Starting phenix.real_space_refine
on Mon Jun  9 07:22:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9iuc_60897/06_2025/9iuc_60897.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9iuc_60897/06_2025/9iuc_60897.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9iuc_60897/06_2025/9iuc_60897.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9iuc_60897/06_2025/9iuc_60897.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9iuc_60897/06_2025/9iuc_60897.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9iuc_60897/06_2025/9iuc_60897.cif"
  }
  resolution = 3.8
  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=   0.011
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: 5
    Type Number    sf(0)   Gaussians
     P      18      5.49       5
     S      40      5.16       5
     C    6996      2.51       5
     N    1566      2.21       5
     O    1740      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 10360
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4765
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 570, 4765
          Classifications: {'peptide': 570}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 552}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 4765
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 570, 4765
          Classifications: {'peptide': 570}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 552}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 443
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 443
          Unusual residues: {'3PE': 3, 'ACD': 1, 'CLR': 7, 'IHP': 1, 'PLM': 2}
          Classifications: {'undetermined': 14}
          Link IDs: {None: 13}
    Chain: "B"
      Number of atoms: 387
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 387
          Unusual residues: {'3PE': 3, 'ACD': 1, 'CLR': 5, 'IHP': 1, 'PLM': 2}
          Classifications: {'undetermined': 12}
          Link IDs: {None: 11}
  Time building chain proxies: 7.19, per 1000 atoms: 0.69
  Number of scatterers: 10360
  At special positions: 0
  Unit cell: (99.16, 126.54, 101.38, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      40     16.00
     P      18     15.00
     O    1740      8.00
     N    1566      7.00
     C    6996      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 415 " - pdb=" SG  CYS A 440 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 415 " - pdb=" SG  CYS B 440 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.03
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2192

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 0 sheets defined
      80.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 10
      removed outlier: 4.055A  pdb=" N   SER A   8 " --> pdb=" O   ALA A   4 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 12 through 16
    Processing helix  chain 'A' and resid 21 through 35
      removed outlier: 3.749A  pdb=" N   PHE A  25 " --> pdb=" O   GLN A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 58
    Processing helix  chain 'A' and resid 60 through 89
    Processing helix  chain 'A' and resid 90 through 99
    Processing helix  chain 'A' and resid 120 through 167
      removed outlier: 4.195A  pdb=" N   ASN A 152 " --> pdb=" O   TYR A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 179
    Processing helix  chain 'A' and resid 183 through 188
      removed outlier: 3.668A  pdb=" N   CYS A 188 " --> pdb=" O   PRO A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 205
      removed outlier: 3.881A  pdb=" N   GLN A 193 " --> pdb=" O   LYS A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 258
      removed outlier: 3.566A  pdb=" N   THR A 234 " --> pdb=" O   PRO A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 296
      removed outlier: 5.527A  pdb=" N   GLY A 274 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   GLY A 275 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   PHE A 276 " --> pdb=" O   TYR A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 303
      removed outlier: 3.506A  pdb=" N   ILE A 302 " --> pdb=" O   ASN A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 337
      removed outlier: 3.694A  pdb=" N   LEU A 316 " --> pdb=" O   SER A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 361
      removed outlier: 4.214A  pdb=" N   LEU A 349 " --> pdb=" O   TYR A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 383
    Processing helix  chain 'A' and resid 390 through 400
    Processing helix  chain 'A' and resid 403 through 420
      removed outlier: 3.941A  pdb=" N   LEU A 407 " --> pdb=" O   LEU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 445
      No H-bonds generated for 'chain 'A' and resid 443 through 445'
    Processing helix  chain 'A' and resid 446 through 471
      Proline residue:  A 455  - end of helix
    Processing helix  chain 'A' and resid 472 through 477
      removed outlier: 3.882A  pdb=" N   HIS A 476 " --> pdb=" O   ARG A 472 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU A 477 " --> pdb=" O   ALA A 473 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 472 through 477'
    Processing helix  chain 'A' and resid 477 through 503
      removed outlier: 5.024A  pdb=" N   THR A 486 " --> pdb=" O   LYS A 482 " (cutoff:3.500A)
      removed outlier: 4.879A  pdb=" N   PHE A 487 " --> pdb=" O   TYR A 483 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   PHE A 488 " --> pdb=" O   SER A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 532
      removed outlier: 3.657A  pdb=" N   ILE A 519 " --> pdb=" O   ILE A 515 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ILE A 520 " --> pdb=" O   VAL A 516 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   THR A 525 " --> pdb=" O   SER A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 580
      removed outlier: 4.089A  pdb=" N   TYR A 559 " --> pdb=" O   GLN A 555 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   PHE A 571 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   ALA A 572 " --> pdb=" O   ILE A 568 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   THR A 574 " --> pdb=" O   ARG A 570 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   ILE A 575 " --> pdb=" O   PHE A 571 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   THR A 580 " --> pdb=" O   GLN A 576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 619
      removed outlier: 3.551A  pdb=" N   ASP A 590 " --> pdb=" O   PRO A 586 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ALA A 593 " --> pdb=" O   GLY A 589 " (cutoff:3.500A)
      Proline residue:  A 598  - end of helix
      removed outlier: 3.748A  pdb=" N   VAL A 601 " --> pdb=" O   ALA A 597 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   PHE A 602 " --> pdb=" O   PRO A 598 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   PHE A 610 " --> pdb=" O   VAL A 606 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   LEU A 612 " --> pdb=" O   ASN A 608 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   GLU A 613 " --> pdb=" O   PHE A 609 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 7 through 11
    Processing helix  chain 'B' and resid 12 through 16
    Processing helix  chain 'B' and resid 21 through 28
      removed outlier: 4.014A  pdb=" N   ASP B  27 " --> pdb=" O   GLU B  23 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   MET B  28 " --> pdb=" O   ALA B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 35
      removed outlier: 4.077A  pdb=" N   ALA B  32 " --> pdb=" O   MET B  28 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   GLN B  33 " --> pdb=" O   LEU B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 99
      removed outlier: 4.225A  pdb=" N   PHE B  58 " --> pdb=" O   PHE B  54 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   PHE B  59 " --> pdb=" O   GLU B  55 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   SER B  93 " --> pdb=" O   ASN B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 167
      removed outlier: 3.538A  pdb=" N   LEU B 145 " --> pdb=" O   SER B 141 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   GLN B 146 " --> pdb=" O   LEU B 142 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ASN B 147 " --> pdb=" O   ILE B 143 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   ASN B 152 " --> pdb=" O   TYR B 148 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ARG B 157 " --> pdb=" O   PHE B 153 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ILE B 159 " --> pdb=" O   GLY B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 179
      removed outlier: 3.953A  pdb=" N   VAL B 177 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 182
      No H-bonds generated for 'chain 'B' and resid 180 through 182'
    Processing helix  chain 'B' and resid 183 through 188
      removed outlier: 3.611A  pdb=" N   CYS B 188 " --> pdb=" O   PRO B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 205
      removed outlier: 3.617A  pdb=" N   GLN B 193 " --> pdb=" O   LYS B 189 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ILE B 195 " --> pdb=" O   ILE B 191 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   SER B 196 " --> pdb=" O   ASN B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 257
      removed outlier: 3.622A  pdb=" N   VAL B 237 " --> pdb=" O   THR B 233 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   PHE B 244 " --> pdb=" O   PHE B 240 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ILE B 245 " --> pdb=" O   CYS B 241 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ILE B 249 " --> pdb=" O   ILE B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 296
      removed outlier: 4.938A  pdb=" N   GLY B 274 " --> pdb=" O   ARG B 270 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   GLY B 275 " --> pdb=" O   ILE B 271 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   PHE B 276 " --> pdb=" O   TYR B 272 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LEU B 277 " --> pdb=" O   ARG B 273 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LEU B 278 " --> pdb=" O   GLY B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 303
    Processing helix  chain 'B' and resid 312 through 337
      removed outlier: 3.538A  pdb=" N   LEU B 316 " --> pdb=" O   SER B 312 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ILE B 319 " --> pdb=" O   HIS B 315 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   PHE B 336 " --> pdb=" O   LEU B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 345 through 360
      removed outlier: 4.550A  pdb=" N   LEU B 349 " --> pdb=" O   TYR B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 383
      removed outlier: 3.597A  pdb=" N   PHE B 372 " --> pdb=" O   TYR B 368 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   TRP B 373 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU B 374 " --> pdb=" O   SER B 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 390 through 400
    Processing helix  chain 'B' and resid 403 through 420
      removed outlier: 4.009A  pdb=" N   LEU B 407 " --> pdb=" O   LEU B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 438 through 442
    Processing helix  chain 'B' and resid 443 through 445
      No H-bonds generated for 'chain 'B' and resid 443 through 445'
    Processing helix  chain 'B' and resid 446 through 453
    Processing helix  chain 'B' and resid 453 through 468
      removed outlier: 3.563A  pdb=" N   ARG B 459 " --> pdb=" O   PRO B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 477 through 503
      removed outlier: 4.872A  pdb=" N   THR B 486 " --> pdb=" O   LYS B 482 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   PHE B 487 " --> pdb=" O   TYR B 483 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   PHE B 488 " --> pdb=" O   SER B 484 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ALA B 493 " --> pdb=" O   MET B 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 530
      removed outlier: 3.520A  pdb=" N   PHE B 510 " --> pdb=" O   ASP B 506 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ILE B 519 " --> pdb=" O   ILE B 515 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ILE B 520 " --> pdb=" O   VAL B 516 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   SER B 521 " --> pdb=" O   PHE B 517 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 556 through 580
      removed outlier: 3.594A  pdb=" N   TYR B 560 " --> pdb=" O   LYS B 556 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE B 564 " --> pdb=" O   TYR B 560 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   VAL B 567 " --> pdb=" O   ILE B 563 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ARG B 570 " --> pdb=" O   ASP B 566 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ALA B 572 " --> pdb=" O   ILE B 568 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   THR B 574 " --> pdb=" O   ARG B 570 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   ILE B 575 " --> pdb=" O   PHE B 571 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   GLN B 576 " --> pdb=" O   ALA B 572 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   SER B 578 " --> pdb=" O   THR B 574 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   THR B 580 " --> pdb=" O   GLN B 576 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 592 through 618
      Proline residue:  B 598  - end of helix
      removed outlier: 3.504A  pdb=" N   VAL B 601 " --> pdb=" O   ALA B 597 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   PHE B 602 " --> pdb=" O   PRO B 598 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   PHE B 609 " --> pdb=" O   PHE B 605 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   PHE B 610 " --> pdb=" O   VAL B 606 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   LEU B 612 " --> pdb=" O   ASN B 608 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   GLU B 613 " --> pdb=" O   PHE B 609 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   ASN B 618 " --> pdb=" O   ASN B 614 " (cutoff:3.500A)

    611 hydrogen bonds defined for protein.
    1809 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: 2.69

  Time building geometry restraints manager: 3.50 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1632
        1.33 -     1.45: 2936
        1.45 -     1.57: 6016
        1.57 -     1.69: 24
        1.69 -     1.81: 56
  Bond restraints: 10664
  Sorted by residual:
  bond pdb=" C   THR B  86 "
       pdb=" O   THR B  86 "
    ideal  model  delta    sigma   weight residual
    1.237  1.209  0.028 1.19e-02 7.06e+03 5.35e+00
  bond pdb=" N   PHE A 366 "
       pdb=" CA  PHE A 366 "
    ideal  model  delta    sigma   weight residual
    1.457  1.484 -0.026 1.29e-02 6.01e+03 4.11e+00
  bond pdb=" C   PHE A  58 "
       pdb=" O   PHE A  58 "
    ideal  model  delta    sigma   weight residual
    1.236  1.211  0.025 1.39e-02 5.18e+03 3.27e+00
  bond pdb=" C   PHE A 156 "
       pdb=" O   PHE A 156 "
    ideal  model  delta    sigma   weight residual
    1.236  1.216  0.020 1.15e-02 7.56e+03 3.16e+00
  bond pdb=" C   ASP B 590 "
       pdb=" O   ASP B 590 "
    ideal  model  delta    sigma   weight residual
    1.235  1.216  0.019 1.26e-02 6.30e+03 2.38e+00
  ... (remaining 10659 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.19: 14119
        2.19 -     4.37: 230
        4.37 -     6.56: 56
        6.56 -     8.75: 15
        8.75 -    10.93: 8
  Bond angle restraints: 14428
  Sorted by residual:
  angle pdb=" N   PHE A  59 "
        pdb=" CA  PHE A  59 "
        pdb=" C   PHE A  59 "
      ideal   model   delta    sigma   weight residual
     113.28  103.37    9.91 1.22e+00 6.72e-01 6.59e+01
  angle pdb=" N   GLN A  60 "
        pdb=" CA  GLN A  60 "
        pdb=" C   GLN A  60 "
      ideal   model   delta    sigma   weight residual
     113.50  106.68    6.82 1.23e+00 6.61e-01 3.08e+01
  angle pdb=" N   GLN B  88 "
        pdb=" CA  GLN B  88 "
        pdb=" C   GLN B  88 "
      ideal   model   delta    sigma   weight residual
     111.07  105.53    5.54 1.07e+00 8.73e-01 2.68e+01
  angle pdb=" N   ASP A 590 "
        pdb=" CA  ASP A 590 "
        pdb=" C   ASP A 590 "
      ideal   model   delta    sigma   weight residual
     111.14  116.55   -5.41 1.08e+00 8.57e-01 2.51e+01
  angle pdb=" N   ILE A 591 "
        pdb=" CA  ILE A 591 "
        pdb=" C   ILE A 591 "
      ideal   model   delta    sigma   weight residual
     110.42  115.05   -4.63 9.60e-01 1.09e+00 2.33e+01
  ... (remaining 14423 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.79: 6483
       32.79 -    65.58: 370
       65.58 -    98.38: 29
       98.38 -   131.17: 28
      131.17 -   163.96: 8
  Dihedral angle restraints: 6918
    sinusoidal: 3538
      harmonic: 3380
  Sorted by residual:
  dihedral pdb=" CA  MET A   1 "
           pdb=" C   MET A   1 "
           pdb=" N   LYS A   2 "
           pdb=" CA  LYS A   2 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.68   27.32     0      5.00e+00 4.00e-02 2.98e+01
  dihedral pdb=" CA  MET B   1 "
           pdb=" C   MET B   1 "
           pdb=" N   LYS B   2 "
           pdb=" CA  LYS B   2 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.03   22.97     0      5.00e+00 4.00e-02 2.11e+01
  dihedral pdb=" O14 IHP A 802 "
           pdb=" C4  IHP A 802 "
           pdb=" C5  IHP A 802 "
           pdb=" O15 IHP A 802 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -52.79  111.17 -163.96     1      3.00e+01 1.11e-03 2.09e+01
  ... (remaining 6915 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.995: 1546
       0.995 -    1.990: 0
       1.990 -    2.985: 0
       2.985 -    3.979: 0
       3.979 -    4.974: 8
  Chirality restraints: 1554
  Sorted by residual:
  chirality pdb=" C2  IHP A 802 "
            pdb=" C1  IHP A 802 "
            pdb=" C3  IHP A 802 "
            pdb=" O12 IHP A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52    2.46   -4.97 2.00e-01 2.50e+01 6.19e+02
  chirality pdb=" C2  IHP B 903 "
            pdb=" C1  IHP B 903 "
            pdb=" C3  IHP B 903 "
            pdb=" O12 IHP B 903 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52    2.45   -4.96 2.00e-01 2.50e+01 6.16e+02
  chirality pdb=" C6  IHP A 802 "
            pdb=" C1  IHP A 802 "
            pdb=" C5  IHP A 802 "
            pdb=" O16 IHP A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50    2.39   -4.89 2.00e-01 2.50e+01 5.98e+02
  ... (remaining 1551 not shown)

  Planarity restraints: 1670
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 512 "    0.026 2.00e-02 2.50e+03   1.90e-02 7.24e+00
        pdb=" CG  TYR A 512 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 512 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 512 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 512 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 512 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 512 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 512 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  58 "    0.021 2.00e-02 2.50e+03   1.52e-02 4.06e+00
        pdb=" CG  PHE A  58 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  58 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  58 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  58 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  58 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  58 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 372 "   -0.013 2.00e-02 2.50e+03   1.44e-02 3.64e+00
        pdb=" CG  PHE A 372 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 372 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 372 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 372 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 372 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 372 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1667 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2236
        2.78 -     3.31: 10535
        3.31 -     3.84: 17455
        3.84 -     4.37: 20592
        4.37 -     4.90: 32815
  Nonbonded interactions: 83633
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A 548 "
            pdb=" OE2 GLU A 613 "
     model   vdw
     2.247 3.120
  nonbonded pdb=" O   LEU A 133 "
            pdb=" OG  SER A 136 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   TRP B 534 "
            pdb=" NH1 ARG B 548 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" OD1 ASP A 533 "
            pdb=" NH1 ARG A 611 "
     model   vdw
     2.271 3.120
  nonbonded pdb=" NE1 TRP B 514 "
            pdb=" OG  SER B 578 "
     model   vdw
     2.281 3.120
  ... (remaining 83628 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 625 or resid 805 through 812))
  selection = (chain 'B' and (resid 1 through 625 or resid 905 through 912))
}

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 group one per residue
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:             2.900
  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:          0.390
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     26.810
  Find NCS groups from input model:        0.450
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
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      :  0.003   0.029  10666  Z= 0.176
  Angle     :  0.761  10.934  14432  Z= 0.395
  Chirality :  0.350   4.974   1554
  Planarity :  0.004   0.046   1670
  Dihedral  : 21.286 163.959   4720
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  : 24.61 %
    Favored  : 75.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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: -0.05 (0.25), residues: 1120
  helix:  0.36 (0.18), residues: 838
  sheet:  None (None), residues: 0
  loop : -0.92 (0.37), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 607 
 HIS   0.007   0.001   HIS A  10 
 PHE   0.034   0.002   PHE A 372 
 TYR   0.046   0.002   TYR A 512 
 ARG   0.013   0.000   ARG A 308 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.23500 (  611)
  hydrogen bonds       : angle       7.34355 ( 1809)
  SS BOND              : bond        0.00135 (    2)
  SS BOND              : angle       0.73363 (    4)
  covalent geometry    : bond        0.00343 (10664)
  covalent geometry    : angle       0.76059 (14428)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 153
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 154
  average time/residue: 0.2528
  time to fit residues: 54.4239
Evaluate side-chains
  139 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 29 optimal weight:    0.2980
   chunk 58 optimal weight:    0.3980
   chunk 46 optimal weight:    0.7980
   chunk 89 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 66 optimal weight:    6.9990
   chunk 103 optimal weight:    2.9990
   overall best weight:    0.6984

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

Flipped N/Q/H residues before XYZ refinement:
** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 387 HIS
B  92 GLN
** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 387 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4719 r_free = 0.4719 target = 0.233287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.174559 restraints weight = 14645.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.173433 restraints weight = 12470.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.176028 restraints weight = 9565.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.4163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.1306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10666  Z= 0.157
  Angle     :  0.705  11.578  14432  Z= 0.340
  Chirality :  0.047   0.474   1554
  Planarity :  0.004   0.052   1670
  Dihedral  : 16.014 135.004   2488
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 22.15 %
    Favored  : 76.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  0.28 (0.25), residues: 1120
  helix:  0.58 (0.18), residues: 836
  sheet:  None (None), residues: 0
  loop : -0.75 (0.39), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 514 
 HIS   0.008   0.001   HIS B 125 
 PHE   0.035   0.002   PHE A 372 
 TYR   0.043   0.002   TYR A 512 
 ARG   0.010   0.001   ARG A 157 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06352 (  611)
  hydrogen bonds       : angle       5.07366 ( 1809)
  SS BOND              : bond        0.00243 (    2)
  SS BOND              : angle       0.84963 (    4)
  covalent geometry    : bond        0.00315 (10664)
  covalent geometry    : angle       0.70489 (14428)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 165
  time to evaluate  : 1.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6394 (ppp) cc_final: 0.6161 (tmm)
REVERT: A  326 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8007 (tt)
REVERT: A  368 TYR cc_start: 0.7453 (p90) cc_final: 0.7100 (p90)
REVERT: B    1 MET cc_start: 0.7003 (ppp) cc_final: 0.5346 (tmm)
REVERT: B  157 ARG cc_start: 0.8382 (ptp-110) cc_final: 0.7974 (ptp-110)
REVERT: B  258 LYS cc_start: 0.6780 (mmtm) cc_final: 0.6508 (tptt)
REVERT: B  355 MET cc_start: 0.8282 (mtt) cc_final: 0.8065 (mtt)
REVERT: B  457 TRP cc_start: 0.8261 (t-100) cc_final: 0.7942 (t60)
REVERT: B  518 TYR cc_start: 0.7890 (t80) cc_final: 0.7647 (t80)
  outliers start: 18
  outliers final: 8
  residues processed: 175
  average time/residue: 0.2939
  time to fit residues: 72.2541
Evaluate side-chains
  149 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 140
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  248 ASN
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain B residue  334 CYS
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  519 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 20 optimal weight:    0.1980
   chunk 41 optimal weight:    6.9990
   chunk 81 optimal weight:    0.0470
   chunk 68 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   chunk 61 optimal weight:    9.9990
   chunk 8 optimal weight:   10.0000
   chunk 87 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 94 optimal weight:    7.9990
   chunk 33 optimal weight:    3.9990
   overall best weight:    0.8080

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

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
A  92 GLN
** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 HIS
** B  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  92 GLN
** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4717 r_free = 0.4717 target = 0.232805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.174153 restraints weight = 14845.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.174259 restraints weight = 15504.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.176394 restraints weight = 11390.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.4164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
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   0.033  10666  Z= 0.142
  Angle     :  0.607  10.244  14432  Z= 0.305
  Chirality :  0.041   0.292   1554
  Planarity :  0.004   0.044   1670
  Dihedral  : 15.062 127.794   2488
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 22.44 %
    Favored  : 74.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.25 (0.25), residues: 1120
  helix:  0.61 (0.18), residues: 846
  sheet:  None (None), residues: 0
  loop : -0.98 (0.38), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 607 
 HIS   0.007   0.001   HIS B 125 
 PHE   0.038   0.002   PHE A 372 
 TYR   0.046   0.002   TYR A 512 
 ARG   0.004   0.000   ARG A 157 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05460 (  611)
  hydrogen bonds       : angle       4.76416 ( 1809)
  SS BOND              : bond        0.00185 (    2)
  SS BOND              : angle       0.65669 (    4)
  covalent geometry    : bond        0.00302 (10664)
  covalent geometry    : angle       0.60688 (14428)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 162
  time to evaluate  : 1.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  258 LYS cc_start: 0.7288 (tppt) cc_final: 0.6618 (tptt)
REVERT: A  326 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8076 (tt)
REVERT: B  132 LYS cc_start: 0.7455 (mtpt) cc_final: 0.7174 (mmtt)
REVERT: B  146 GLN cc_start: 0.8280 (pm20) cc_final: 0.7848 (pm20)
REVERT: B  195 ILE cc_start: 0.5278 (OUTLIER) cc_final: 0.4984 (mp)
REVERT: B  457 TRP cc_start: 0.8150 (t-100) cc_final: 0.7802 (t60)
REVERT: B  518 TYR cc_start: 0.7751 (t80) cc_final: 0.7549 (t80)
  outliers start: 30
  outliers final: 10
  residues processed: 183
  average time/residue: 0.2667
  time to fit residues: 70.0695
Evaluate side-chains
  156 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 144
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  248 ASN
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain B residue  195 ILE
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  579 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 85 optimal weight:    0.0040
   chunk 62 optimal weight:   20.0000
   chunk 106 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 68 optimal weight:    7.9990
   chunk 17 optimal weight:    8.9990
   chunk 111 optimal weight:    0.1980
   chunk 98 optimal weight:    6.9990
   chunk 84 optimal weight:    0.9980
   chunk 70 optimal weight:    0.0040
   overall best weight:    0.4204

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

Flipped N/Q/H residues before XYZ refinement:
** A  10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 540 ASN
B  81 GLN
B  92 GLN
B 119 HIS
** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4731 r_free = 0.4731 target = 0.234333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.176914 restraints weight = 14731.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.174602 restraints weight = 14701.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.177583 restraints weight = 10709.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.4185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.2299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  10666  Z= 0.123
  Angle     :  0.584   9.210  14432  Z= 0.298
  Chirality :  0.041   0.241   1554
  Planarity :  0.005   0.084   1670
  Dihedral  : 14.803 122.799   2488
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 23.33 %
    Favored  : 74.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.47 (0.25), residues: 1120
  helix:  0.79 (0.18), residues: 848
  sheet:  None (None), residues: 0
  loop : -1.00 (0.38), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 607 
 HIS   0.007   0.001   HIS B 125 
 PHE   0.040   0.002   PHE A 372 
 TYR   0.048   0.002   TYR A 512 
 ARG   0.006   0.000   ARG A 308 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04867 (  611)
  hydrogen bonds       : angle       4.58534 ( 1809)
  SS BOND              : bond        0.00184 (    2)
  SS BOND              : angle       0.55782 (    4)
  covalent geometry    : bond        0.00248 (10664)
  covalent geometry    : angle       0.58408 (14428)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 167
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 GLN cc_start: 0.8267 (mm-40) cc_final: 0.7875 (mm-40)
REVERT: A  258 LYS cc_start: 0.7203 (tppt) cc_final: 0.6585 (tptt)
REVERT: A  326 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8047 (tt)
REVERT: B   62 CYS cc_start: 0.8664 (m) cc_final: 0.8061 (m)
REVERT: B  195 ILE cc_start: 0.5253 (OUTLIER) cc_final: 0.4952 (mp)
REVERT: B  457 TRP cc_start: 0.8148 (t-100) cc_final: 0.7779 (t60)
REVERT: B  615 GLU cc_start: 0.7867 (tp30) cc_final: 0.7301 (tp30)
  outliers start: 25
  outliers final: 10
  residues processed: 181
  average time/residue: 0.2297
  time to fit residues: 58.4798
Evaluate side-chains
  161 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 149
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ILE
Chi-restraints excluded: chain A residue   55 GLU
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  248 ASN
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue  195 ILE
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  575 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 83 optimal weight:    0.6980
   chunk 79 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 111 optimal weight:    0.6980
   chunk 63 optimal weight:    7.9990
   chunk 41 optimal weight:    3.9990
   chunk 28 optimal weight:    0.4980
   chunk 13 optimal weight:    8.9990
   chunk 12 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 540 ASN
B  10 HIS
B  92 GLN
B 248 ASN
** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4723 r_free = 0.4723 target = 0.233513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.178313 restraints weight = 14705.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.175993 restraints weight = 17326.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.180164 restraints weight = 12136.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.4208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  10666  Z= 0.135
  Angle     :  0.600  11.094  14432  Z= 0.306
  Chirality :  0.040   0.201   1554
  Planarity :  0.004   0.048   1670
  Dihedral  : 14.743 120.649   2488
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 22.83 %
    Favored  : 74.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.48 (0.25), residues: 1120
  helix:  0.82 (0.18), residues: 848
  sheet:  None (None), residues: 0
  loop : -1.08 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 607 
 HIS   0.007   0.001   HIS B 125 
 PHE   0.026   0.001   PHE A 153 
 TYR   0.048   0.002   TYR A 512 
 ARG   0.007   0.000   ARG A 157 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04832 (  611)
  hydrogen bonds       : angle       4.53551 ( 1809)
  SS BOND              : bond        0.00153 (    2)
  SS BOND              : angle       0.53116 (    4)
  covalent geometry    : bond        0.00294 (10664)
  covalent geometry    : angle       0.60028 (14428)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 153
  time to evaluate  : 1.069 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  258 LYS cc_start: 0.7276 (tppt) cc_final: 0.6683 (tptt)
REVERT: A  326 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8073 (tt)
REVERT: B  157 ARG cc_start: 0.8290 (ptp-110) cc_final: 0.8035 (ptp-170)
REVERT: B  457 TRP cc_start: 0.8159 (t-100) cc_final: 0.7788 (t60)
REVERT: B  615 GLU cc_start: 0.7868 (tp30) cc_final: 0.7292 (tp30)
  outliers start: 24
  outliers final: 13
  residues processed: 169
  average time/residue: 0.2396
  time to fit residues: 56.5099
Evaluate side-chains
  149 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 135
  time to evaluate  : 1.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ILE
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  248 ASN
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  328 CYS
Chi-restraints excluded: chain A residue  574 THR
Chi-restraints excluded: chain A residue  587 HIS
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  575 ILE
Chi-restraints excluded: chain B residue  579 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 111 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   chunk 108 optimal weight:    0.9990
   chunk 1 optimal weight:    4.9990
   chunk 47 optimal weight:    0.4980
   chunk 14 optimal weight:   10.0000
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 476 HIS
** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  92 GLN
B 149 GLN
** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4713 r_free = 0.4713 target = 0.232538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.175590 restraints weight = 14778.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.174224 restraints weight = 15088.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.176725 restraints weight = 11230.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.4172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.2715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10666  Z= 0.142
  Angle     :  0.610   8.909  14432  Z= 0.310
  Chirality :  0.040   0.185   1554
  Planarity :  0.004   0.046   1670
  Dihedral  : 14.700 119.375   2488
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 23.62 %
    Favored  : 73.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.55 (0.25), residues: 1120
  helix:  0.86 (0.18), residues: 846
  sheet:  None (None), residues: 0
  loop : -1.00 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 607 
 HIS   0.007   0.001   HIS B 125 
 PHE   0.024   0.001   PHE A  59 
 TYR   0.047   0.002   TYR A 512 
 ARG   0.010   0.001   ARG B 176 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04901 (  611)
  hydrogen bonds       : angle       4.52162 ( 1809)
  SS BOND              : bond        0.00146 (    2)
  SS BOND              : angle       0.52927 (    4)
  covalent geometry    : bond        0.00316 (10664)
  covalent geometry    : angle       0.61020 (14428)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 149
  time to evaluate  : 1.078 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  158 LYS cc_start: 0.9010 (mmmt) cc_final: 0.8792 (mmtt)
REVERT: A  258 LYS cc_start: 0.7318 (tppt) cc_final: 0.6726 (tptt)
REVERT: A  326 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7880 (tt)
REVERT: A  482 LYS cc_start: 0.8880 (tmmt) cc_final: 0.8434 (tmmt)
REVERT: B  146 GLN cc_start: 0.8176 (pm20) cc_final: 0.7682 (pm20)
REVERT: B  165 LYS cc_start: 0.8938 (mtmm) cc_final: 0.8407 (pttm)
REVERT: B  237 VAL cc_start: 0.7864 (OUTLIER) cc_final: 0.7117 (m)
REVERT: B  379 PHE cc_start: 0.6363 (t80) cc_final: 0.5862 (t80)
REVERT: B  457 TRP cc_start: 0.8186 (t-100) cc_final: 0.7780 (t60)
REVERT: B  613 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7333 (mm-30)
REVERT: B  615 GLU cc_start: 0.7937 (tp30) cc_final: 0.7416 (tp30)
  outliers start: 26
  outliers final: 15
  residues processed: 167
  average time/residue: 0.2655
  time to fit residues: 62.0584
Evaluate side-chains
  160 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 143
  time to evaluate  : 1.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ILE
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  248 ASN
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  328 CYS
Chi-restraints excluded: chain A residue  519 ILE
Chi-restraints excluded: chain A residue  574 THR
Chi-restraints excluded: chain A residue  587 HIS
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain B residue   92 GLN
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  575 ILE
Chi-restraints excluded: chain B residue  579 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 58 optimal weight:    7.9990
   chunk 60 optimal weight:   10.0000
   chunk 107 optimal weight:    0.9980
   chunk 81 optimal weight:    0.6980
   chunk 97 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 108 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   chunk 72 optimal weight:    9.9990
   chunk 94 optimal weight:    1.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4696 r_free = 0.4696 target = 0.230583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.175970 restraints weight = 15039.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.172335 restraints weight = 16819.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.176393 restraints weight = 13208.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.4161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.2846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10666  Z= 0.173
  Angle     :  0.631   8.721  14432  Z= 0.324
  Chirality :  0.042   0.297   1554
  Planarity :  0.004   0.044   1670
  Dihedral  : 14.753 118.416   2488
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 25.20 %
    Favored  : 72.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.25), residues: 1120
  helix:  0.82 (0.18), residues: 846
  sheet:  None (None), residues: 0
  loop : -1.00 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 607 
 HIS   0.007   0.001   HIS B 125 
 PHE   0.014   0.002   PHE A  72 
 TYR   0.047   0.002   TYR B 512 
 ARG   0.008   0.001   ARG A 308 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05237 (  611)
  hydrogen bonds       : angle       4.57078 ( 1809)
  SS BOND              : bond        0.00120 (    2)
  SS BOND              : angle       0.58414 (    4)
  covalent geometry    : bond        0.00394 (10664)
  covalent geometry    : angle       0.63125 (14428)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 148
  time to evaluate  : 1.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  258 LYS cc_start: 0.7380 (tppt) cc_final: 0.6757 (tptt)
REVERT: A  326 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7906 (tt)
REVERT: B  157 ARG cc_start: 0.8458 (ptp-110) cc_final: 0.8052 (ptp-170)
REVERT: B  165 LYS cc_start: 0.9023 (mtmm) cc_final: 0.8459 (pttm)
REVERT: B  326 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8172 (tt)
REVERT: B  379 PHE cc_start: 0.6434 (t80) cc_final: 0.5879 (t80)
REVERT: B  457 TRP cc_start: 0.8176 (t-100) cc_final: 0.7771 (t60)
REVERT: B  508 MET cc_start: 0.7641 (ptp) cc_final: 0.7194 (ptp)
REVERT: B  532 MET cc_start: 0.8137 (ptp) cc_final: 0.7879 (ptp)
REVERT: B  615 GLU cc_start: 0.8019 (tp30) cc_final: 0.7513 (tp30)
  outliers start: 22
  outliers final: 12
  residues processed: 164
  average time/residue: 0.2690
  time to fit residues: 61.9917
Evaluate side-chains
  155 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 141
  time to evaluate  : 1.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ILE
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  248 ASN
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  328 CYS
Chi-restraints excluded: chain A residue  574 THR
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain A residue  587 HIS
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  453 CYS
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  579 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9980
   chunk 66 optimal weight:    6.9990
   chunk 4 optimal weight:    6.9990
   chunk 38 optimal weight:    7.9990
   chunk 95 optimal weight:   10.0000
   chunk 62 optimal weight:   20.0000
   chunk 39 optimal weight:    0.4980
   chunk 23 optimal weight:    0.6980
   chunk 110 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 441 HIS
** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4677 r_free = 0.4677 target = 0.228772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.176019 restraints weight = 14796.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.172975 restraints weight = 18768.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.176203 restraints weight = 15730.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.4158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.3047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10666  Z= 0.167
  Angle     :  0.634   8.962  14432  Z= 0.325
  Chirality :  0.041   0.206   1554
  Planarity :  0.004   0.046   1670
  Dihedral  : 14.692 116.698   2488
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 25.69 %
    Favored  : 72.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.25), residues: 1120
  helix:  0.83 (0.18), residues: 848
  sheet:  None (None), residues: 0
  loop : -1.01 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 175 
 HIS   0.007   0.001   HIS B 179 
 PHE   0.019   0.002   PHE B  59 
 TYR   0.045   0.002   TYR B 512 
 ARG   0.008   0.001   ARG A 308 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05266 (  611)
  hydrogen bonds       : angle       4.53560 ( 1809)
  SS BOND              : bond        0.00195 (    2)
  SS BOND              : angle       0.62191 (    4)
  covalent geometry    : bond        0.00379 (10664)
  covalent geometry    : angle       0.63415 (14428)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 1.012 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  258 LYS cc_start: 0.7443 (tppt) cc_final: 0.6886 (tptt)
REVERT: A  326 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7953 (tt)
REVERT: B  146 GLN cc_start: 0.8169 (pm20) cc_final: 0.7913 (pm20)
REVERT: B  165 LYS cc_start: 0.8830 (mtmm) cc_final: 0.8315 (pttm)
REVERT: B  326 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8191 (tt)
REVERT: B  457 TRP cc_start: 0.8148 (t-100) cc_final: 0.7749 (t60)
REVERT: B  508 MET cc_start: 0.7469 (ptp) cc_final: 0.7090 (ptp)
REVERT: B  532 MET cc_start: 0.8212 (ptp) cc_final: 0.7996 (ptp)
REVERT: B  615 GLU cc_start: 0.8006 (tp30) cc_final: 0.7504 (tp30)
  outliers start: 20
  outliers final: 14
  residues processed: 163
  average time/residue: 0.2351
  time to fit residues: 53.4067
Evaluate side-chains
  158 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 142
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ILE
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  248 ASN
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  328 CYS
Chi-restraints excluded: chain A residue  574 THR
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain A residue  587 HIS
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  453 CYS
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  579 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 101 optimal weight:    6.9990
   chunk 70 optimal weight:    6.9990
   chunk 74 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   chunk 51 optimal weight:    0.8980
   chunk 67 optimal weight:    7.9990
   chunk 89 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 540 ASN
B  81 GLN
** B  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 314 GLN ** 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 = 0.4676 r_free = 0.4676 target = 0.228827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.172972 restraints weight = 14926.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.172057 restraints weight = 15926.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.175077 restraints weight = 12815.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.4154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.3202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10666  Z= 0.160
  Angle     :  0.640   9.510  14432  Z= 0.326
  Chirality :  0.041   0.218   1554
  Planarity :  0.004   0.047   1670
  Dihedral  : 14.545 115.370   2488
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 26.28 %
    Favored  : 72.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.56 (0.25), residues: 1120
  helix:  0.87 (0.18), residues: 846
  sheet:  None (None), residues: 0
  loop : -0.99 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP B 175 
 HIS   0.007   0.001   HIS B 125 
 PHE   0.015   0.001   PHE B 153 
 TYR   0.047   0.002   TYR B 512 
 ARG   0.009   0.000   ARG A 308 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05160 (  611)
  hydrogen bonds       : angle       4.51205 ( 1809)
  SS BOND              : bond        0.00157 (    2)
  SS BOND              : angle       0.65470 (    4)
  covalent geometry    : bond        0.00361 (10664)
  covalent geometry    : angle       0.63983 (14428)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 147
  time to evaluate  : 1.015 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  258 LYS cc_start: 0.7481 (tppt) cc_final: 0.6850 (tptt)
REVERT: A  326 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7964 (tt)
REVERT: B  157 ARG cc_start: 0.8351 (ptp-170) cc_final: 0.7933 (ptp-110)
REVERT: B  165 LYS cc_start: 0.8872 (mtmm) cc_final: 0.8426 (pttm)
REVERT: B  326 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8145 (tt)
REVERT: B  457 TRP cc_start: 0.8201 (t-100) cc_final: 0.7761 (t60)
REVERT: B  508 MET cc_start: 0.7528 (ptp) cc_final: 0.7130 (ptp)
REVERT: B  532 MET cc_start: 0.8253 (ptp) cc_final: 0.8044 (ptp)
REVERT: B  615 GLU cc_start: 0.8070 (tp30) cc_final: 0.7574 (tp30)
  outliers start: 16
  outliers final: 14
  residues processed: 159
  average time/residue: 0.2427
  time to fit residues: 53.8555
Evaluate side-chains
  157 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 141
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ILE
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  248 ASN
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  328 CYS
Chi-restraints excluded: chain A residue  574 THR
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain A residue  587 HIS
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  453 CYS
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  579 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 73 optimal weight:    9.9990
   chunk 86 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 78 optimal weight:    0.6980
   chunk 69 optimal weight:    0.6980
   chunk 103 optimal weight:    1.9990
   chunk 3 optimal weight:   10.0000
   chunk 108 optimal weight:    0.6980
   chunk 42 optimal weight:    0.7980
   chunk 37 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 608 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4689 r_free = 0.4689 target = 0.230331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.177121 restraints weight = 14833.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.175182 restraints weight = 17940.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.178309 restraints weight = 14946.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.4185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.3346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10666  Z= 0.142
  Angle     :  0.640  10.209  14432  Z= 0.330
  Chirality :  0.041   0.238   1554
  Planarity :  0.004   0.046   1670
  Dihedral  : 14.293 113.947   2488
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 26.08 %
    Favored  : 72.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.25), residues: 1120
  helix:  0.90 (0.18), residues: 848
  sheet:  None (None), residues: 0
  loop : -0.97 (0.38), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.001   TRP B 175 
 HIS   0.007   0.001   HIS B 125 
 PHE   0.016   0.001   PHE B  59 
 TYR   0.046   0.002   TYR B 512 
 ARG   0.010   0.000   ARG A 308 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04938 (  611)
  hydrogen bonds       : angle       4.44889 ( 1809)
  SS BOND              : bond        0.00198 (    2)
  SS BOND              : angle       0.62088 (    4)
  covalent geometry    : bond        0.00308 (10664)
  covalent geometry    : angle       0.63999 (14428)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 147
  time to evaluate  : 1.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  258 LYS cc_start: 0.7481 (tppt) cc_final: 0.6873 (tptt)
REVERT: A  326 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7923 (tt)
REVERT: B  146 GLN cc_start: 0.8169 (pm20) cc_final: 0.7669 (pm20)
REVERT: B  165 LYS cc_start: 0.8790 (mtmm) cc_final: 0.8211 (pttm)
REVERT: B  326 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8386 (tt)
REVERT: B  457 TRP cc_start: 0.8167 (t-100) cc_final: 0.7722 (t60)
REVERT: B  508 MET cc_start: 0.7406 (ptp) cc_final: 0.7028 (ptp)
  outliers start: 16
  outliers final: 10
  residues processed: 157
  average time/residue: 0.2356
  time to fit residues: 51.7051
Evaluate side-chains
  150 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 138
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  248 ASN
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  328 CYS
Chi-restraints excluded: chain A residue  574 THR
Chi-restraints excluded: chain A residue  587 HIS
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  453 CYS
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  579 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 79 optimal weight:    0.6980
   chunk 72 optimal weight:    6.9990
   chunk 7 optimal weight:    4.9990
   chunk 84 optimal weight:    0.6980
   chunk 16 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9980
   chunk 65 optimal weight:   30.0000
   chunk 49 optimal weight:    0.9990
   chunk 73 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9990
   chunk 98 optimal weight:    0.0270
   overall best weight:    0.6840

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4693 r_free = 0.4693 target = 0.230792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.174277 restraints weight = 14725.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.173776 restraints weight = 16859.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.176517 restraints weight = 11828.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.4173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.3535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10666  Z= 0.136
  Angle     :  0.636  10.687  14432  Z= 0.327
  Chirality :  0.041   0.223   1554
  Planarity :  0.004   0.045   1670
  Dihedral  : 14.030 112.248   2488
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 26.87 %
    Favored  : 71.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.74 (0.25), residues: 1120
  helix:  0.99 (0.18), residues: 848
  sheet:  None (None), residues: 0
  loop : -0.92 (0.38), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.001   TRP B 175 
 HIS   0.007   0.001   HIS B 125 
 PHE   0.021   0.001   PHE B  59 
 TYR   0.045   0.002   TYR B 512 
 ARG   0.010   0.000   ARG A 308 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04790 (  611)
  hydrogen bonds       : angle       4.38617 ( 1809)
  SS BOND              : bond        0.00182 (    2)
  SS BOND              : angle       0.58184 (    4)
  covalent geometry    : bond        0.00293 (10664)
  covalent geometry    : angle       0.63591 (14428)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3543.69 seconds
wall clock time: 63 minutes 57.22 seconds (3837.22 seconds total)