N  27 
 TYR   0.014   0.001   TYR A 391 
 ARG   0.003   0.000   ARG A  38 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.809 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  249 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7835 (t70)
REVERT: A  368 ASP cc_start: 0.8597 (t0) cc_final: 0.7959 (t0)
REVERT: R   54 MET cc_start: 0.7722 (mmt) cc_final: 0.7497 (mmt)
REVERT: B  227 SER cc_start: 0.8676 (t) cc_final: 0.8005 (p)
REVERT: B  308 LEU cc_start: 0.7585 (mm) cc_final: 0.7016 (tt)
REVERT: N   39 GLN cc_start: 0.8391 (tp40) cc_final: 0.8092 (tp40)
REVERT: N   53 GLN cc_start: 0.8448 (mp10) cc_final: 0.8202 (mp10)
REVERT: N   80 TYR cc_start: 0.6405 (m-80) cc_final: 0.6068 (m-80)
  outliers start: 16
  outliers final: 9
  residues processed: 128
  average time/residue: 0.1608
  time to fit residues: 29.3490
Evaluate side-chains
  123 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain R residue  153 VAL
Chi-restraints excluded: chain R residue  171 THR
Chi-restraints excluded: chain R residue  182 ILE
Chi-restraints excluded: chain R residue  202 VAL
Chi-restraints excluded: chain R residue  252 VAL
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue   99 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 82 optimal weight:    6.9990
   chunk 62 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 63 optimal weight:    8.9990
   chunk 30 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 57 optimal weight:    5.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
R 284 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.132504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.113774 restraints weight = 15771.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 3.31
r_work: 0.3516 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.2626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   7376  Z= 0.234
  Angle     :  0.541   7.528  10067  Z= 0.285
  Chirality :  0.043   0.138   1177
  Planarity :  0.003   0.044   1255
  Dihedral  :  4.087  21.506   1029
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 15.86 %
    Favored  : 82.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.28), residues: 934
  helix:  1.69 (0.27), residues: 349
  sheet:  0.42 (0.35), residues: 207
  loop : -0.58 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B 332 
 HIS   0.006   0.001   HIS R 108 
 PHE   0.011   0.001   PHE R 264 
 TYR   0.013   0.001   TYR A 391 
 ARG   0.003   0.000   ARG A  38 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  249 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7834 (t70)
REVERT: A  368 ASP cc_start: 0.8625 (t0) cc_final: 0.7959 (t0)
REVERT: B  227 SER cc_start: 0.8736 (t) cc_final: 0.8065 (p)
REVERT: B  308 LEU cc_start: 0.7793 (mm) cc_final: 0.7234 (tt)
REVERT: N   39 GLN cc_start: 0.8413 (tp40) cc_final: 0.7844 (tp40)
REVERT: N   53 GLN cc_start: 0.8502 (mp10) cc_final: 0.8243 (mp10)
  outliers start: 13
  outliers final: 11
  residues processed: 130
  average time/residue: 0.1581
  time to fit residues: 29.3888
Evaluate side-chains
  127 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain R residue  153 VAL
Chi-restraints excluded: chain R residue  171 THR
Chi-restraints excluded: chain R residue  182 ILE
Chi-restraints excluded: chain R residue  202 VAL
Chi-restraints excluded: chain R residue  252 VAL
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue   99 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 82 optimal weight:    9.9990
   chunk 22 optimal weight:    0.4980
   chunk 36 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 86 optimal weight:    0.0470
   chunk 26 optimal weight:    2.9990
   chunk 73 optimal weight:    0.0970
   overall best weight:    0.4476

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.136017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.117238 restraints weight = 15694.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 3.35
r_work: 0.3566 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.2620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.062   7376  Z= 0.146
  Angle     :  0.493   6.875  10067  Z= 0.257
  Chirality :  0.041   0.134   1177
  Planarity :  0.003   0.042   1255
  Dihedral  :  3.825  19.850   1029
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 16.71 %
    Favored  : 81.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.28), residues: 934
  helix:  2.05 (0.28), residues: 349
  sheet:  0.48 (0.35), residues: 205
  loop : -0.60 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 332 
 HIS   0.004   0.001   HIS R 108 
 PHE   0.010   0.001   PHE B 241 
 TYR   0.010   0.001   TYR N  95 
 ARG   0.002   0.000   ARG A  38 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.751 
Fit side-chains
REVERT: A  368 ASP cc_start: 0.8590 (t0) cc_final: 0.7921 (t0)
REVERT: B  227 SER cc_start: 0.8638 (t) cc_final: 0.7981 (p)
REVERT: B  308 LEU cc_start: 0.7763 (mm) cc_final: 0.7209 (tt)
REVERT: B  325 MET cc_start: 0.6897 (ptt) cc_final: 0.6592 (ptt)
REVERT: N   34 MET cc_start: 0.7482 (mtp) cc_final: 0.7171 (mtt)
REVERT: N   39 GLN cc_start: 0.8443 (tp40) cc_final: 0.7805 (tp40)
REVERT: N   53 GLN cc_start: 0.8490 (mp10) cc_final: 0.8245 (mp10)
REVERT: N   80 TYR cc_start: 0.6343 (m-80) cc_final: 0.6047 (m-80)
  outliers start: 13
  outliers final: 6
  residues processed: 127
  average time/residue: 0.1669
  time to fit residues: 29.8529
Evaluate side-chains
  121 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 115
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain R residue   94 VAL
Chi-restraints excluded: chain R residue  202 VAL
Chi-restraints excluded: chain R residue  270 LEU
Chi-restraints excluded: chain N residue   73 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 57 optimal weight:    6.9990
   chunk 63 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 69 optimal weight:   10.0000
   chunk 62 optimal weight:    6.9990
   chunk 79 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 49 optimal weight:    0.0070
   overall best weight:    0.9200

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.135070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.116162 restraints weight = 15524.985|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 3.34
r_work: 0.3556 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.2741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   7376  Z= 0.189
  Angle     :  0.528   6.732  10067  Z= 0.273
  Chirality :  0.042   0.138   1177
  Planarity :  0.003   0.041   1255
  Dihedral  :  3.847  18.872   1029
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 16.57 %
    Favored  : 81.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.28), residues: 934
  helix:  2.04 (0.28), residues: 349
  sheet:  0.59 (0.36), residues: 205
  loop : -0.56 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 332 
 HIS   0.005   0.001   HIS R 108 
 PHE   0.010   0.001   PHE R 264 
 TYR   0.011   0.001   TYR N  95 
 ARG   0.002   0.000   ARG A  38 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
REVERT: A  368 ASP cc_start: 0.8641 (t0) cc_final: 0.7983 (t0)
REVERT: B  227 SER cc_start: 0.8702 (t) cc_final: 0.8045 (p)
REVERT: B  308 LEU cc_start: 0.7830 (mm) cc_final: 0.7234 (tt)
REVERT: N   39 GLN cc_start: 0.8433 (tp40) cc_final: 0.7843 (tp40)
REVERT: N   53 GLN cc_start: 0.8507 (mp10) cc_final: 0.8261 (mp10)
REVERT: N   80 TYR cc_start: 0.6376 (m-80) cc_final: 0.6037 (m-80)
  outliers start: 12
  outliers final: 11
  residues processed: 125
  average time/residue: 0.2059
  time to fit residues: 36.7455
Evaluate side-chains
  129 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 1.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  358 TYR
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue   94 VAL
Chi-restraints excluded: chain R residue  153 VAL
Chi-restraints excluded: chain R residue  202 VAL
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  108 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 71 optimal weight:   20.0000
   chunk 70 optimal weight:    0.6980
   chunk 50 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 54 optimal weight:    3.9990
   chunk 43 optimal weight:    0.0670
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.6918

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.136403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.117438 restraints weight = 15703.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 3.38
r_work: 0.3568 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.2765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.059   7376  Z= 0.165
  Angle     :  0.513   6.593  10067  Z= 0.264
  Chirality :  0.042   0.134   1177
  Planarity :  0.003   0.041   1255
  Dihedral  :  3.782  19.534   1029
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 17.43 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.28), residues: 934
  helix:  2.20 (0.28), residues: 350
  sheet:  0.63 (0.36), residues: 204
  loop : -0.54 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 332 
 HIS   0.003   0.001   HIS R 108 
 PHE   0.010   0.001   PHE B 292 
 TYR   0.010   0.001   TYR A 391 
 ARG   0.003   0.000   ARG B 314 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
REVERT: A  333 ARG cc_start: 0.4655 (OUTLIER) cc_final: 0.4131 (mmm160)
REVERT: A  368 ASP cc_start: 0.8633 (t0) cc_final: 0.8000 (t0)
REVERT: B  227 SER cc_start: 0.8692 (t) cc_final: 0.8041 (p)
REVERT: B  308 LEU cc_start: 0.7820 (mm) cc_final: 0.7246 (tt)
REVERT: N   34 MET cc_start: 0.7496 (mtp) cc_final: 0.7177 (mtm)
REVERT: N   39 GLN cc_start: 0.8425 (tp40) cc_final: 0.7798 (tp40)
REVERT: N   53 GLN cc_start: 0.8495 (mp10) cc_final: 0.8248 (mp10)
REVERT: N   80 TYR cc_start: 0.6375 (m-80) cc_final: 0.6043 (m-80)
  outliers start: 13
  outliers final: 12
  residues processed: 124
  average time/residue: 0.1952
  time to fit residues: 33.6247
Evaluate side-chains
  131 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  333 ARG
Chi-restraints excluded: chain R residue   56 ILE
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue   94 VAL
Chi-restraints excluded: chain R residue  153 VAL
Chi-restraints excluded: chain R residue  202 VAL
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  108 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0670
   chunk 48 optimal weight:    0.3980
   chunk 53 optimal weight:    5.9990
   chunk 27 optimal weight:    0.4980
   chunk 44 optimal weight:    0.6980
   chunk 46 optimal weight:    0.8980
   chunk 64 optimal weight:    0.0470
   chunk 84 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    0.3416

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.138384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.119553 restraints weight = 15454.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3709 rms_B_bonded: 3.34
r_work: 0.3600 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.2812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049   7376  Z= 0.139
  Angle     :  0.499   6.882  10067  Z= 0.255
  Chirality :  0.041   0.134   1177
  Planarity :  0.003   0.040   1255
  Dihedral  :  3.606  17.542   1029
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 18.14 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.28), residues: 934
  helix:  2.33 (0.28), residues: 351
  sheet:  0.66 (0.36), residues: 205
  loop : -0.48 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 332 
 HIS   0.003   0.001   HIS R 108 
 PHE   0.010   0.001   PHE R 268 
 TYR   0.009   0.001   TYR A 391 
 ARG   0.003   0.000   ARG B 314 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 122
  time to evaluate  : 0.753 
Fit side-chains
REVERT: A  368 ASP cc_start: 0.8548 (t0) cc_final: 0.7867 (t0)
REVERT: B  227 SER cc_start: 0.8565 (t) cc_final: 0.7897 (p)
REVERT: B  308 LEU cc_start: 0.7774 (mm) cc_final: 0.7211 (tt)
REVERT: B  325 MET cc_start: 0.6930 (ptt) cc_final: 0.6432 (ptt)
REVERT: N   34 MET cc_start: 0.7453 (mtp) cc_final: 0.7142 (mtm)
REVERT: N   39 GLN cc_start: 0.8359 (tp40) cc_final: 0.7745 (tp40)
REVERT: N   53 GLN cc_start: 0.8481 (mp10) cc_final: 0.8233 (mp10)
REVERT: N   80 TYR cc_start: 0.6347 (m-80) cc_final: 0.6055 (m-80)
  outliers start: 10
  outliers final: 8
  residues processed: 126
  average time/residue: 0.1575
  time to fit residues: 28.2216
Evaluate side-chains
  123 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  358 TYR
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue   94 VAL
Chi-restraints excluded: chain R residue  202 VAL
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue   99 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 84 optimal weight:    5.9990
   chunk 74 optimal weight:    0.0020
   chunk 42 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 90 optimal weight:   10.0000
   chunk 78 optimal weight:    7.9990
   chunk 83 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   overall best weight:    1.1994

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

Flipped N/Q/H residues before XYZ refinement:
** R 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.134628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.115473 restraints weight = 15964.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3645 rms_B_bonded: 3.41
r_work: 0.3536 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.2895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   7376  Z= 0.221
  Angle     :  0.544   7.123  10067  Z= 0.282
  Chirality :  0.043   0.141   1177
  Planarity :  0.003   0.039   1255
  Dihedral  :  3.810  19.093   1029
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 18.29 %
    Favored  : 79.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.28), residues: 934
  helix:  2.19 (0.28), residues: 352
  sheet:  0.72 (0.36), residues: 201
  loop : -0.48 (0.33), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 332 
 HIS   0.003   0.001   HIS R 197 
 PHE   0.013   0.001   PHE R 264 
 TYR   0.012   0.001   TYR A 391 
 ARG   0.005   0.000   ARG N  38 

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

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

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1868 Ramachandran restraints generated.
    934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
REVERT: A  368 ASP cc_start: 0.8668 (t0) cc_final: 0.8027 (t0)
REVERT: B  183 HIS cc_start: 0.7424 (OUTLIER) cc_final: 0.7143 (m90)
REVERT: B  227 SER cc_start: 0.8737 (t) cc_final: 0.8081 (p)
REVERT: B  308 LEU cc_start: 0.7911 (mm) cc_final: 0.7309 (tt)
REVERT: N   39 GLN cc_start: 0.8358 (tp40) cc_final: 0.7986 (tp40)
REVERT: N   80 TYR cc_start: 0.6422 (m-80) cc_final: 0.6068 (m-80)
  outliers start: 13
  outliers final: 10
  residues processed: 127
  average time/residue: 0.1690
  time to fit residues: 30.2808
Evaluate side-chains
  130 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain R residue   81 MET
Chi-restraints excluded: chain R residue   94 VAL
Chi-restraints excluded: chain R residue  153 VAL
Chi-restraints excluded: chain R residue  202 VAL
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue   99 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 80 optimal weight:    0.0870
   chunk 28 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 52 optimal weight:    4.9990
   chunk 45 optimal weight:    0.3980
   chunk 64 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   overall best weight:    1.2964

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

Flipped N/Q/H residues before XYZ refinement:
** R 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.134114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.114987 restraints weight = 15663.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.3673 rms_B_bonded: 3.36
r_work: 0.3565 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.2990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   7376  Z= 0.228
  Angle     :  0.555   7.162  10067  Z= 0.287
  Chirality :  0.043   0.139   1177
  Planarity :  0.003   0.040   1255
  Dihedral  :  3.898  19.516   1029
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 17.86 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.28), residues: 934
  helix:  2.10 (0.28), residues: 352
  sheet:  0.63 (0.36), residues: 203
  loop : -0.46 (0.33), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 332 
 HIS   0.003   0.001   HIS R 197 
 PHE   0.012   0.001   PHE R 264 
 TYR   0.013   0.001   TYR A 391 
 ARG   0.002   0.000   ARG B 314 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3338.41 seconds
wall clock time: 59 minutes 14.02 seconds (3554.02 seconds total)