Starting phenix.real_space_refine
on Thu Feb 13 16:47:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zdk_14652/02_2025/7zdk_14652.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zdk_14652/02_2025/7zdk_14652.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zdk_14652/02_2025/7zdk_14652.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zdk_14652/02_2025/7zdk_14652.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zdk_14652/02_2025/7zdk_14652.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zdk_14652/02_2025/7zdk_14652.cif"
  }
  resolution = 3.01
  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=   0.007
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      30      5.16       5
     C    5804      2.51       5
     N    1600      2.21       5
     O    1647      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 88 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9089
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 4433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 573, 4433
          Classifications: {'peptide': 573}
          Link IDs: {'PTRANS': 18, 'TRANS': 554}
    Chain: "D"
      Number of atoms: 4592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 588, 4592
          Classifications: {'peptide': 588}
          Link IDs: {'PTRANS': 27, 'TRANS': 560}
    Chain: "C"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.33, per 1000 atoms: 0.59
  Number of scatterers: 9089
  At special positions: 0
  Unit cell: (117.18, 80.352, 114.669, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      30     16.00
     P       6     15.00
     Mg      2     11.99
     O    1647      8.00
     N    1600      7.00
     C    5804      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: 2.29
  Conformation dependent library (CDL) restraints added in 995.4 milliseconds
  

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2148

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 6 sheets defined
      68.3% alpha, 9.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.06
  Creating SS restraints...
    Processing helix  chain 'C' and resid 4 through 9
    Processing helix  chain 'C' and resid 14 through 50
    Processing helix  chain 'C' and resid 59 through 104
      removed outlier: 3.556A  pdb=" N   ARG C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   THR C  74 " --> pdb=" O   ALA C  70 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   HIS C  94 " --> pdb=" O   ARG C  90 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 115 through 132
      removed outlier: 3.513A  pdb=" N   LEU C 120 " --> pdb=" O   GLN C 116 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   ASN C 121 " --> pdb=" O   GLY C 117 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ARG C 122 " --> pdb=" O   GLU C 118 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 132 through 137
    Processing helix  chain 'C' and resid 137 through 157
      removed outlier: 3.849A  pdb=" N   PHE C 157 " --> pdb=" O   ILE C 153 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 159 through 176
      removed outlier: 3.612A  pdb=" N   THR C 165 " --> pdb=" O   THR C 161 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ILE C 169 " --> pdb=" O   THR C 165 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 176 through 185
    Processing helix  chain 'C' and resid 185 through 209
    Processing helix  chain 'C' and resid 209 through 216
    Processing helix  chain 'C' and resid 218 through 269
      removed outlier: 3.586A  pdb=" N   LEU C 243 " --> pdb=" O   ARG C 239 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   SER C 267 " --> pdb=" O   LEU C 263 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLY C 268 " --> pdb=" O   TRP C 264 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   GLY C 269 " --> pdb=" O   MET C 265 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 277 through 290
      removed outlier: 4.347A  pdb=" N   ALA C 281 " --> pdb=" O   GLY C 277 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LEU C 282 " --> pdb=" O   ALA C 278 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 291 through 293
      No H-bonds generated for 'chain 'C' and resid 291 through 293'
    Processing helix  chain 'C' and resid 294 through 319
      removed outlier: 4.335A  pdb=" N   GLY C 299 " --> pdb=" O   ALA C 295 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ALA C 300 " --> pdb=" O   PRO C 296 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   PHE C 301 " --> pdb=" O   VAL C 297 " (cutoff:3.500A)
      removed outlier: 5.378A  pdb=" N   GLN C 302 " --> pdb=" O   THR C 298 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 379 through 387
      removed outlier: 3.665A  pdb=" N   GLN C 385 " --> pdb=" O   THR C 381 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU C 386 " --> pdb=" O   LEU C 382 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 407
      No H-bonds generated for 'chain 'C' and resid 405 through 407'
    Processing helix  chain 'C' and resid 408 through 415
    Processing helix  chain 'C' and resid 429 through 436
      removed outlier: 3.815A  pdb=" N   LEU C 436 " --> pdb=" O   ASP C 432 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 442 through 453
    Processing helix  chain 'C' and resid 456 through 460
    Processing helix  chain 'C' and resid 462 through 466
      removed outlier: 3.622A  pdb=" N   ASN C 465 " --> pdb=" O   ALA C 462 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   SER C 466 " --> pdb=" O   GLY C 463 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 462 through 466'
    Processing helix  chain 'C' and resid 476 through 492
      removed outlier: 3.675A  pdb=" N   LEU C 483 " --> pdb=" O   GLU C 479 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 506 through 521
      removed outlier: 3.675A  pdb=" N   GLN C 512 " --> pdb=" O   THR C 508 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 555 through 562
    Processing helix  chain 'C' and resid 564 through 572
    Processing helix  chain 'D' and resid 2 through 17
      removed outlier: 3.556A  pdb=" N   GLU D   8 " --> pdb=" O   SER D   4 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLN D  15 " --> pdb=" O   ARG D  11 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 20 through 54
      removed outlier: 3.584A  pdb=" N   PHE D  32 " --> pdb=" O   ARG D  28 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 58 through 61
    Processing helix  chain 'D' and resid 62 through 110
    Processing helix  chain 'D' and resid 110 through 115
    Processing helix  chain 'D' and resid 118 through 127
    Processing helix  chain 'D' and resid 127 through 132
    Processing helix  chain 'D' and resid 133 through 139
      removed outlier: 3.620A  pdb=" N   TYR D 137 " --> pdb=" O   MET D 133 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 139 through 162
      removed outlier: 3.670A  pdb=" N   VAL D 148 " --> pdb=" O   MET D 144 " (cutoff:3.500A)
      Proline residue:  D 151  - end of helix
      Proline residue:  D 160  - end of helix
    Processing helix  chain 'D' and resid 162 through 173
      removed outlier: 3.605A  pdb=" N   THR D 172 " --> pdb=" O   ILE D 168 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ALA D 173 " --> pdb=" O   LEU D 169 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 174 through 203
      removed outlier: 3.643A  pdb=" N   LEU D 178 " --> pdb=" O   PRO D 174 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ASP D 189 " --> pdb=" O   MET D 185 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   LEU D 196 " --> pdb=" O   ARG D 192 " (cutoff:3.500A)
      removed outlier: 5.004A  pdb=" N   ALA D 197 " --> pdb=" O   ARG D 193 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   GLY D 203 " --> pdb=" O   ALA D 199 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 203 through 210
    Processing helix  chain 'D' and resid 211 through 218
    Processing helix  chain 'D' and resid 220 through 274
      removed outlier: 3.784A  pdb=" N   GLU D 226 " --> pdb=" O   GLU D 222 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   SER D 227 " --> pdb=" O   ALA D 223 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   GLU D 241 " --> pdb=" O   GLN D 237 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   VAL D 242 " --> pdb=" O   ARG D 238 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   LEU D 245 " --> pdb=" O   GLU D 241 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   LEU D 248 " --> pdb=" O   ARG D 244 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   LEU D 253 " --> pdb=" O   SER D 249 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   GLU D 254 " --> pdb=" O   SER D 250 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   SER D 258 " --> pdb=" O   GLU D 254 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LEU D 273 " --> pdb=" O   GLY D 269 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 286 through 310
      removed outlier: 3.532A  pdb=" N   GLY D 290 " --> pdb=" O   THR D 286 " (cutoff:3.500A)
      Proline residue:  D 298  - end of helix
      removed outlier: 4.098A  pdb=" N   PHE D 301 " --> pdb=" O   ALA D 297 " (cutoff:3.500A)
      Proline residue:  D 303  - end of helix
      removed outlier: 3.538A  pdb=" N   THR D 309 " --> pdb=" O   ARG D 305 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 311 through 330
      removed outlier: 3.795A  pdb=" N   ALA D 315 " --> pdb=" O   TYR D 311 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ALA D 317 " --> pdb=" O   ALA D 313 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 388 through 397
    Processing helix  chain 'D' and resid 417 through 422
    Processing helix  chain 'D' and resid 438 through 444
    Processing helix  chain 'D' and resid 451 through 462
    Processing helix  chain 'D' and resid 473 through 477
      removed outlier: 3.598A  pdb=" N   THR D 477 " --> pdb=" O   GLY D 474 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 487 through 501
    Processing helix  chain 'D' and resid 517 through 532
    Processing helix  chain 'D' and resid 566 through 573
      removed outlier: 3.739A  pdb=" N   VAL D 572 " --> pdb=" O   ALA D 568 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 575 through 583
    Processing sheet with id=AA1, first strand: chain 'C' and resid 362 through 363
    Processing sheet with id=AA2, first strand: chain 'C' and resid 344 through 347
      removed outlier: 6.709A  pdb=" N   VAL C 344 " --> pdb=" O   LYS C 357 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   LYS C 357 " --> pdb=" O   VAL C 344 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   PHE C 346 " --> pdb=" O   ALA C 355 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 416 through 419
      removed outlier: 6.455A  pdb=" N   VAL C 496 " --> pdb=" O   LEU C 527 " (cutoff:3.500A)
      removed outlier: 7.483A  pdb=" N   VAL C 529 " --> pdb=" O   VAL C 496 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   LEU C 498 " --> pdb=" O   VAL C 529 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   GLU C 552 " --> pdb=" O   VAL C 544 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   ASP C 546 " --> pdb=" O   ILE C 550 " (cutoff:3.500A)
      removed outlier: 5.378A  pdb=" N   ILE C 550 " --> pdb=" O   ASP C 546 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 364 through 373
      removed outlier: 6.477A  pdb=" N   ILE D 357 " --> pdb=" O   LEU D 365 " (cutoff:3.500A)
      removed outlier: 5.125A  pdb=" N   GLY D 367 " --> pdb=" O   LEU D 355 " (cutoff:3.500A)
      removed outlier: 5.134A  pdb=" N   LEU D 355 " --> pdb=" O   GLY D 367 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   LEU D 369 " --> pdb=" O   GLU D 353 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   GLU D 353 " --> pdb=" O   LEU D 369 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   PHE D 371 " --> pdb=" O   GLU D 351 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   GLU D 351 " --> pdb=" O   PHE D 371 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   SER D 401 " --> pdb=" O   THR D 358 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 364 through 373
      removed outlier: 6.477A  pdb=" N   ILE D 357 " --> pdb=" O   LEU D 365 " (cutoff:3.500A)
      removed outlier: 5.125A  pdb=" N   GLY D 367 " --> pdb=" O   LEU D 355 " (cutoff:3.500A)
      removed outlier: 5.134A  pdb=" N   LEU D 355 " --> pdb=" O   GLY D 367 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   LEU D 369 " --> pdb=" O   GLU D 353 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   GLU D 353 " --> pdb=" O   LEU D 369 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   PHE D 371 " --> pdb=" O   GLU D 351 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   GLU D 351 " --> pdb=" O   PHE D 371 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 425 through 428
      removed outlier: 6.889A  pdb=" N   SER D 426 " --> pdb=" O   LEU D 508 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   ASP D 510 " --> pdb=" O   SER D 426 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   VAL D 428 " --> pdb=" O   ASP D 510 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   LEU D 507 " --> pdb=" O   LEU D 538 " (cutoff:3.500A)
      removed outlier: 7.928A  pdb=" N   VAL D 540 " --> pdb=" O   LEU D 507 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   LEU D 509 " --> pdb=" O   VAL D 540 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ARG D 378 " --> pdb=" O   VAL D 552 " (cutoff:3.500A)
      removed outlier: 8.043A  pdb=" N   TRP D 554 " --> pdb=" O   ARG D 378 " (cutoff:3.500A)
      removed outlier: 6.055A  pdb=" N   VAL D 380 " --> pdb=" O   TRP D 554 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   MET D 556 " --> pdb=" O   VAL D 380 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   VAL D 382 " --> pdb=" O   MET D 556 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   ILE D 553 " --> pdb=" O   GLN D 564 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   GLN D 564 " --> pdb=" O   ILE D 553 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   VAL D 555 " --> pdb=" O   ILE D 562 " (cutoff:3.500A)

    570 hydrogen bonds defined for protein.
    1677 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: 2.84

  Time building geometry restraints manager: 2.63 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2482
        1.33 -     1.45: 1557
        1.45 -     1.57: 5163
        1.57 -     1.69: 10
        1.69 -     1.81: 57
  Bond restraints: 9269
  Sorted by residual:
  bond pdb=" N3B ANP D 602 "
       pdb=" PG  ANP D 602 "
    ideal  model  delta    sigma   weight residual
    1.795  1.626  0.169 2.00e-02 2.50e+03 7.12e+01
  bond pdb=" N3B ANP C 602 "
       pdb=" PG  ANP C 602 "
    ideal  model  delta    sigma   weight residual
    1.795  1.628  0.167 2.00e-02 2.50e+03 6.99e+01
  bond pdb=" O3A ANP C 602 "
       pdb=" PB  ANP C 602 "
    ideal  model  delta    sigma   weight residual
    1.700  1.596  0.104 2.00e-02 2.50e+03 2.70e+01
  bond pdb=" O3A ANP D 602 "
       pdb=" PB  ANP D 602 "
    ideal  model  delta    sigma   weight residual
    1.700  1.602  0.098 2.00e-02 2.50e+03 2.41e+01
  bond pdb=" N   GLU C 500 "
       pdb=" CA  GLU C 500 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 7.40e-03 1.83e+04 1.69e+01
  ... (remaining 9264 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 12316
        2.27 -     4.55: 242
        4.55 -     6.82: 38
        6.82 -     9.09: 7
        9.09 -    11.36: 1
  Bond angle restraints: 12604
  Sorted by residual:
  angle pdb=" N   GLU C 515 "
        pdb=" CA  GLU C 515 "
        pdb=" C   GLU C 515 "
      ideal   model   delta    sigma   weight residual
     111.36  105.54    5.82 1.09e+00 8.42e-01 2.86e+01
  angle pdb=" C   GLU C 500 "
        pdb=" CA  GLU C 500 "
        pdb=" CB  GLU C 500 "
      ideal   model   delta    sigma   weight residual
     111.00  114.48   -3.48 8.70e-01 1.32e+00 1.60e+01
  angle pdb=" N   TYR C  11 "
        pdb=" CA  TYR C  11 "
        pdb=" C   TYR C  11 "
      ideal   model   delta    sigma   weight residual
     112.89  108.04    4.85 1.24e+00 6.50e-01 1.53e+01
  angle pdb=" N   LYS C  12 "
        pdb=" CA  LYS C  12 "
        pdb=" C   LYS C  12 "
      ideal   model   delta    sigma   weight residual
     111.28  107.08    4.20 1.09e+00 8.42e-01 1.48e+01
  angle pdb=" N   ARG D  11 "
        pdb=" CA  ARG D  11 "
        pdb=" C   ARG D  11 "
      ideal   model   delta    sigma   weight residual
     111.82  107.40    4.42 1.16e+00 7.43e-01 1.45e+01
  ... (remaining 12599 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.57: 5037
       19.57 -    39.13: 412
       39.13 -    58.70: 71
       58.70 -    78.27: 26
       78.27 -    97.83: 18
  Dihedral angle restraints: 5564
    sinusoidal: 2233
      harmonic: 3331
  Sorted by residual:
  dihedral pdb=" CA  LEU D 209 "
           pdb=" C   LEU D 209 "
           pdb=" N   ARG D 210 "
           pdb=" CA  ARG D 210 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.97   25.03     0      5.00e+00 4.00e-02 2.51e+01
  dihedral pdb=" O2' ANP D 602 "
           pdb=" C2' ANP D 602 "
           pdb=" C3' ANP D 602 "
           pdb=" O3' ANP D 602 "
      ideal   model   delta sinusoidal    sigma   weight residual
      47.90  -49.93   97.83     1      3.00e+01 1.11e-03 1.21e+01
  dihedral pdb=" C1' ANP D 602 "
           pdb=" C2' ANP D 602 "
           pdb=" C3' ANP D 602 "
           pdb=" O3' ANP D 602 "
      ideal   model   delta sinusoidal    sigma   weight residual
     164.59   69.72   94.87     1      3.00e+01 1.11e-03 1.16e+01
  ... (remaining 5561 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.089: 1348
       0.089 -    0.179: 103
       0.179 -    0.268: 8
       0.268 -    0.357: 0
       0.357 -    0.446: 2
  Chirality restraints: 1461
  Sorted by residual:
  chirality pdb=" C3' ANP C 602 "
            pdb=" C2' ANP C 602 "
            pdb=" C4' ANP C 602 "
            pdb=" O3' ANP C 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.80    0.45 2.00e-01 2.50e+01 4.98e+00
  chirality pdb=" C3' ANP D 602 "
            pdb=" C2' ANP D 602 "
            pdb=" C4' ANP D 602 "
            pdb=" O3' ANP D 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.80    0.44 2.00e-01 2.50e+01 4.81e+00
  chirality pdb=" CA  VAL D 428 "
            pdb=" N   VAL D 428 "
            pdb=" C   VAL D 428 "
            pdb=" CB  VAL D 428 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.70   -0.26 2.00e-01 2.50e+01 1.71e+00
  ... (remaining 1458 not shown)

  Planarity restraints: 1604
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D 428 "    0.012 2.00e-02 2.50e+03   2.55e-02 6.51e+00
        pdb=" C   VAL D 428 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   VAL D 428 "    0.017 2.00e-02 2.50e+03
        pdb=" N   GLY D 429 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C 497 "    0.008 2.00e-02 2.50e+03   1.70e-02 2.89e+00
        pdb=" C   LEU C 497 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   LEU C 497 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LEU C 498 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU D 511 "    0.027 5.00e-02 4.00e+02   4.00e-02 2.56e+00
        pdb=" N   PRO D 512 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO D 512 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D 512 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1601 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1431
        2.75 -     3.29: 8840
        3.29 -     3.83: 14871
        3.83 -     4.36: 19151
        4.36 -     4.90: 32283
  Nonbonded interactions: 76576
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D 438 "
            pdb=" OD1 ASP D 441 "
     model   vdw
     2.219 3.040
  nonbonded pdb="MG    MG D 601 "
            pdb=" O1G ANP D 602 "
     model   vdw
     2.220 2.170
  nonbonded pdb="MG    MG C 601 "
            pdb=" O1B ANP C 602 "
     model   vdw
     2.222 2.170
  nonbonded pdb=" OG  SER C 380 "
            pdb="MG    MG C 601 "
     model   vdw
     2.223 2.170
  nonbonded pdb="MG    MG C 601 "
            pdb=" O2G ANP C 602 "
     model   vdw
     2.224 2.170
  ... (remaining 76571 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     23.000
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
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      :  0.007   0.169   9269  Z= 0.432
  Angle     :  0.783  11.363  12604  Z= 0.460
  Chirality :  0.051   0.446   1461
  Planarity :  0.004   0.040   1604
  Dihedral  : 16.142  97.831   3416
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  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: -1.50 (0.23), residues: 1157
  helix: -1.19 (0.18), residues: 723
  sheet:  0.39 (0.63), residues: 62
  loop : -0.40 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D  81 
 HIS   0.004   0.001   HIS C  14 
 PHE   0.014   0.002   PHE D 467 
 TYR   0.012   0.002   TYR D  88 
 ARG   0.008   0.001   ARG C  96 

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.966 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.3417
  time to fit residues: 49.3058
Evaluate side-chains
  104 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 1.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    0.4980
   chunk 87 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 46 optimal weight:    4.9990
   chunk 90 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9980
   chunk 104 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
C 225 GLN
D   2 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.112852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.090490 restraints weight = 11061.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.2936 rms_B_bonded: 1.52
r_work: 0.2810 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2673 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.2673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8709
moved from start:          0.1224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9269  Z= 0.222
  Angle     :  0.598   6.979  12604  Z= 0.306
  Chirality :  0.041   0.157   1461
  Planarity :  0.005   0.041   1604
  Dihedral  : 10.319  73.197   1329
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  5.73 %
    Favored  : 93.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.24), residues: 1157
  helix:  0.72 (0.19), residues: 721
  sheet:  0.29 (0.62), residues: 62
  loop : -0.35 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D 427 
 HIS   0.003   0.001   HIS D  51 
 PHE   0.014   0.001   PHE C 164 
 TYR   0.013   0.001   TYR D  88 
 ARG   0.004   0.000   ARG D 493 

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 117
  time to evaluate  : 1.033 
Fit side-chains
REVERT: D  154 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8574 (mt)
REVERT: D  207 ASP cc_start: 0.8231 (t0) cc_final: 0.7926 (t0)
REVERT: D  240 MET cc_start: 0.8739 (mmm) cc_final: 0.8362 (mmm)
REVERT: D  277 ASP cc_start: 0.7697 (t0) cc_final: 0.7407 (t0)
  outliers start: 9
  outliers final: 5
  residues processed: 123
  average time/residue: 0.2914
  time to fit residues: 46.6758
Evaluate side-chains
  110 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 104
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  360 SER
Chi-restraints excluded: chain C residue  448 GLU
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  233 GLU
Chi-restraints excluded: chain D residue  475 VAL
Chi-restraints excluded: chain D residue  487 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 61 optimal weight:    0.6980
   chunk 35 optimal weight:    0.0970
   chunk 41 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 114 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
C 225 GLN
C 474 GLN
C 541 GLN
C 553 GLN
D 143 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.110661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.088284 restraints weight = 11194.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.2922 rms_B_bonded: 1.51
r_work: 0.2794 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2655 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.2655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8741
moved from start:          0.1459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   9269  Z= 0.331
  Angle     :  0.611   7.650  12604  Z= 0.306
  Chirality :  0.043   0.188   1461
  Planarity :  0.005   0.048   1604
  Dihedral  :  8.501  74.110   1329
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  :  9.23 %
    Favored  : 89.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.25), residues: 1157
  helix:  1.28 (0.19), residues: 721
  sheet:  0.14 (0.63), residues: 59
  loop : -0.46 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP D  81 
 HIS   0.004   0.001   HIS C 424 
 PHE   0.018   0.002   PHE D 467 
 TYR   0.018   0.002   TYR D  88 
 ARG   0.005   0.000   ARG C  96 

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 1.027 
Fit side-chains
REVERT: C  183 ARG cc_start: 0.8050 (ttm110) cc_final: 0.7848 (ttp-110)
REVERT: C  515 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7464 (tm-30)
REVERT: D    1 MET cc_start: 0.5909 (ptt) cc_final: 0.5265 (tpt)
REVERT: D  154 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8706 (mt)
REVERT: D  167 LEU cc_start: 0.8915 (tp) cc_final: 0.8627 (tp)
REVERT: D  277 ASP cc_start: 0.7729 (t0) cc_final: 0.7353 (t0)
  outliers start: 14
  outliers final: 11
  residues processed: 119
  average time/residue: 0.2907
  time to fit residues: 45.5170
Evaluate side-chains
  120 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain C residue  360 SER
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  448 GLU
Chi-restraints excluded: chain C residue  529 VAL
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  202 SER
Chi-restraints excluded: chain D residue  233 GLU
Chi-restraints excluded: chain D residue  475 VAL
Chi-restraints excluded: chain D residue  487 SER
Chi-restraints excluded: chain D residue  546 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   chunk 103 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 109 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 111 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 80 optimal weight:    0.8980
   chunk 87 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
C 306 GLN
C 474 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.113035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.090756 restraints weight = 10977.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.2956 rms_B_bonded: 1.50
r_work: 0.2829 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2690 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.2690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8712
moved from start:          0.1662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9269  Z= 0.203
  Angle     :  0.533   7.092  12604  Z= 0.269
  Chirality :  0.040   0.149   1461
  Planarity :  0.004   0.042   1604
  Dihedral  :  7.407  74.573   1329
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  :  9.97 %
    Favored  : 88.34 %
  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:  1.35 (0.25), residues: 1157
  helix:  1.67 (0.19), residues: 722
  sheet:  0.05 (0.63), residues: 59
  loop : -0.41 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP D  81 
 HIS   0.003   0.001   HIS C 424 
 PHE   0.014   0.001   PHE D 467 
 TYR   0.018   0.001   TYR D  88 
 ARG   0.003   0.000   ARG C 522 

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 0.997 
Fit side-chains
REVERT: C  515 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7506 (tm-30)
REVERT: D    1 MET cc_start: 0.5830 (ptt) cc_final: 0.5243 (tpt)
REVERT: D   11 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7724 (ttt180)
REVERT: D  167 LEU cc_start: 0.8929 (tp) cc_final: 0.8609 (tp)
REVERT: D  207 ASP cc_start: 0.8210 (t0) cc_final: 0.7873 (t0)
REVERT: D  277 ASP cc_start: 0.7742 (t0) cc_final: 0.7427 (t0)
  outliers start: 16
  outliers final: 10
  residues processed: 120
  average time/residue: 0.2975
  time to fit residues: 46.9060
Evaluate side-chains
  116 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain C residue  360 SER
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain D residue   11 ARG
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  202 SER
Chi-restraints excluded: chain D residue  233 GLU
Chi-restraints excluded: chain D residue  351 GLU
Chi-restraints excluded: chain D residue  475 VAL
Chi-restraints excluded: chain D residue  487 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 41 optimal weight:    0.7980
   chunk 62 optimal weight:    5.9990
   chunk 102 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 103 optimal weight:    5.9990
   chunk 43 optimal weight:    0.0270
   chunk 90 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.7242

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

Flipped N/Q/H residues before XYZ refinement:
C 306 GLN
D 482 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.113692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.091330 restraints weight = 11011.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.2976 rms_B_bonded: 1.50
r_work: 0.2849 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2712 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8697
moved from start:          0.1783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9269  Z= 0.190
  Angle     :  0.510   6.811  12604  Z= 0.259
  Chirality :  0.040   0.151   1461
  Planarity :  0.004   0.043   1604
  Dihedral  :  6.763  73.336   1329
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 10.60 %
    Favored  : 87.59 %
  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:  1.58 (0.25), residues: 1157
  helix:  1.87 (0.20), residues: 722
  sheet:  0.04 (0.65), residues: 59
  loop : -0.36 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP D  81 
 HIS   0.003   0.001   HIS C  85 
 PHE   0.013   0.001   PHE D 467 
 TYR   0.018   0.001   TYR D  88 
 ARG   0.004   0.000   ARG D 193 

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 1.081 
Fit side-chains
REVERT: C  515 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7498 (tm-30)
REVERT: D    1 MET cc_start: 0.5759 (ptt) cc_final: 0.5236 (tpt)
REVERT: D   11 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7682 (ttt180)
REVERT: D  207 ASP cc_start: 0.8217 (t0) cc_final: 0.7891 (t0)
REVERT: D  277 ASP cc_start: 0.7669 (t0) cc_final: 0.7385 (t0)
  outliers start: 17
  outliers final: 12
  residues processed: 120
  average time/residue: 0.2806
  time to fit residues: 44.1518
Evaluate side-chains
  117 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  360 SER
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  448 GLU
Chi-restraints excluded: chain D residue   11 ARG
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  202 SER
Chi-restraints excluded: chain D residue  351 GLU
Chi-restraints excluded: chain D residue  475 VAL
Chi-restraints excluded: chain D residue  487 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 87 optimal weight:    0.7980
   chunk 89 optimal weight:    0.7980
   chunk 88 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 111 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
C 306 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.113472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.091118 restraints weight = 10978.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.2954 rms_B_bonded: 1.49
r_work: 0.2827 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2689 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.2689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8701
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9269  Z= 0.213
  Angle     :  0.513   7.026  12604  Z= 0.261
  Chirality :  0.040   0.157   1461
  Planarity :  0.004   0.042   1604
  Dihedral  :  6.506  73.252   1329
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 11.03 %
    Favored  : 86.85 %
  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:  1.67 (0.25), residues: 1157
  helix:  1.95 (0.19), residues: 723
  sheet:  0.02 (0.65), residues: 59
  loop : -0.32 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP D 427 
 HIS   0.003   0.001   HIS C  85 
 PHE   0.014   0.001   PHE D 467 
 TYR   0.019   0.001   TYR D  88 
 ARG   0.004   0.000   ARG C 522 

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 1.080 
Fit side-chains
REVERT: C  515 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7474 (tm-30)
REVERT: D    1 MET cc_start: 0.5749 (ptt) cc_final: 0.5141 (tpt)
REVERT: D   11 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7677 (ttt180)
REVERT: D  207 ASP cc_start: 0.8225 (t0) cc_final: 0.7883 (t0)
  outliers start: 20
  outliers final: 16
  residues processed: 121
  average time/residue: 0.2877
  time to fit residues: 45.9144
Evaluate side-chains
  121 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 1.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  360 SER
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  448 GLU
Chi-restraints excluded: chain C residue  468 LEU
Chi-restraints excluded: chain C residue  521 MET
Chi-restraints excluded: chain D residue   11 ARG
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  202 SER
Chi-restraints excluded: chain D residue  233 GLU
Chi-restraints excluded: chain D residue  351 GLU
Chi-restraints excluded: chain D residue  475 VAL
Chi-restraints excluded: chain D residue  487 SER
Chi-restraints excluded: chain D residue  546 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 67 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 90 optimal weight:    0.9990
   chunk 89 optimal weight:    0.5980
   chunk 88 optimal weight:    0.9990
   chunk 82 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
C 306 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.114053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.091653 restraints weight = 11055.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.2990 rms_B_bonded: 1.50
r_work: 0.2859 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2720 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8734
moved from start:          0.1892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9269  Z= 0.200
  Angle     :  0.505   6.866  12604  Z= 0.258
  Chirality :  0.040   0.146   1461
  Planarity :  0.004   0.043   1604
  Dihedral  :  6.378  72.738   1329
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 11.56 %
    Favored  : 86.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.25), residues: 1157
  helix:  2.04 (0.19), residues: 723
  sheet:  0.06 (0.65), residues: 59
  loop : -0.29 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP D  81 
 HIS   0.003   0.001   HIS C  85 
 PHE   0.013   0.001   PHE D 467 
 TYR   0.018   0.001   TYR D  88 
 ARG   0.004   0.000   ARG C 122 

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.968 
Fit side-chains
REVERT: C  515 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7506 (tm-30)
REVERT: D    1 MET cc_start: 0.5756 (ptt) cc_final: 0.5162 (tpt)
REVERT: D   11 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7777 (ttt180)
REVERT: D  207 ASP cc_start: 0.8189 (t0) cc_final: 0.7886 (t0)
REVERT: D  216 ARG cc_start: 0.8526 (ttp-170) cc_final: 0.8168 (ptt90)
REVERT: D  585 GLN cc_start: 0.7475 (mt0) cc_final: 0.7166 (mm110)
  outliers start: 19
  outliers final: 17
  residues processed: 121
  average time/residue: 0.2889
  time to fit residues: 45.4309
Evaluate side-chains
  123 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 1.040 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  360 SER
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  448 GLU
Chi-restraints excluded: chain C residue  468 LEU
Chi-restraints excluded: chain C residue  521 MET
Chi-restraints excluded: chain D residue   11 ARG
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  202 SER
Chi-restraints excluded: chain D residue  233 GLU
Chi-restraints excluded: chain D residue  351 GLU
Chi-restraints excluded: chain D residue  475 VAL
Chi-restraints excluded: chain D residue  487 SER
Chi-restraints excluded: chain D residue  546 ASP
Chi-restraints excluded: chain D residue  581 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 53 optimal weight:    0.4980
   chunk 35 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 95 optimal weight:    3.9990
   chunk 89 optimal weight:    0.3980
   chunk 41 optimal weight:    0.7980
   chunk 45 optimal weight:    0.2980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
C 303 HIS
C 306 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.115328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.092936 restraints weight = 11197.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.3001 rms_B_bonded: 1.52
r_work: 0.2874 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2736 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8673
moved from start:          0.2053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9269  Z= 0.160
  Angle     :  0.478   6.790  12604  Z= 0.245
  Chirality :  0.038   0.142   1461
  Planarity :  0.004   0.044   1604
  Dihedral  :  6.143  69.418   1329
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 12.09 %
    Favored  : 86.11 %
  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:  1.98 (0.25), residues: 1157
  helix:  2.21 (0.19), residues: 723
  sheet:  0.16 (0.66), residues: 59
  loop : -0.26 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP D  81 
 HIS   0.004   0.000   HIS C  85 
 PHE   0.012   0.001   PHE D 467 
 TYR   0.018   0.001   TYR D  88 
 ARG   0.003   0.000   ARG C 122 

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 1.079 
Fit side-chains
REVERT: D    1 MET cc_start: 0.5770 (ptt) cc_final: 0.5142 (tpt)
REVERT: D   11 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7776 (ttt180)
REVERT: D  216 ARG cc_start: 0.8461 (ttp-110) cc_final: 0.8151 (ptt90)
REVERT: D  240 MET cc_start: 0.8872 (mmm) cc_final: 0.8577 (mmm)
REVERT: D  526 GLU cc_start: 0.8307 (tt0) cc_final: 0.7882 (mt-10)
REVERT: D  585 GLN cc_start: 0.7446 (mt0) cc_final: 0.7147 (mm110)
  outliers start: 17
  outliers final: 14
  residues processed: 124
  average time/residue: 0.2759
  time to fit residues: 45.2771
Evaluate side-chains
  121 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  360 SER
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  448 GLU
Chi-restraints excluded: chain D residue   11 ARG
Chi-restraints excluded: chain D residue  202 SER
Chi-restraints excluded: chain D residue  233 GLU
Chi-restraints excluded: chain D residue  351 GLU
Chi-restraints excluded: chain D residue  475 VAL
Chi-restraints excluded: chain D residue  487 SER
Chi-restraints excluded: chain D residue  546 ASP
Chi-restraints excluded: chain D residue  581 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 82 optimal weight:    0.5980
   chunk 114 optimal weight:    4.9990
   chunk 110 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 87 optimal weight:    0.8980
   chunk 72 optimal weight:    0.8980
   chunk 111 optimal weight:    0.0270
   chunk 66 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
C 306 GLN
C 541 GLN
D  15 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.115675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.093383 restraints weight = 10975.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.3023 rms_B_bonded: 1.50
r_work: 0.2896 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2758 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8708
moved from start:          0.2106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9269  Z= 0.167
  Angle     :  0.490   6.925  12604  Z= 0.249
  Chirality :  0.039   0.144   1461
  Planarity :  0.004   0.044   1604
  Dihedral  :  6.053  67.628   1329
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 12.41 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: 1157
  helix:  2.29 (0.19), residues: 723
  sheet:  0.17 (0.66), residues: 59
  loop : -0.24 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP D  81 
 HIS   0.004   0.001   HIS C  85 
 PHE   0.012   0.001   PHE D 467 
 TYR   0.018   0.001   TYR D  88 
 ARG   0.003   0.000   ARG D 139 

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 0.972 
Fit side-chains
REVERT: D    1 MET cc_start: 0.5711 (ptt) cc_final: 0.5150 (tpt)
REVERT: D   11 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.8029 (ttm-80)
REVERT: D  216 ARG cc_start: 0.8483 (ttp-110) cc_final: 0.8205 (ptt90)
REVERT: D  240 MET cc_start: 0.8898 (mmm) cc_final: 0.8613 (mmm)
REVERT: D  526 GLU cc_start: 0.8326 (tt0) cc_final: 0.7939 (mt-10)
REVERT: D  585 GLN cc_start: 0.7431 (mt0) cc_final: 0.7178 (mm110)
  outliers start: 16
  outliers final: 15
  residues processed: 121
  average time/residue: 0.3238
  time to fit residues: 52.3500
Evaluate side-chains
  121 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 1.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  360 SER
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  448 GLU
Chi-restraints excluded: chain C residue  468 LEU
Chi-restraints excluded: chain D residue   11 ARG
Chi-restraints excluded: chain D residue  202 SER
Chi-restraints excluded: chain D residue  233 GLU
Chi-restraints excluded: chain D residue  351 GLU
Chi-restraints excluded: chain D residue  475 VAL
Chi-restraints excluded: chain D residue  487 SER
Chi-restraints excluded: chain D residue  546 ASP
Chi-restraints excluded: chain D residue  581 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 104 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 100 optimal weight:    0.0030
   chunk 40 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 37 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.6390

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

Flipped N/Q/H residues before XYZ refinement:
C 306 GLN
C 531 HIS
D  15 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.115827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.093444 restraints weight = 11043.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.2953 rms_B_bonded: 1.51
r_work: 0.2828 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2691 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8669
moved from start:          0.2131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9269  Z= 0.173
  Angle     :  0.497   8.393  12604  Z= 0.251
  Chirality :  0.039   0.144   1461
  Planarity :  0.004   0.044   1604
  Dihedral  :  6.009  66.697   1329
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 12.30 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.10 (0.25), residues: 1157
  helix:  2.30 (0.19), residues: 723
  sheet:  0.23 (0.66), residues: 59
  loop : -0.20 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D  81 
 HIS   0.003   0.001   HIS C  85 
 PHE   0.012   0.001   PHE D 467 
 TYR   0.018   0.001   TYR D  88 
 ARG   0.003   0.000   ARG D 139 

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

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

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2314 Ramachandran restraints generated.
    1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 112
  time to evaluate  : 0.983 
Fit side-chains
REVERT: D    1 MET cc_start: 0.5677 (ptt) cc_final: 0.5106 (tpt)
REVERT: D   11 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7915 (ttm-80)
REVERT: D  216 ARG cc_start: 0.8476 (ttp-110) cc_final: 0.8184 (ptt90)
REVERT: D  240 MET cc_start: 0.8874 (mmm) cc_final: 0.8587 (mmm)
REVERT: D  275 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7807 (mp0)
REVERT: D  526 GLU cc_start: 0.8305 (tt0) cc_final: 0.7907 (mt-10)
REVERT: D  585 GLN cc_start: 0.7406 (mt0) cc_final: 0.7143 (mm110)
  outliers start: 17
  outliers final: 16
  residues processed: 123
  average time/residue: 0.2925
  time to fit residues: 47.0745
Evaluate side-chains
  126 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 109
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  360 SER
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  448 GLU
Chi-restraints excluded: chain C residue  468 LEU
Chi-restraints excluded: chain C residue  531 HIS
Chi-restraints excluded: chain D residue   11 ARG
Chi-restraints excluded: chain D residue  202 SER
Chi-restraints excluded: chain D residue  233 GLU
Chi-restraints excluded: chain D residue  351 GLU
Chi-restraints excluded: chain D residue  475 VAL
Chi-restraints excluded: chain D residue  487 SER
Chi-restraints excluded: chain D residue  546 ASP
Chi-restraints excluded: chain D residue  581 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 17 optimal weight:    0.5980
   chunk 89 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 29 optimal weight:    0.2980
   chunk 62 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   chunk 64 optimal weight:    0.6980
   chunk 86 optimal weight:    0.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
C 306 GLN
C 531 HIS
C 541 GLN
D  15 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.116262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.093954 restraints weight = 10980.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.2962 rms_B_bonded: 1.50
r_work: 0.2838 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2701 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8646
moved from start:          0.2158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9269  Z= 0.161
  Angle     :  0.497   8.032  12604  Z= 0.250
  Chirality :  0.039   0.144   1461
  Planarity :  0.004   0.044   1604
  Dihedral  :  5.958  65.860   1329
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 12.20 %
    Favored  : 86.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.15 (0.25), residues: 1157
  helix:  2.34 (0.19), residues: 723
  sheet:  0.20 (0.66), residues: 59
  loop : -0.17 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP D  81 
 HIS   0.007   0.001   HIS C 531 
 PHE   0.011   0.001   PHE D 467 
 TYR   0.018   0.001   TYR D  88 
 ARG   0.004   0.000   ARG D 139 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4661.17 seconds
wall clock time: 83 minutes 17.90 seconds (4997.90 seconds total)