Starting phenix.real_space_refine
on Fri Nov 15 02:42:32 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmv_34903/11_2024/8hmv_34903.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmv_34903/11_2024/8hmv_34903.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.91
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmv_34903/11_2024/8hmv_34903.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmv_34903/11_2024/8hmv_34903.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmv_34903/11_2024/8hmv_34903.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmv_34903/11_2024/8hmv_34903.cif"
  }
  resolution = 2.91
  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=  -0.000 sd=   0.035
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      52      5.16       5
     C    5168      2.51       5
     N    1410      2.21       5
     O    1497      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 8127
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2237
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 2237
          Classifications: {'peptide': 274}
          Link IDs: {'PTRANS': 10, 'TRANS': 263}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1892
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1892
          Classifications: {'peptide': 227}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 220}
          Chain breaks: 3
    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: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
  Time building chain proxies: 5.93, per 1000 atoms: 0.73
  Number of scatterers: 8127
  At special positions: 0
  Unit cell: (79.9, 103.7, 128.35, 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    1497      8.00
     N    1410      7.00
     C    5168      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    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=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.09
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1932

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 10 sheets defined
      42.9% alpha, 20.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 30 through 55
    Processing helix  chain 'A' and resid 63 through 82
      removed outlier: 4.155A  pdb=" N   PHE A  67 " --> pdb=" O   THR A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 90
    Processing helix  chain 'A' and resid 97 through 133
      removed outlier: 3.579A  pdb=" N   PHE A 107 " --> pdb=" O   GLN A 103 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   SER A 124 " --> pdb=" O   LEU A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 141
    Processing helix  chain 'A' and resid 142 through 161
      removed outlier: 3.952A  pdb=" N   PHE A 161 " --> pdb=" O   SER A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 165
    Processing helix  chain 'A' and resid 173 through 177
      removed outlier: 3.627A  pdb=" N   ASP A 176 " --> pdb=" O   TYR A 173 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   VAL A 177 " --> pdb=" O   HIS A 174 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 173 through 177'
    Processing helix  chain 'A' and resid 188 through 233
      removed outlier: 5.055A  pdb=" N   ALA A 201 " --> pdb=" O   MET A 197 " (cutoff:3.500A)
      Proline residue:  A 202  - end of helix
      removed outlier: 3.866A  pdb=" N   VAL A 207 " --> pdb=" O   ALA A 203 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ARG A 231 " --> pdb=" O   GLU A 227 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   PHE A 232 " --> pdb=" O   ARG A 228 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   SER A 233 " --> pdb=" O   GLN A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 278
      removed outlier: 3.535A  pdb=" N   ARG A 256 " --> pdb=" O   MET A 252 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   VAL A 260 " --> pdb=" O   ARG A 256 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   PHE A 261 " --> pdb=" O   ILE A 257 " (cutoff:3.500A)
      removed outlier: 4.785A  pdb=" N   TYR A 262 " --> pdb=" O   THR A 258 " (cutoff:3.500A)
      Proline residue:  A 267  - end of helix
    Processing helix  chain 'A' and resid 282 through 306
      removed outlier: 4.038A  pdb=" N   PHE A 287 " --> pdb=" O   ARG A 283 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   LEU A 288 " --> pdb=" O   PHE A 284 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   SER A 297 " --> pdb=" O   ALA A 293 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   PHE A 298 " --> pdb=" O   ILE A 294 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   CYS A 301 " --> pdb=" O   SER A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 317
    Processing helix  chain 'C' and resid 12 through 39
      removed outlier: 3.956A  pdb=" N   ALA C  39 " --> pdb=" O   GLN C  35 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 49 through 51
      No H-bonds generated for 'chain 'C' and resid 49 through 51'
    Processing helix  chain 'C' and resid 52 through 60
      removed outlier: 3.569A  pdb=" N   ILE C  56 " --> pdb=" O   GLY C  52 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 239
      removed outlier: 3.617A  pdb=" N   GLN C 236 " --> pdb=" O   LYS C 233 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   CYS C 237 " --> pdb=" O   TRP C 234 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   PHE C 238 " --> pdb=" O   ILE C 235 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ASN C 239 " --> pdb=" O   GLN C 236 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 233 through 239'
    Processing helix  chain 'C' and resid 264 through 279
      removed outlier: 3.934A  pdb=" N   GLU C 268 " --> pdb=" O   ASN C 264 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 280 through 283
      removed outlier: 4.188A  pdb=" N   ARG C 283 " --> pdb=" O   ARG C 280 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 280 through 283'
    Processing helix  chain 'C' and resid 295 through 303
      removed outlier: 3.540A  pdb=" N   LEU C 302 " --> pdb=" O   ALA C 298 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 307 through 311
    Processing helix  chain 'C' and resid 314 through 318
    Processing helix  chain 'C' and resid 331 through 350
      removed outlier: 3.735A  pdb=" N   THR C 335 " --> pdb=" O   ASP C 331 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   ALA C 337 " --> pdb=" O   ARG C 333 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 24
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 8 through 24
      removed outlier: 3.838A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.696A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.863A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
    Processing sheet with id=AA1, first strand: chain 'C' and resid 210 through 214
      removed outlier: 6.362A  pdb=" N   HIS C  41 " --> pdb=" O   HIS C 220 " (cutoff:3.500A)
      removed outlier: 7.993A  pdb=" N   PHE C 222 " --> pdb=" O   HIS C  41 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   LEU C  43 " --> pdb=" O   PHE C 222 " (cutoff:3.500A)
      removed outlier: 9.659A  pdb=" N   ALA C 243 " --> pdb=" O   THR C  40 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   ARG C  42 " --> pdb=" O   ALA C 243 " (cutoff:3.500A)
      removed outlier: 8.250A  pdb=" N   ILE C 245 " --> pdb=" O   ARG C  42 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   LEU C  44 " --> pdb=" O   ILE C 245 " (cutoff:3.500A)
      removed outlier: 7.677A  pdb=" N   VAL C 247 " --> pdb=" O   LEU C  44 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   LEU C  46 " --> pdb=" O   VAL C 247 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   ILE C 244 " --> pdb=" O   ILE C 288 " (cutoff:3.500A)
      removed outlier: 7.363A  pdb=" N   PHE C 290 " --> pdb=" O   ILE C 244 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   PHE C 246 " --> pdb=" O   PHE C 290 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   VAL C 287 " --> pdb=" O   TYR C 360 " (cutoff:3.500A)
      removed outlier: 7.863A  pdb=" N   HIS C 362 " --> pdb=" O   VAL C 287 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   LEU C 289 " --> pdb=" O   HIS C 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.632A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.028A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.253A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.680A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.886A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.685A  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: 6.643A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.238A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.400A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.625A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.629A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.606A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.765A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.747A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.591A  pdb=" N   SER N  71 " --> pdb=" O   TYR N  80 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11
      removed outlier: 6.889A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    387 hydrogen bonds defined for protein.
    1104 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: 2.39

  Time building geometry restraints manager: 2.43 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2638
        1.34 -     1.46: 1404
        1.46 -     1.57: 4192
        1.57 -     1.69: 0
        1.69 -     1.81: 71
  Bond restraints: 8305
  Sorted by residual:
  bond pdb=" CG1 ILE B  58 "
       pdb=" CD1 ILE B  58 "
    ideal  model  delta    sigma   weight residual
    1.513  1.463  0.050 3.90e-02 6.57e+02 1.64e+00
  bond pdb=" CG1 ILE B 123 "
       pdb=" CD1 ILE B 123 "
    ideal  model  delta    sigma   weight residual
    1.513  1.470  0.043 3.90e-02 6.57e+02 1.23e+00
  bond pdb=" C   HIS A  61 "
       pdb=" O   HIS A  61 "
    ideal  model  delta    sigma   weight residual
    1.235  1.246 -0.011 1.10e-02 8.26e+03 1.07e+00
  bond pdb=" CB  ASN C 239 "
       pdb=" CG  ASN C 239 "
    ideal  model  delta    sigma   weight residual
    1.516  1.492  0.024 2.50e-02 1.60e+03 9.50e-01
  bond pdb=" CB  THR B 274 "
       pdb=" CG2 THR B 274 "
    ideal  model  delta    sigma   weight residual
    1.521  1.491  0.030 3.30e-02 9.18e+02 8.48e-01
  ... (remaining 8300 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 11002
        1.76 -     3.53: 223
        3.53 -     5.29: 22
        5.29 -     7.06: 6
        7.06 -     8.82: 3
  Bond angle restraints: 11256
  Sorted by residual:
  angle pdb=" N   ASN A  60 "
        pdb=" CA  ASN A  60 "
        pdb=" C   ASN A  60 "
      ideal   model   delta    sigma   weight residual
     111.71  107.92    3.79 1.34e+00 5.57e-01 8.01e+00
  angle pdb=" N   PHE B 234 "
        pdb=" CA  PHE B 234 "
        pdb=" C   PHE B 234 "
      ideal   model   delta    sigma   weight residual
     110.50  114.31   -3.81 1.41e+00 5.03e-01 7.32e+00
  angle pdb=" C   SER B  74 "
        pdb=" N   GLN B  75 "
        pdb=" CA  GLN B  75 "
      ideal   model   delta    sigma   weight residual
     120.31  124.27   -3.96 1.52e+00 4.33e-01 6.79e+00
  angle pdb=" C   GLY A 169 "
        pdb=" N   LYS A 170 "
        pdb=" CA  LYS A 170 "
      ideal   model   delta    sigma   weight residual
     121.59  130.41   -8.82 3.54e+00 7.98e-02 6.21e+00
  angle pdb=" CA  GLN A 103 "
        pdb=" CB  GLN A 103 "
        pdb=" CG  GLN A 103 "
      ideal   model   delta    sigma   weight residual
     114.10  118.76   -4.66 2.00e+00 2.50e-01 5.43e+00
  ... (remaining 11251 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.26: 4470
       17.26 -    34.51: 373
       34.51 -    51.77: 59
       51.77 -    69.02: 12
       69.02 -    86.28: 8
  Dihedral angle restraints: 4922
    sinusoidal: 1940
      harmonic: 2982
  Sorted by residual:
  dihedral pdb=" CA  PRO A  57 "
           pdb=" C   PRO A  57 "
           pdb=" N   LEU A  58 "
           pdb=" CA  LEU A  58 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -143.08  -36.92     0      5.00e+00 4.00e-02 5.45e+01
  dihedral pdb=" CA  LEU C 291 "
           pdb=" C   LEU C 291 "
           pdb=" N   ASN C 292 "
           pdb=" CA  ASN C 292 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.38  -27.62     0      5.00e+00 4.00e-02 3.05e+01
  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 -153.96  -26.04     0      5.00e+00 4.00e-02 2.71e+01
  ... (remaining 4919 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 639
       0.028 -    0.056: 372
       0.056 -    0.084: 162
       0.084 -    0.112: 68
       0.112 -    0.140: 24
  Chirality restraints: 1265
  Sorted by residual:
  chirality pdb=" CA  ILE B  43 "
            pdb=" N   ILE B  43 "
            pdb=" C   ILE B  43 "
            pdb=" CB  ILE B  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.92e-01
  chirality pdb=" CA  TRP A 291 "
            pdb=" N   TRP A 291 "
            pdb=" C   TRP A 291 "
            pdb=" CB  TRP A 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.51e-01
  chirality pdb=" CA  PRO N 100 "
            pdb=" N   PRO N 100 "
            pdb=" C   PRO N 100 "
            pdb=" CB  PRO N 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.13 2.00e-01 2.50e+01 4.47e-01
  ... (remaining 1262 not shown)

  Planarity restraints: 1431
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A  56 "   -0.045 5.00e-02 4.00e+02   6.93e-02 7.68e+00
        pdb=" N   PRO A  57 "    0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO A  57 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A  57 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 266 "    0.031 5.00e-02 4.00e+02   4.60e-02 3.38e+00
        pdb=" N   PRO A 267 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A 267 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 267 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 162 "   -0.025 5.00e-02 4.00e+02   3.80e-02 2.30e+00
        pdb=" N   PRO A 163 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A 163 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 163 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1428 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 203
        2.70 -     3.25: 7636
        3.25 -     3.80: 12121
        3.80 -     4.35: 16263
        4.35 -     4.90: 28420
  Nonbonded interactions: 64643
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.150 3.040
  nonbonded pdb=" OH  TYR C 318 "
            pdb=" OD2 ASP C 343 "
     model   vdw
     2.155 3.040
  nonbonded pdb=" OD1 ASP B 228 "
            pdb=" OH  TYR N 117 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" OD1 ASN C 239 "
            pdb=" NZ  LYS B  57 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" O   GLY B 310 "
            pdb=" NZ  LYS B 337 "
     model   vdw
     2.240 3.120
  ... (remaining 64638 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:                  0.010
  Normalize map: mean=0, sd=1:             1.930
  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:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     22.740
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.040
  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:             0.010
  Load rotamer database and sin/cos tables:12.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
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   0.050   8305  Z= 0.337
  Angle     :  0.635   8.822  11256  Z= 0.361
  Chirality :  0.045   0.140   1265
  Planarity :  0.004   0.069   1431
  Dihedral  : 13.376  86.277   2984
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.72 (0.26), residues: 1004
  helix:  0.72 (0.26), residues: 400
  sheet: -1.04 (0.32), residues: 229
  loop : -1.30 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 291 
 HIS   0.010   0.001   HIS C 357 
 PHE   0.018   0.002   PHE A 272 
 TYR   0.016   0.002   TYR C 358 
 ARG   0.005   0.000   ARG C 265 

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.983 
Fit side-chains
REVERT: C  274 LYS cc_start: 0.8181 (ttmt) cc_final: 0.7930 (ttmt)
REVERT: B   36 ASN cc_start: 0.7654 (m-40) cc_final: 0.7354 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 1.7982
  time to fit residues: 184.1310
Evaluate side-chains
  83 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    4.9990
   chunk 75 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 89 optimal weight:    0.8980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
C  31 GLN
** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 268 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.0892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8305  Z= 0.266
  Angle     :  0.565   8.781  11256  Z= 0.302
  Chirality :  0.044   0.137   1265
  Planarity :  0.004   0.064   1431
  Dihedral  :  4.748  38.322   1116
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  7.77 %
    Favored  : 91.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.21 (0.26), residues: 1004
  helix:  1.25 (0.27), residues: 400
  sheet: -0.46 (0.33), residues: 216
  loop : -1.39 (0.30), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 291 
 HIS   0.009   0.001   HIS C 357 
 PHE   0.015   0.002   PHE B 151 
 TYR   0.015   0.001   TYR C 339 
 ARG   0.004   0.000   ARG N  72 

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.909 
Fit side-chains
REVERT: B   25 CYS cc_start: 0.7743 (t) cc_final: 0.7439 (t)
REVERT: B   36 ASN cc_start: 0.7698 (m-40) cc_final: 0.7427 (m-40)
REVERT: B  197 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7676 (mmt180)
REVERT: B  217 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7415 (ptt)
  outliers start: 10
  outliers final: 4
  residues processed: 95
  average time/residue: 1.7810
  time to fit residues: 177.3882
Evaluate side-chains
  93 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 87
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ILE
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  314 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 90 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 80 optimal weight:    0.6980
   chunk 89 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 72 optimal weight:    0.1980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
C  31 GLN
** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN
N  31 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.1244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8305  Z= 0.195
  Angle     :  0.500   7.639  11256  Z= 0.268
  Chirality :  0.042   0.130   1265
  Planarity :  0.004   0.061   1431
  Dihedral  :  4.405  36.423   1116
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 10.92 %
    Favored  : 87.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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:  0.19 (0.26), residues: 1004
  helix:  1.65 (0.27), residues: 400
  sheet: -0.13 (0.34), residues: 214
  loop : -1.34 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 291 
 HIS   0.007   0.001   HIS C 357 
 PHE   0.014   0.001   PHE B 151 
 TYR   0.013   0.001   TYR C 339 
 ARG   0.002   0.000   ARG A 317 

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.906 
Fit side-chains
REVERT: C  268 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6956 (tp30)
REVERT: C  294 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.6798 (mp10)
REVERT: B   36 ASN cc_start: 0.7717 (m-40) cc_final: 0.7468 (m-40)
REVERT: B   52 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7487 (mtp-110)
REVERT: B  217 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7375 (ptt)
  outliers start: 11
  outliers final: 5
  residues processed: 100
  average time/residue: 1.5973
  time to fit residues: 167.9052
Evaluate side-chains
  99 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  185 TRP
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain C residue  268 GLU
Chi-restraints excluded: chain C residue  294 GLN
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  314 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 88 optimal weight:    5.9990
   chunk 67 optimal weight:    0.0670
   chunk 46 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 42 optimal weight:    5.9990
   chunk 60 optimal weight:    3.9990
   chunk 90 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9980
   chunk 47 optimal weight:    0.5980
   chunk 85 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
C  31 GLN
** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 268 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.1517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8305  Z= 0.151
  Angle     :  0.465   7.074  11256  Z= 0.250
  Chirality :  0.041   0.127   1265
  Planarity :  0.004   0.060   1431
  Dihedral  :  4.147  34.391   1116
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 2.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 11.71 %
    Favored  : 86.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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:  0.51 (0.27), residues: 1004
  helix:  1.93 (0.27), residues: 401
  sheet:  0.12 (0.35), residues: 214
  loop : -1.25 (0.30), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 291 
 HIS   0.006   0.001   HIS C 357 
 PHE   0.012   0.001   PHE B 292 
 TYR   0.011   0.001   TYR C 358 
 ARG   0.002   0.000   ARG C 356 

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.892 
Fit side-chains
REVERT: C  268 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6906 (tp30)
REVERT: C  294 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.6716 (mp10)
REVERT: B   36 ASN cc_start: 0.7729 (m-40) cc_final: 0.7503 (m-40)
REVERT: B   52 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7474 (mtp-110)
  outliers start: 14
  outliers final: 7
  residues processed: 99
  average time/residue: 1.5727
  time to fit residues: 163.8015
Evaluate side-chains
  98 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  185 TRP
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain C residue  268 GLU
Chi-restraints excluded: chain C residue  294 GLN
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  314 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 1 optimal weight:    6.9990
   chunk 71 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 66 optimal weight:    0.0670
   chunk 0 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9980
   chunk 85 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   overall best weight:    1.7322

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

Flipped N/Q/H residues before XYZ refinement:
C  31 GLN
** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  16 ASN
B 268 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.1365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   8305  Z= 0.331
  Angle     :  0.572   8.354  11256  Z= 0.304
  Chirality :  0.044   0.142   1265
  Planarity :  0.004   0.058   1431
  Dihedral  :  4.473  33.788   1116
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 12.73 %
    Favored  : 85.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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:  0.28 (0.27), residues: 1004
  helix:  1.73 (0.26), residues: 400
  sheet: -0.10 (0.34), residues: 218
  loop : -1.30 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 185 
 HIS   0.010   0.001   HIS C 357 
 PHE   0.017   0.002   PHE B 234 
 TYR   0.020   0.002   TYR B 105 
 ARG   0.004   0.000   ARG N 118 

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 1.005 
Fit side-chains
REVERT: C  268 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7018 (tp30)
REVERT: B   36 ASN cc_start: 0.7740 (m-40) cc_final: 0.7509 (m-40)
REVERT: B   46 ARG cc_start: 0.7698 (mmt-90) cc_final: 0.7425 (mmt-90)
REVERT: B   52 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7508 (mtp-110)
  outliers start: 15
  outliers final: 7
  residues processed: 95
  average time/residue: 1.6908
  time to fit residues: 168.3804
Evaluate side-chains
  96 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  185 TRP
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain C residue   60 MET
Chi-restraints excluded: chain C residue  268 GLU
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  314 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 56 optimal weight:    0.4980
   chunk 23 optimal weight:    6.9990
   chunk 95 optimal weight:    0.9990
   chunk 79 optimal weight:    4.9990
   chunk 44 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
C  31 GLN
** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.1580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8305  Z= 0.172
  Angle     :  0.482   7.235  11256  Z= 0.258
  Chirality :  0.041   0.132   1265
  Planarity :  0.004   0.058   1431
  Dihedral  :  4.192  33.330   1116
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 13.29 %
    Favored  : 84.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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:  0.52 (0.27), residues: 1004
  helix:  1.95 (0.27), residues: 400
  sheet:  0.10 (0.35), residues: 214
  loop : -1.23 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 291 
 HIS   0.006   0.001   HIS C 357 
 PHE   0.017   0.001   PHE A 298 
 TYR   0.012   0.001   TYR C 339 
 ARG   0.004   0.000   ARG B  42 

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.926 
Fit side-chains
REVERT: C   60 MET cc_start: 0.5879 (OUTLIER) cc_final: 0.5507 (mpt)
REVERT: C  268 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6972 (tp30)
REVERT: C  294 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.6706 (mp10)
REVERT: B   36 ASN cc_start: 0.7760 (m-40) cc_final: 0.7548 (m-40)
  outliers start: 17
  outliers final: 7
  residues processed: 99
  average time/residue: 1.6918
  time to fit residues: 175.5273
Evaluate side-chains
  95 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  185 TRP
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain C residue   60 MET
Chi-restraints excluded: chain C residue  268 GLU
Chi-restraints excluded: chain C residue  294 GLN
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain N residue   83 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   chunk 80 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 95 optimal weight:    0.6980
   chunk 59 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
C  31 GLN
** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 268 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.1572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8305  Z= 0.225
  Angle     :  0.512   7.677  11256  Z= 0.272
  Chirality :  0.042   0.140   1265
  Planarity :  0.004   0.057   1431
  Dihedral  :  4.244  31.851   1116
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 14.30 %
    Favored  : 84.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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:  0.49 (0.27), residues: 1004
  helix:  1.95 (0.26), residues: 400
  sheet: -0.03 (0.34), residues: 218
  loop : -1.22 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 291 
 HIS   0.007   0.001   HIS C 357 
 PHE   0.015   0.002   PHE A 298 
 TYR   0.014   0.002   TYR C 339 
 ARG   0.006   0.000   ARG B  42 

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 1.004 
Fit side-chains
REVERT: C  268 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6997 (tp30)
REVERT: C  294 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.6725 (mp10)
REVERT: B   36 ASN cc_start: 0.7771 (m-40) cc_final: 0.7558 (m-40)
REVERT: B   52 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7678 (mtp180)
  outliers start: 15
  outliers final: 11
  residues processed: 94
  average time/residue: 1.7774
  time to fit residues: 175.0114
Evaluate side-chains
  97 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  185 TRP
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain C residue   60 MET
Chi-restraints excluded: chain C residue  268 GLU
Chi-restraints excluded: chain C residue  294 GLN
Chi-restraints excluded: chain C residue  390 GLN
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain N residue   83 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 60 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 75 optimal weight:    3.9990
   chunk 86 optimal weight:    0.0000
   chunk 91 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   overall best weight:    0.5984

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

Flipped N/Q/H residues before XYZ refinement:
C  31 GLN
** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 268 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.1775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8305  Z= 0.147
  Angle     :  0.459   6.943  11256  Z= 0.246
  Chirality :  0.041   0.140   1265
  Planarity :  0.004   0.057   1431
  Dihedral  :  4.008  31.014   1116
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 14.41 %
    Favored  : 83.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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:  0.66 (0.27), residues: 1004
  helix:  2.12 (0.27), residues: 401
  sheet:  0.17 (0.35), residues: 210
  loop : -1.22 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 291 
 HIS   0.005   0.001   HIS C 357 
 PHE   0.014   0.001   PHE A 298 
 TYR   0.013   0.001   TYR B  59 
 ARG   0.007   0.000   ARG B  42 

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.986 
Fit side-chains
REVERT: C   60 MET cc_start: 0.5905 (OUTLIER) cc_final: 0.5644 (mpt)
REVERT: C  268 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6907 (tp30)
REVERT: B   52 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7653 (mtp180)
REVERT: B  181 THR cc_start: 0.8799 (p) cc_final: 0.8595 (p)
  outliers start: 16
  outliers final: 7
  residues processed: 103
  average time/residue: 1.8218
  time to fit residues: 196.6534
Evaluate side-chains
  97 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  185 TRP
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain C residue   60 MET
Chi-restraints excluded: chain C residue  268 GLU
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  314 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 91 optimal weight:    0.8980
   chunk 53 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 80 optimal weight:    0.5980
   chunk 84 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 94 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0370
   overall best weight:    0.9060

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

Flipped N/Q/H residues before XYZ refinement:
C  31 GLN
** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 390 GLN
B 268 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.1766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8305  Z= 0.196
  Angle     :  0.490   7.159  11256  Z= 0.261
  Chirality :  0.042   0.149   1265
  Planarity :  0.004   0.056   1431
  Dihedral  :  4.057  29.760   1116
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 14.86 %
    Favored  : 83.56 %
  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 (0.27), residues: 1004
  helix:  2.07 (0.26), residues: 402
  sheet:  0.09 (0.35), residues: 212
  loop : -1.20 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 291 
 HIS   0.006   0.001   HIS C 357 
 PHE   0.014   0.001   PHE A 298 
 TYR   0.015   0.001   TYR B  59 
 ARG   0.002   0.000   ARG B 251 

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 1.026 
Fit side-chains
REVERT: C   60 MET cc_start: 0.5949 (OUTLIER) cc_final: 0.5706 (mpt)
REVERT: C  239 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.8198 (p0)
REVERT: C  268 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6977 (tp30)
REVERT: B   52 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7658 (mtp180)
  outliers start: 14
  outliers final: 8
  residues processed: 93
  average time/residue: 1.6788
  time to fit residues: 164.1746
Evaluate side-chains
  95 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  146 LEU
Chi-restraints excluded: chain A residue  185 TRP
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain C residue   60 MET
Chi-restraints excluded: chain C residue  239 ASN
Chi-restraints excluded: chain C residue  268 GLU
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  314 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 98 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   chunk 78 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0570
   chunk 60 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 62 optimal weight:    0.6980
   chunk 83 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
A  60 ASN
A  69 GLN
C  31 GLN
** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 390 GLN
B 268 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.1915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8305  Z= 0.146
  Angle     :  0.460   6.629  11256  Z= 0.246
  Chirality :  0.041   0.138   1265
  Planarity :  0.003   0.056   1431
  Dihedral  :  3.917  29.143   1116
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 14.86 %
    Favored  : 83.45 %
  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:  0.79 (0.27), residues: 1004
  helix:  2.25 (0.27), residues: 399
  sheet:  0.08 (0.35), residues: 217
  loop : -1.07 (0.30), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 291 
 HIS   0.005   0.001   HIS C 357 
 PHE   0.013   0.001   PHE A 298 
 TYR   0.014   0.001   TYR B  59 
 ARG   0.003   0.000   ARG B  19 

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

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

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2008 Ramachandran restraints generated.
    1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.909 
Fit side-chains
REVERT: C   60 MET cc_start: 0.5954 (OUTLIER) cc_final: 0.5724 (mpt)
REVERT: C  268 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6915 (tp30)
REVERT: B   52 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7665 (mtp180)
  outliers start: 15
  outliers final: 8
  residues processed: 96
  average time/residue: 1.5480
  time to fit residues: 156.5057
Evaluate side-chains
  96 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  185 TRP
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain C residue   60 MET
Chi-restraints excluded: chain C residue  268 GLU
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  314 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 78 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 80 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   chunk 14 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
C  31 GLN
C 294 GLN
B 268 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.143183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.110520 restraints weight = 9704.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 1.96
r_work: 0.3118 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.1903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8305  Z= 0.164
  Angle     :  0.472   6.793  11256  Z= 0.252
  Chirality :  0.041   0.139   1265
  Planarity :  0.003   0.055   1431
  Dihedral  :  3.913  27.685   1116
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 14.98 %
    Favored  : 83.56 %
  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:  0.81 (0.27), residues: 1004
  helix:  2.18 (0.26), residues: 406
  sheet:  0.06 (0.35), residues: 217
  loop : -0.99 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 291 
 HIS   0.005   0.001   HIS C 357 
 PHE   0.020   0.001   PHE A 298 
 TYR   0.015   0.001   TYR B  59 
 ARG   0.003   0.000   ARG B  19 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3506.65 seconds
wall clock time: 63 minutes 43.16 seconds (3823.16 seconds total)