Starting phenix.real_space_refine
on Mon May 12 06:43:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fv8_50792/05_2025/9fv8_50792.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fv8_50792/05_2025/9fv8_50792.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fv8_50792/05_2025/9fv8_50792.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fv8_50792/05_2025/9fv8_50792.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fv8_50792/05_2025/9fv8_50792.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fv8_50792/05_2025/9fv8_50792.cif"
  }
  resolution = 3.4
  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=   0.015
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      54      5.16       5
     C    5590      2.51       5
     N    1536      2.21       5
     O    1642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8822
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4411
          Classifications: {'peptide': 569}
          Link IDs: {'PTRANS': 13, 'TRANS': 555}
    Chain: "B"
      Number of atoms: 4411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4411
          Classifications: {'peptide': 569}
          Link IDs: {'PTRANS': 13, 'TRANS': 555}
  Time building chain proxies: 5.88, per 1000 atoms: 0.67
  Number of scatterers: 8822
  At special positions: 0
  Unit cell: (120.36, 106.08, 138.04, 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      54     16.00
     O    1642      8.00
     N    1536      7.00
     C    5590      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 2.00
  Conformation dependent library (CDL) restraints added in 975.4 milliseconds
  

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2128

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 4 sheets defined
      54.0% alpha, 5.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 21
      removed outlier: 3.613A  pdb=" N   ILE A  20 " --> pdb=" O   LEU A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 34 through 39
    Processing helix  chain 'A' and resid 47 through 53
    Processing helix  chain 'A' and resid 62 through 91
      removed outlier: 3.858A  pdb=" N   TRP A  66 " --> pdb=" O   SER A  62 " (cutoff:3.500A)
      Proline residue:  A  68  - end of helix
      removed outlier: 3.755A  pdb=" N   ILE A  72 " --> pdb=" O   PRO A  68 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   MET A  75 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ILE A  76 " --> pdb=" O   ILE A  72 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   LEU A  77 " --> pdb=" O   GLY A  73 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   SER A  82 " --> pdb=" O   ARG A  78 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   SER A  85 " --> pdb=" O   THR A  81 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   SER A  86 " --> pdb=" O   SER A  82 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   CYS A  88 " --> pdb=" O   VAL A  84 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   ILE A  89 " --> pdb=" O   SER A  85 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   SER A  90 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 105
      removed outlier: 3.606A  pdb=" N   ARG A 102 " --> pdb=" O   MET A  98 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   ARG A 103 " --> pdb=" O   THR A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 116
    Processing helix  chain 'A' and resid 121 through 127
    Processing helix  chain 'A' and resid 147 through 163
      removed outlier: 5.311A  pdb=" N   ILE A 153 " --> pdb=" O   GLU A 149 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   ILE A 154 " --> pdb=" O   GLY A 150 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ILE A 158 " --> pdb=" O   ILE A 154 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   PHE A 161 " --> pdb=" O   PHE A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 209
      removed outlier: 3.793A  pdb=" N   ILE A 170 " --> pdb=" O   GLN A 166 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU A 174 " --> pdb=" O   ILE A 170 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   ALA A 175 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
      Proline residue:  A 176  - end of helix
      removed outlier: 3.761A  pdb=" N   ARG A 188 " --> pdb=" O   VAL A 184 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   PHE A 189 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   SER A 193 " --> pdb=" O   PHE A 189 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   GLY A 201 " --> pdb=" O   GLN A 197 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   GLN A 202 " --> pdb=" O   ASN A 198 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   VAL A 203 " --> pdb=" O   THR A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 221
      removed outlier: 3.655A  pdb=" N   ILE A 219 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 238
    Processing helix  chain 'A' and resid 250 through 259
      removed outlier: 3.856A  pdb=" N   ILE A 254 " --> pdb=" O   ILE A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 270
      removed outlier: 3.517A  pdb=" N   PHE A 265 " --> pdb=" O   LEU A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 290
    Processing helix  chain 'A' and resid 294 through 302
      removed outlier: 3.562A  pdb=" N   LEU A 298 " --> pdb=" O   LEU A 294 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   THR A 302 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 305
      No H-bonds generated for 'chain 'A' and resid 303 through 305'
    Processing helix  chain 'A' and resid 313 through 323
      removed outlier: 4.253A  pdb=" N   PHE A 319 " --> pdb=" O   CYS A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 390
      removed outlier: 4.013A  pdb=" N   LEU A 388 " --> pdb=" O   THR A 384 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   ILE A 389 " --> pdb=" O   ILE A 385 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   THR A 390 " --> pdb=" O   ALA A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 416
    Processing helix  chain 'A' and resid 432 through 438
    Processing helix  chain 'A' and resid 446 through 457
    Processing helix  chain 'A' and resid 459 through 465
      removed outlier: 3.597A  pdb=" N   ILE A 463 " --> pdb=" O   ALA A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 498
      removed outlier: 3.646A  pdb=" N   ARG A 488 " --> pdb=" O   GLY A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 527
    Processing helix  chain 'A' and resid 538 through 545
      removed outlier: 3.682A  pdb=" N   ILE A 542 " --> pdb=" O   ARG A 538 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LYS A 544 " --> pdb=" O   SER A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 562 through 568
    Processing helix  chain 'A' and resid 571 through 580
    Processing helix  chain 'B' and resid 16 through 21
    Processing helix  chain 'B' and resid 34 through 39
    Processing helix  chain 'B' and resid 44 through 46
      No H-bonds generated for 'chain 'B' and resid 44 through 46'
    Processing helix  chain 'B' and resid 47 through 54
    Processing helix  chain 'B' and resid 62 through 73
      removed outlier: 3.923A  pdb=" N   TRP B  66 " --> pdb=" O   SER B  62 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   MET B  67 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
      Proline residue:  B  68  - end of helix
      removed outlier: 3.710A  pdb=" N   ILE B  72 " --> pdb=" O   PRO B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 84
      removed outlier: 3.536A  pdb=" N   THR B  81 " --> pdb=" O   LEU B  77 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   SER B  82 " --> pdb=" O   ARG B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 91 through 105
      removed outlier: 3.511A  pdb=" N   LYS B  95 " --> pdb=" O   TRP B  91 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   VAL B  97 " --> pdb=" O   SER B  93 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   THR B  99 " --> pdb=" O   LYS B  95 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   MET B 100 " --> pdb=" O   VAL B  96 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ARG B 103 " --> pdb=" O   THR B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 118
      removed outlier: 4.042A  pdb=" N   LYS B 118 " --> pdb=" O   SER B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 124 through 128
    Processing helix  chain 'B' and resid 140 through 149
      removed outlier: 3.828A  pdb=" N   THR B 145 " --> pdb=" O   GLY B 141 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   VAL B 146 " --> pdb=" O   ALA B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 164
      removed outlier: 4.244A  pdb=" N   MET B 160 " --> pdb=" O   LEU B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 212
      removed outlier: 3.744A  pdb=" N   ILE B 170 " --> pdb=" O   GLN B 166 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ALA B 175 " --> pdb=" O   LEU B 171 " (cutoff:3.500A)
      Proline residue:  B 176  - end of helix
      removed outlier: 3.719A  pdb=" N   ARG B 188 " --> pdb=" O   VAL B 184 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   PHE B 189 " --> pdb=" O   VAL B 185 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   THR B 199 " --> pdb=" O   ASN B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 221
      removed outlier: 3.757A  pdb=" N   ILE B 219 " --> pdb=" O   LYS B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 228
    Processing helix  chain 'B' and resid 234 through 239
    Processing helix  chain 'B' and resid 244 through 249
    Processing helix  chain 'B' and resid 250 through 272
      removed outlier: 3.857A  pdb=" N   ILE B 254 " --> pdb=" O   ILE B 250 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ALA B 262 " --> pdb=" O   ILE B 258 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU B 263 " --> pdb=" O   ALA B 259 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   SER B 271 " --> pdb=" O   LEU B 267 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   PHE B 272 " --> pdb=" O   TYR B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 293
      removed outlier: 3.604A  pdb=" N   MET B 291 " --> pdb=" O   VAL B 287 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ILE B 292 " --> pdb=" O   PHE B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 300
      removed outlier: 3.785A  pdb=" N   SER B 300 " --> pdb=" O   ARG B 296 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 303 through 308
    Processing helix  chain 'B' and resid 312 through 317
    Processing helix  chain 'B' and resid 317 through 322
    Processing helix  chain 'B' and resid 381 through 390
      removed outlier: 4.074A  pdb=" N   ILE B 385 " --> pdb=" O   GLY B 381 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ALA B 386 " --> pdb=" O   LYS B 382 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ILE B 389 " --> pdb=" O   ILE B 385 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   THR B 390 " --> pdb=" O   ALA B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 417
      removed outlier: 3.837A  pdb=" N   ASN B 417 " --> pdb=" O   ALA B 413 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 457
      removed outlier: 3.569A  pdb=" N   ILE B 450 " --> pdb=" O   SER B 446 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLU B 452 " --> pdb=" O   GLU B 448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 465
    Processing helix  chain 'B' and resid 482 through 498
    Processing helix  chain 'B' and resid 515 through 527
    Processing helix  chain 'B' and resid 538 through 544
      removed outlier: 3.769A  pdb=" N   ILE B 542 " --> pdb=" O   ARG B 538 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LYS B 544 " --> pdb=" O   SER B 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 561 through 568
    Processing helix  chain 'B' and resid 570 through 580
    Processing sheet with id=AA1, first strand: chain 'A' and resid 363 through 366
      removed outlier: 3.876A  pdb=" N   VAL A 342 " --> pdb=" O   ILE A 366 " (cutoff:3.500A)
      removed outlier: 5.485A  pdb=" N   PHE A 344 " --> pdb=" O   LEU A 401 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   LEU A 401 " --> pdb=" O   PHE A 344 " (cutoff:3.500A)
      removed outlier: 5.052A  pdb=" N   ASN A 346 " --> pdb=" O   GLU A 399 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   GLU A 399 " --> pdb=" O   ASN A 346 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 419 through 420
      removed outlier: 6.774A  pdb=" N   ALA A 420 " --> pdb=" O   ILE A 503 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   LEU A 502 " --> pdb=" O   LEU A 533 " (cutoff:3.500A)
      removed outlier: 7.562A  pdb=" N   ILE A 535 " --> pdb=" O   LEU A 502 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   LEU A 504 " --> pdb=" O   ILE A 535 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   VAL A 372 " --> pdb=" O   VAL A 534 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLU A 547 " --> pdb=" O   THR A 371 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ILE A 548 " --> pdb=" O   GLY A 560 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   GLY A 560 " --> pdb=" O   ILE A 548 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 359 through 362
      removed outlier: 3.893A  pdb=" N   ASN B 361 " --> pdb=" O   VAL B 347 " (cutoff:3.500A)
      removed outlier: 6.223A  pdb=" N   VAL B 347 " --> pdb=" O   ASN B 361 " (cutoff:3.500A)
      removed outlier: 5.291A  pdb=" N   PHE B 344 " --> pdb=" O   LEU B 401 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   LEU B 401 " --> pdb=" O   PHE B 344 " (cutoff:3.500A)
      removed outlier: 4.947A  pdb=" N   ASN B 346 " --> pdb=" O   GLU B 399 " (cutoff:3.500A)
      removed outlier: 5.086A  pdb=" N   GLU B 399 " --> pdb=" O   ASN B 346 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 419 through 422
      removed outlier: 6.727A  pdb=" N   ALA B 420 " --> pdb=" O   ILE B 503 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   LEU B 502 " --> pdb=" O   LEU B 533 " (cutoff:3.500A)
      removed outlier: 7.510A  pdb=" N   ILE B 535 " --> pdb=" O   LEU B 502 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   LEU B 504 " --> pdb=" O   ILE B 535 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   VAL B 372 " --> pdb=" O   VAL B 534 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   GLU B 547 " --> pdb=" O   ALA B 373 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   VAL B 375 " --> pdb=" O   GLU B 547 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   VAL B 549 " --> pdb=" O   VAL B 375 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

    311 hydrogen bonds defined for protein.
    894 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: 2.35 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: 2844
        1.34 -     1.46: 1357
        1.46 -     1.58: 4645
        1.58 -     1.70: 0
        1.70 -     1.82: 104
  Bond restraints: 8950
  Sorted by residual:
  bond pdb=" N   VAL B 113 "
       pdb=" CA  VAL B 113 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.25e-02 6.40e+03 9.30e+00
  bond pdb=" N   VAL A 433 "
       pdb=" CA  VAL A 433 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 1.19e-02 7.06e+03 8.84e+00
  bond pdb=" N   ILE B 389 "
       pdb=" CA  ILE B 389 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 1.17e-02 7.31e+03 8.37e+00
  bond pdb=" N   ILE B 170 "
       pdb=" CA  ILE B 170 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.034 1.21e-02 6.83e+03 7.95e+00
  bond pdb=" N   VAL B 433 "
       pdb=" CA  VAL B 433 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.90e+00
  ... (remaining 8945 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 11205
        1.64 -     3.27: 745
        3.27 -     4.91: 107
        4.91 -     6.54: 33
        6.54 -     8.18: 2
  Bond angle restraints: 12092
  Sorted by residual:
  angle pdb=" N   PHE A  43 "
        pdb=" CA  PHE A  43 "
        pdb=" C   PHE A  43 "
      ideal   model   delta    sigma   weight residual
     113.72  105.54    8.18 1.30e+00 5.92e-01 3.96e+01
  angle pdb=" N   VAL A 245 "
        pdb=" CA  VAL A 245 "
        pdb=" C   VAL A 245 "
      ideal   model   delta    sigma   weight residual
     112.96  107.92    5.04 1.00e+00 1.00e+00 2.54e+01
  angle pdb=" N   VAL B  97 "
        pdb=" CA  VAL B  97 "
        pdb=" C   VAL B  97 "
      ideal   model   delta    sigma   weight residual
     111.81  107.48    4.33 8.60e-01 1.35e+00 2.53e+01
  angle pdb=" N   ARG A 127 "
        pdb=" CA  ARG A 127 "
        pdb=" C   ARG A 127 "
      ideal   model   delta    sigma   weight residual
     113.88  108.28    5.60 1.23e+00 6.61e-01 2.07e+01
  angle pdb=" N   VAL A 571 "
        pdb=" CA  VAL A 571 "
        pdb=" C   VAL A 571 "
      ideal   model   delta    sigma   weight residual
     113.71  109.79    3.92 9.50e-01 1.11e+00 1.70e+01
  ... (remaining 12087 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.87: 4616
       16.87 -    33.74: 621
       33.74 -    50.62: 173
       50.62 -    67.49: 36
       67.49 -    84.36: 8
  Dihedral angle restraints: 5454
    sinusoidal: 2164
      harmonic: 3290
  Sorted by residual:
  dihedral pdb=" CA  ASN A 529 "
           pdb=" C   ASN A 529 "
           pdb=" N   ARG A 530 "
           pdb=" CA  ARG A 530 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.81   29.19     0      5.00e+00 4.00e-02 3.41e+01
  dihedral pdb=" CA  MET B  75 "
           pdb=" C   MET B  75 "
           pdb=" N   ILE B  76 "
           pdb=" CA  ILE B  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.34   28.66     0      5.00e+00 4.00e-02 3.29e+01
  dihedral pdb=" CA  ARG B  14 "
           pdb=" C   ARG B  14 "
           pdb=" N   ARG B  15 "
           pdb=" CA  ARG B  15 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.45   27.55     0      5.00e+00 4.00e-02 3.04e+01
  ... (remaining 5451 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 1238
       0.064 -    0.128: 170
       0.128 -    0.192: 30
       0.192 -    0.255: 1
       0.255 -    0.319: 1
  Chirality restraints: 1440
  Sorted by residual:
  chirality pdb=" CB  VAL B 433 "
            pdb=" CA  VAL B 433 "
            pdb=" CG1 VAL B 433 "
            pdb=" CG2 VAL B 433 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.31   -0.32 2.00e-01 2.50e+01 2.55e+00
  chirality pdb=" CA  PHE A  13 "
            pdb=" N   PHE A  13 "
            pdb=" C   PHE A  13 "
            pdb=" CB  PHE A  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.23e-01
  chirality pdb=" CA  LEU B 322 "
            pdb=" N   LEU B 322 "
            pdb=" C   LEU B 322 "
            pdb=" CB  LEU B 322 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 8.80e-01
  ... (remaining 1437 not shown)

  Planarity restraints: 1532
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 127 "   -0.216 9.50e-02 1.11e+02   9.71e-02 6.35e+00
        pdb=" NE  ARG B 127 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 127 "   -0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 127 "    0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 127 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A  42 "    0.010 2.00e-02 2.50e+03   1.97e-02 3.88e+00
        pdb=" C   THR A  42 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   THR A  42 "    0.013 2.00e-02 2.50e+03
        pdb=" N   PHE A  43 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A  67 "   -0.029 5.00e-02 4.00e+02   4.35e-02 3.03e+00
        pdb=" N   PRO A  68 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO A  68 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A  68 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1529 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 2130
        2.80 -     3.32: 8369
        3.32 -     3.85: 13668
        3.85 -     4.37: 16516
        4.37 -     4.90: 27844
  Nonbonded interactions: 68527
  Sorted by model distance:
  nonbonded pdb=" O   THR B 317 "
            pdb=" OG1 THR B 320 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" OD1 ASN B 435 "
            pdb=" OG1 THR B 442 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" O   PRO A 357 "
            pdb=" NH1 ARG A 360 "
     model   vdw
     2.318 3.120
  nonbonded pdb=" OD1 ASP A 431 "
            pdb=" N   THR A 432 "
     model   vdw
     2.329 3.120
  nonbonded pdb=" O   MET A 402 "
            pdb=" OH  TYR A 410 "
     model   vdw
     2.331 3.040
  ... (remaining 68522 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             5.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          2.420
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     20.080
  Find NCS groups from input model:        0.270
  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:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
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   0.042   8950  Z= 0.291
  Angle     :  0.912   8.180  12092  Z= 0.541
  Chirality :  0.049   0.319   1440
  Planarity :  0.005   0.097   1532
  Dihedral  : 16.943  84.360   3326
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.88 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 21.49 %
    Favored  : 78.20 %
  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: -3.46 (0.23), residues: 1134
  helix: -2.34 (0.18), residues: 674
  sheet: -2.12 (0.71), residues: 46
  loop : -1.90 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  66 
 HIS   0.008   0.001   HIS B 107 
 PHE   0.030   0.002   PHE A 115 
 TYR   0.010   0.001   TYR B 572 
 ARG   0.013   0.001   ARG B 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21635 (  311)
  hydrogen bonds       : angle       7.93639 (  894)
  covalent geometry    : bond        0.00526 ( 8950)
  covalent geometry    : angle       0.91189 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 125
  time to evaluate  : 0.889 
Fit side-chains
  outliers start: 3
  outliers final: 0
  residues processed: 127
  average time/residue: 0.2331
  time to fit residues: 39.5642
Evaluate side-chains
  109 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.0470
   chunk 84 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 57 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9990
   overall best weight:    0.7284

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

Flipped N/Q/H residues before XYZ refinement:
A 436 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.192487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.160799 restraints weight = 10638.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3879 rms_B_bonded: 1.71
r_work: 0.3580 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3448 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.1418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8950  Z= 0.132
  Angle     :  0.614   8.064  12092  Z= 0.325
  Chirality :  0.043   0.144   1440
  Planarity :  0.004   0.037   1532
  Dihedral  :  5.644  26.812   1238
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 23.45 %
    Favored  : 74.07 %
  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: -2.93 (0.24), residues: 1134
  helix: -1.96 (0.18), residues: 710
  sheet: -1.20 (0.65), residues: 64
  loop : -1.60 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  66 
 HIS   0.003   0.001   HIS A 576 
 PHE   0.016   0.001   PHE B 115 
 TYR   0.017   0.001   TYR B 410 
 ARG   0.008   0.000   ARG B 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03736 (  311)
  hydrogen bonds       : angle       4.89467 (  894)
  covalent geometry    : bond        0.00296 ( 8950)
  covalent geometry    : angle       0.61357 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 118
  time to evaluate  : 0.925 
Fit side-chains
REVERT: A   14 ARG cc_start: 0.6273 (mpp-170) cc_final: 0.5660 (mpt180)
REVERT: A   23 PHE cc_start: 0.7241 (m-80) cc_final: 0.7028 (m-10)
REVERT: A  267 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8238 (mp)
REVERT: B   98 MET cc_start: 0.8263 (ttp) cc_final: 0.7965 (ttp)
REVERT: B  462 PHE cc_start: 0.6531 (m-10) cc_final: 0.6273 (m-10)
REVERT: B  488 ARG cc_start: 0.7088 (ttm170) cc_final: 0.6777 (ttp-170)
  outliers start: 24
  outliers final: 18
  residues processed: 134
  average time/residue: 0.2384
  time to fit residues: 42.5792
Evaluate side-chains
  127 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  436 ASN
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  291 MET
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  502 LEU
Chi-restraints excluded: chain B residue  534 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:    0.0060
   chunk 79 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0980
   chunk 52 optimal weight:    0.6980
   chunk 16 optimal weight:    0.4980
   chunk 48 optimal weight:    4.9990
   chunk 82 optimal weight:    2.9990
   overall best weight:    0.3996

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

Flipped N/Q/H residues before XYZ refinement:
A 436 ASN
B 576 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.194563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.163177 restraints weight = 10595.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3902 rms_B_bonded: 1.71
r_work: 0.3613 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3476 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.1806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8950  Z= 0.106
  Angle     :  0.555   7.436  12092  Z= 0.294
  Chirality :  0.041   0.146   1440
  Planarity :  0.003   0.035   1532
  Dihedral  :  5.256  25.860   1238
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 25.31 %
    Favored  : 71.59 %
  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: -2.47 (0.25), residues: 1134
  helix: -1.54 (0.19), residues: 722
  sheet: -1.02 (0.66), residues: 66
  loop : -1.53 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  17 
 HIS   0.002   0.000   HIS B 214 
 PHE   0.010   0.001   PHE A 462 
 TYR   0.009   0.001   TYR B 572 
 ARG   0.008   0.000   ARG B 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03204 (  311)
  hydrogen bonds       : angle       4.37784 (  894)
  covalent geometry    : bond        0.00223 ( 8950)
  covalent geometry    : angle       0.55452 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 115
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 ARG cc_start: 0.6245 (mpp-170) cc_final: 0.5720 (mpt180)
REVERT: A  202 GLN cc_start: 0.8089 (tt0) cc_final: 0.7802 (tp40)
REVERT: A  267 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8077 (mp)
REVERT: B   48 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7930 (mp)
REVERT: B  126 SER cc_start: 0.8845 (OUTLIER) cc_final: 0.8352 (t)
REVERT: B  196 MET cc_start: 0.7849 (tpp) cc_final: 0.7487 (mmt)
REVERT: B  388 LEU cc_start: 0.8468 (mp) cc_final: 0.8233 (tp)
REVERT: B  462 PHE cc_start: 0.6357 (m-10) cc_final: 0.6021 (m-10)
REVERT: B  466 MET cc_start: 0.5554 (mtt) cc_final: 0.4916 (mmm)
REVERT: B  488 ARG cc_start: 0.6976 (ttm170) cc_final: 0.6617 (ttp-170)
  outliers start: 30
  outliers final: 18
  residues processed: 134
  average time/residue: 0.2549
  time to fit residues: 45.1122
Evaluate side-chains
  127 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 106
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue  126 SER
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  291 MET
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  502 LEU
Chi-restraints excluded: chain B residue  534 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 5 optimal weight:    0.2980
   chunk 23 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9980
   chunk 39 optimal weight:    5.9990
   chunk 16 optimal weight:    0.8980
   chunk 92 optimal weight:    9.9990
   chunk 99 optimal weight:    1.9990
   chunk 107 optimal weight:    0.2980
   chunk 2 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 405 HIS
A 576 HIS
B 520 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.193323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.160630 restraints weight = 10589.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3869 rms_B_bonded: 1.63
r_work: 0.3584 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3450 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8950  Z= 0.114
  Angle     :  0.548   6.518  12092  Z= 0.290
  Chirality :  0.041   0.144   1440
  Planarity :  0.003   0.034   1532
  Dihedral  :  5.106  25.440   1238
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 24.38 %
    Favored  : 71.07 %
  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: -2.23 (0.25), residues: 1134
  helix: -1.35 (0.19), residues: 724
  sheet: -0.85 (0.69), residues: 66
  loop : -1.47 (0.35), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  17 
 HIS   0.002   0.000   HIS A 405 
 PHE   0.008   0.001   PHE A 115 
 TYR   0.018   0.001   TYR B  87 
 ARG   0.008   0.000   ARG B 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03117 (  311)
  hydrogen bonds       : angle       4.12073 (  894)
  covalent geometry    : bond        0.00254 ( 8950)
  covalent geometry    : angle       0.54848 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 112
  time to evaluate  : 0.893 
Fit side-chains
REVERT: A   14 ARG cc_start: 0.6300 (mpp-170) cc_final: 0.5802 (mpt180)
REVERT: A  202 GLN cc_start: 0.8123 (tt0) cc_final: 0.7815 (tp40)
REVERT: A  267 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8107 (mp)
REVERT: B   48 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7938 (mp)
REVERT: B   98 MET cc_start: 0.8228 (ttp) cc_final: 0.7972 (ttp)
REVERT: B  115 PHE cc_start: 0.7795 (t80) cc_final: 0.7335 (t80)
REVERT: B  126 SER cc_start: 0.8930 (OUTLIER) cc_final: 0.8509 (t)
REVERT: B  196 MET cc_start: 0.7826 (tpp) cc_final: 0.7426 (mmt)
REVERT: B  388 LEU cc_start: 0.8509 (mp) cc_final: 0.8279 (tp)
REVERT: B  488 ARG cc_start: 0.6958 (ttm170) cc_final: 0.6678 (ttm170)
REVERT: B  520 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7690 (mm110)
REVERT: B  578 MET cc_start: 0.6741 (OUTLIER) cc_final: 0.6437 (mmp)
  outliers start: 44
  outliers final: 31
  residues processed: 139
  average time/residue: 0.2395
  time to fit residues: 45.0390
Evaluate side-chains
  145 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 109
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ASP
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  234 SER
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  456 MET
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue  126 SER
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  291 MET
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  502 LEU
Chi-restraints excluded: chain B residue  520 GLN
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  578 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 78 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   chunk 89 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 70 optimal weight:    0.3980
   chunk 65 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 60 optimal weight:    0.8980
   chunk 66 optimal weight:    0.4980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 576 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.193153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.160720 restraints weight = 10553.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.3870 rms_B_bonded: 1.73
r_work: 0.3574 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3437 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.2182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8950  Z= 0.113
  Angle     :  0.548  10.410  12092  Z= 0.288
  Chirality :  0.041   0.143   1440
  Planarity :  0.003   0.033   1532
  Dihedral  :  5.036  25.341   1238
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 23.97 %
    Favored  : 70.45 %
  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: -2.07 (0.25), residues: 1134
  helix: -1.22 (0.19), residues: 724
  sheet: -1.06 (0.65), residues: 76
  loop : -1.36 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  17 
 HIS   0.002   0.000   HIS B 576 
 PHE   0.009   0.001   PHE A 105 
 TYR   0.006   0.001   TYR B 410 
 ARG   0.009   0.000   ARG B 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03047 (  311)
  hydrogen bonds       : angle       4.02093 (  894)
  covalent geometry    : bond        0.00253 ( 8950)
  covalent geometry    : angle       0.54838 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 113
  time to evaluate  : 0.969 
Fit side-chains
REVERT: A   14 ARG cc_start: 0.6357 (mpp-170) cc_final: 0.5885 (mpt180)
REVERT: A  267 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8088 (mp)
REVERT: A  288 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7789 (m-80)
REVERT: A  530 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6664 (ttm110)
REVERT: B   48 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7946 (mp)
REVERT: B  126 SER cc_start: 0.8934 (OUTLIER) cc_final: 0.8568 (t)
REVERT: B  127 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8347 (ttm-80)
REVERT: B  190 ARG cc_start: 0.6904 (ttm110) cc_final: 0.6630 (ttp80)
REVERT: B  196 MET cc_start: 0.7864 (tpp) cc_final: 0.7450 (mmt)
REVERT: B  321 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8543 (mp)
REVERT: B  388 LEU cc_start: 0.8503 (mp) cc_final: 0.8286 (tp)
REVERT: B  460 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7759 (mmm)
REVERT: B  466 MET cc_start: 0.5365 (mtt) cc_final: 0.4985 (mmm)
REVERT: B  488 ARG cc_start: 0.7003 (ttm170) cc_final: 0.6577 (ttm170)
REVERT: B  578 MET cc_start: 0.6723 (OUTLIER) cc_final: 0.6291 (mmp)
  outliers start: 54
  outliers final: 33
  residues processed: 150
  average time/residue: 0.2330
  time to fit residues: 46.8571
Evaluate side-chains
  146 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 104
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ASP
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  234 SER
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  436 ASN
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  530 ARG
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  555 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue  126 SER
Chi-restraints excluded: chain B residue  127 ARG
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  291 MET
Chi-restraints excluded: chain B residue  321 ILE
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  460 MET
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  502 LEU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  578 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 86 optimal weight:    0.7980
   chunk 51 optimal weight:   10.0000
   chunk 55 optimal weight:    6.9990
   chunk 33 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 101 optimal weight:    7.9990
   chunk 106 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 576 HIS
B 405 HIS
** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.191621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.159448 restraints weight = 10525.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.3856 rms_B_bonded: 1.67
r_work: 0.3547 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3411 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.2293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8950  Z= 0.131
  Angle     :  0.589  11.599  12092  Z= 0.302
  Chirality :  0.042   0.140   1440
  Planarity :  0.003   0.033   1532
  Dihedral  :  5.074  25.332   1238
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.53 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  5.89 %
    Allowed  : 23.97 %
    Favored  : 70.14 %
  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: -2.01 (0.25), residues: 1134
  helix: -1.18 (0.20), residues: 724
  sheet: -0.98 (0.66), residues: 76
  loop : -1.31 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  17 
 HIS   0.003   0.001   HIS B 405 
 PHE   0.018   0.001   PHE B 115 
 TYR   0.006   0.001   TYR B 410 
 ARG   0.009   0.000   ARG B 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03173 (  311)
  hydrogen bonds       : angle       4.04326 (  894)
  covalent geometry    : bond        0.00300 ( 8950)
  covalent geometry    : angle       0.58858 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 106
  time to evaluate  : 0.976 
Fit side-chains
REVERT: A   14 ARG cc_start: 0.6390 (mpp-170) cc_final: 0.5935 (mpt180)
REVERT: A  267 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8157 (mp)
REVERT: A  288 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7821 (m-80)
REVERT: B   48 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7934 (mp)
REVERT: B  126 SER cc_start: 0.8934 (OUTLIER) cc_final: 0.8598 (t)
REVERT: B  127 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8292 (ttm-80)
REVERT: B  288 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7927 (m-80)
REVERT: B  388 LEU cc_start: 0.8482 (mp) cc_final: 0.8260 (tp)
REVERT: B  460 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7610 (mmm)
REVERT: B  462 PHE cc_start: 0.6338 (m-10) cc_final: 0.6002 (m-10)
REVERT: B  466 MET cc_start: 0.5487 (mtt) cc_final: 0.5091 (mmm)
REVERT: B  488 ARG cc_start: 0.7043 (ttm170) cc_final: 0.6603 (ttm170)
REVERT: B  578 MET cc_start: 0.6701 (OUTLIER) cc_final: 0.6288 (mmp)
  outliers start: 57
  outliers final: 37
  residues processed: 146
  average time/residue: 0.2374
  time to fit residues: 46.3522
Evaluate side-chains
  148 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 103
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ASP
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  234 SER
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  436 ASN
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  555 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue  126 SER
Chi-restraints excluded: chain B residue  127 ARG
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  288 PHE
Chi-restraints excluded: chain B residue  291 MET
Chi-restraints excluded: chain B residue  383 SER
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  460 MET
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  502 LEU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  578 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 103 optimal weight:    7.9990
   chunk 100 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   chunk 104 optimal weight:    0.9990
   chunk 40 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9980
   chunk 74 optimal weight:    0.7980
   chunk 71 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 107 HIS
A 576 HIS
** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.191180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.158396 restraints weight = 10689.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.3845 rms_B_bonded: 1.60
r_work: 0.3566 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3437 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8950  Z= 0.131
  Angle     :  0.584  10.675  12092  Z= 0.300
  Chirality :  0.042   0.141   1440
  Planarity :  0.003   0.033   1532
  Dihedral  :  5.107  28.870   1238
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.53 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 25.31 %
    Favored  : 69.42 %
  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: -1.96 (0.25), residues: 1134
  helix: -1.14 (0.20), residues: 724
  sheet: -1.02 (0.66), residues: 76
  loop : -1.28 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  17 
 HIS   0.002   0.000   HIS B 576 
 PHE   0.019   0.001   PHE B 115 
 TYR   0.006   0.001   TYR A 572 
 ARG   0.010   0.000   ARG B 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03182 (  311)
  hydrogen bonds       : angle       4.02369 (  894)
  covalent geometry    : bond        0.00302 ( 8950)
  covalent geometry    : angle       0.58369 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 103
  time to evaluate  : 0.964 
Fit side-chains
REVERT: A   14 ARG cc_start: 0.6326 (mpp-170) cc_final: 0.5872 (mpt180)
REVERT: A  267 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8118 (mp)
REVERT: A  288 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.7824 (m-80)
REVERT: A  397 GLU cc_start: 0.7340 (tm-30) cc_final: 0.7043 (tm-30)
REVERT: A  456 MET cc_start: 0.7883 (tpp) cc_final: 0.7565 (tpp)
REVERT: B   48 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7927 (mp)
REVERT: B  126 SER cc_start: 0.8903 (OUTLIER) cc_final: 0.8579 (t)
REVERT: B  127 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8269 (ttm-80)
REVERT: B  190 ARG cc_start: 0.6920 (ttm110) cc_final: 0.6674 (ttp80)
REVERT: B  321 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8515 (mp)
REVERT: B  388 LEU cc_start: 0.8469 (mp) cc_final: 0.8255 (tp)
REVERT: B  460 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7591 (mmm)
REVERT: B  462 PHE cc_start: 0.6443 (m-10) cc_final: 0.6129 (m-10)
REVERT: B  466 MET cc_start: 0.5620 (mtt) cc_final: 0.5236 (mmm)
REVERT: B  488 ARG cc_start: 0.6989 (ttm170) cc_final: 0.6562 (ttm170)
REVERT: B  578 MET cc_start: 0.6545 (OUTLIER) cc_final: 0.6134 (mmp)
  outliers start: 51
  outliers final: 39
  residues processed: 139
  average time/residue: 0.2296
  time to fit residues: 42.8348
Evaluate side-chains
  148 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 101
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ASP
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  234 SER
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  436 ASN
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  555 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue  126 SER
Chi-restraints excluded: chain B residue  127 ARG
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  291 MET
Chi-restraints excluded: chain B residue  321 ILE
Chi-restraints excluded: chain B residue  383 SER
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  460 MET
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  502 LEU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  578 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 96 optimal weight:    4.9990
   chunk 51 optimal weight:   10.0000
   chunk 85 optimal weight:    0.8980
   chunk 43 optimal weight:    4.9990
   chunk 102 optimal weight:    3.9990
   chunk 99 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   chunk 86 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 107 HIS
A 576 HIS
** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.190923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.158165 restraints weight = 10751.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3840 rms_B_bonded: 1.60
r_work: 0.3560 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3428 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.2524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8950  Z= 0.132
  Angle     :  0.584   9.728  12092  Z= 0.301
  Chirality :  0.042   0.141   1440
  Planarity :  0.003   0.036   1532
  Dihedral  :  5.118  27.520   1238
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.79 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 26.14 %
    Favored  : 68.60 %
  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: -1.91 (0.25), residues: 1134
  helix: -1.10 (0.20), residues: 722
  sheet: -1.07 (0.65), residues: 78
  loop : -1.25 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  17 
 HIS   0.003   0.001   HIS A 107 
 PHE   0.019   0.001   PHE B 115 
 TYR   0.006   0.001   TYR A 572 
 ARG   0.009   0.000   ARG B 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03195 (  311)
  hydrogen bonds       : angle       4.02399 (  894)
  covalent geometry    : bond        0.00305 ( 8950)
  covalent geometry    : angle       0.58414 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 105
  time to evaluate  : 0.984 
Fit side-chains
REVERT: A   14 ARG cc_start: 0.6354 (mpp-170) cc_final: 0.5928 (mpt180)
REVERT: A  267 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8111 (mp)
REVERT: A  288 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7832 (m-80)
REVERT: B   48 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7928 (mp)
REVERT: B  126 SER cc_start: 0.8903 (OUTLIER) cc_final: 0.8572 (t)
REVERT: B  127 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8302 (ttm-80)
REVERT: B  190 ARG cc_start: 0.6978 (ttm110) cc_final: 0.6739 (ttp80)
REVERT: B  322 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8322 (tt)
REVERT: B  388 LEU cc_start: 0.8462 (mp) cc_final: 0.8258 (tp)
REVERT: B  460 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7648 (mmm)
REVERT: B  462 PHE cc_start: 0.6520 (m-10) cc_final: 0.6209 (m-10)
REVERT: B  488 ARG cc_start: 0.7023 (ttm170) cc_final: 0.6596 (ttm170)
REVERT: B  578 MET cc_start: 0.6528 (OUTLIER) cc_final: 0.6117 (mmp)
  outliers start: 51
  outliers final: 40
  residues processed: 142
  average time/residue: 0.2444
  time to fit residues: 46.3238
Evaluate side-chains
  151 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 103
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ASP
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  234 SER
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  436 ASN
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  555 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue  126 SER
Chi-restraints excluded: chain B residue  127 ARG
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  291 MET
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  383 SER
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  460 MET
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  502 LEU
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  578 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 74 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 79 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 87 optimal weight:    0.8980
   chunk 77 optimal weight:    0.4980
   chunk 49 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   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 576 HIS
B 477 ASN
B 520 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.191997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.159303 restraints weight = 10581.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.3857 rms_B_bonded: 1.45
r_work: 0.3600 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3471 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.2659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8950  Z= 0.115
  Angle     :  0.573   9.322  12092  Z= 0.296
  Chirality :  0.041   0.140   1440
  Planarity :  0.003   0.034   1532
  Dihedral  :  5.041  28.036   1238
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.26 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 26.65 %
    Favored  : 68.08 %
  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: -1.75 (0.26), residues: 1134
  helix: -0.97 (0.20), residues: 722
  sheet: -1.03 (0.66), residues: 78
  loop : -1.19 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  17 
 HIS   0.002   0.000   HIS B 214 
 PHE   0.019   0.001   PHE B 115 
 TYR   0.007   0.001   TYR A 572 
 ARG   0.010   0.000   ARG B 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02978 (  311)
  hydrogen bonds       : angle       3.95207 (  894)
  covalent geometry    : bond        0.00259 ( 8950)
  covalent geometry    : angle       0.57282 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 108
  time to evaluate  : 1.017 
Fit side-chains
REVERT: A   14 ARG cc_start: 0.6270 (mpp-170) cc_final: 0.5846 (mpt180)
REVERT: A  267 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8026 (mp)
REVERT: A  288 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7801 (m-80)
REVERT: A  312 MET cc_start: 0.8036 (tpp) cc_final: 0.7267 (mmt)
REVERT: A  397 GLU cc_start: 0.7243 (tm-30) cc_final: 0.6903 (tm-30)
REVERT: B   48 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7890 (mp)
REVERT: B  126 SER cc_start: 0.8883 (OUTLIER) cc_final: 0.8558 (t)
REVERT: B  127 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8278 (ttm-80)
REVERT: B  190 ARG cc_start: 0.6922 (ttm110) cc_final: 0.6672 (ttp80)
REVERT: B  288 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7869 (m-80)
REVERT: B  321 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8440 (mp)
REVERT: B  322 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8255 (tt)
REVERT: B  397 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7234 (pm20)
REVERT: B  460 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7537 (mmm)
REVERT: B  488 ARG cc_start: 0.6976 (ttm170) cc_final: 0.6571 (ttm170)
REVERT: B  578 MET cc_start: 0.6562 (OUTLIER) cc_final: 0.6157 (mmp)
  outliers start: 51
  outliers final: 39
  residues processed: 146
  average time/residue: 0.2500
  time to fit residues: 48.5395
Evaluate side-chains
  151 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 102
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ASP
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  234 SER
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  436 ASN
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  555 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue  126 SER
Chi-restraints excluded: chain B residue  127 ARG
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  288 PHE
Chi-restraints excluded: chain B residue  291 MET
Chi-restraints excluded: chain B residue  321 ILE
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  383 SER
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  460 MET
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  502 LEU
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  578 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9980
   chunk 70 optimal weight:    0.7980
   chunk 87 optimal weight:    0.7980
   chunk 15 optimal weight:    0.3980
   chunk 73 optimal weight:    0.6980
   chunk 8 optimal weight:    0.3980
   chunk 88 optimal weight:    4.9990
   chunk 100 optimal weight:    6.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 576 HIS
B 405 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.193365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.161153 restraints weight = 10595.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.3854 rms_B_bonded: 1.52
r_work: 0.3590 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3462 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.2747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8950  Z= 0.112
  Angle     :  0.570   9.063  12092  Z= 0.298
  Chirality :  0.041   0.139   1440
  Planarity :  0.003   0.034   1532
  Dihedral  :  4.994  27.295   1238
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.17 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 26.45 %
    Favored  : 68.18 %
  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: -1.65 (0.26), residues: 1134
  helix: -0.88 (0.20), residues: 722
  sheet: -1.00 (0.66), residues: 78
  loop : -1.21 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  17 
 HIS   0.003   0.000   HIS B 214 
 PHE   0.018   0.001   PHE B 115 
 TYR   0.007   0.001   TYR A 572 
 ARG   0.010   0.000   ARG B 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02927 (  311)
  hydrogen bonds       : angle       3.91473 (  894)
  covalent geometry    : bond        0.00249 ( 8950)
  covalent geometry    : angle       0.56992 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 102
  time to evaluate  : 0.909 
Fit side-chains
REVERT: A   14 ARG cc_start: 0.6188 (mpp-170) cc_final: 0.5793 (mpt180)
REVERT: A  267 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.7989 (mp)
REVERT: A  288 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7762 (m-80)
REVERT: A  312 MET cc_start: 0.8022 (tpp) cc_final: 0.7231 (mmt)
REVERT: A  397 GLU cc_start: 0.7206 (tm-30) cc_final: 0.6865 (tm-30)
REVERT: A  456 MET cc_start: 0.7780 (tpp) cc_final: 0.7515 (tpp)
REVERT: B   48 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7860 (mp)
REVERT: B  126 SER cc_start: 0.8860 (OUTLIER) cc_final: 0.8547 (t)
REVERT: B  172 ILE cc_start: 0.7961 (tp) cc_final: 0.7493 (tp)
REVERT: B  288 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7870 (m-80)
REVERT: B  322 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8259 (tt)
REVERT: B  397 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7283 (pm20)
REVERT: B  456 MET cc_start: 0.7736 (tpp) cc_final: 0.7384 (mmm)
REVERT: B  460 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7491 (mmm)
REVERT: B  488 ARG cc_start: 0.7005 (ttm170) cc_final: 0.6595 (ttm170)
REVERT: B  578 MET cc_start: 0.6526 (OUTLIER) cc_final: 0.6142 (mmp)
  outliers start: 52
  outliers final: 39
  residues processed: 141
  average time/residue: 0.2394
  time to fit residues: 44.9416
Evaluate side-chains
  146 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 99
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ASP
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  234 SER
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  436 ASN
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  555 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue  126 SER
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  288 PHE
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  383 SER
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  460 MET
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  502 LEU
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  578 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 78 optimal weight:    0.2980
   chunk 37 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 53 optimal weight:    6.9990
   chunk 86 optimal weight:    0.6980
   chunk 54 optimal weight:    9.9990
   chunk 111 optimal weight:    9.9990
   chunk 102 optimal weight:    9.9990
   chunk 84 optimal weight:    0.9990
   chunk 87 optimal weight:    2.9990
   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 576 HIS
B 405 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.192692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.159962 restraints weight = 10655.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3868 rms_B_bonded: 1.53
r_work: 0.3609 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3480 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.2829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8950  Z= 0.116
  Angle     :  0.568   8.708  12092  Z= 0.296
  Chirality :  0.041   0.139   1440
  Planarity :  0.003   0.034   1532
  Dihedral  :  4.975  26.807   1238
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.44 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 27.27 %
    Favored  : 67.87 %
  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: -1.63 (0.26), residues: 1134
  helix: -0.84 (0.20), residues: 724
  sheet: -0.98 (0.66), residues: 78
  loop : -1.25 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  17 
 HIS   0.002   0.000   HIS B 214 
 PHE   0.018   0.001   PHE B 115 
 TYR   0.007   0.001   TYR A 572 
 ARG   0.010   0.000   ARG B 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02949 (  311)
  hydrogen bonds       : angle       3.91345 (  894)
  covalent geometry    : bond        0.00260 ( 8950)
  covalent geometry    : angle       0.56782 (12092)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5117.76 seconds
wall clock time: 89 minutes 12.68 seconds (5352.68 seconds total)