Starting phenix.real_space_refine
on Wed Sep 17 18:24:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9iuc_60897/09_2025/9iuc_60897.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9iuc_60897/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9iuc_60897/09_2025/9iuc_60897.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9iuc_60897/09_2025/9iuc_60897.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9iuc_60897/09_2025/9iuc_60897.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9iuc_60897/09_2025/9iuc_60897.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.46, per 1000 atoms: 0.24
  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: 1.10
  Conformation dependent library (CDL) restraints added in 373.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.29
  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: 1.51

  Time building geometry restraints manager: 1.39 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:             4.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.670
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.360
-------------------------------------------------------------------------------
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 : 11.77
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.013   0.000   ARG A 308 
 TYR   0.046   0.002   TYR A 512 
 PHE   0.034   0.002   PHE A 372 
 TRP   0.011   0.001   TRP A 607 
 HIS   0.007   0.001   HIS A  10 

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

*********************** 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  : 0.307 
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: 0.1084
  time to fit residues: 23.2235
Evaluate side-chains
  138 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    0.2980
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.8980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 248 ASN
** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 387 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4697 r_free = 0.4697 target = 0.230920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.172116 restraints weight = 14623.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.171027 restraints weight = 11990.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.173634 restraints weight = 9049.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.174137 restraints weight = 6782.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.174256 restraints weight = 6724.179|
|-----------------------------------------------------------------------------|
r_work (final): 0.4146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.1294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10666  Z= 0.169
  Angle     :  0.707  11.537  14432  Z= 0.344
  Chirality :  0.048   0.456   1554
  Planarity :  0.005   0.055   1670
  Dihedral  : 16.179 136.180   2488
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 21.95 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.25 (0.25), residues: 1120
  helix:  0.56 (0.18), residues: 834
  sheet:  None (None), residues: 0
  loop : -0.75 (0.39), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 157 
 TYR   0.043   0.002   TYR A 512 
 PHE   0.034   0.002   PHE A 372 
 TRP   0.014   0.001   TRP B 514 
 HIS   0.008   0.001   HIS B 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (10664)
  covalent geometry    : angle       0.70654 (14428)
  SS BOND              : bond        0.00257 (    2)
  SS BOND              : angle       0.93617 (    4)
  hydrogen bonds       : bond        0.06401 (  611)
  hydrogen bonds       : angle       5.12924 ( 1809)

*********************** 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
  186 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 166
  time to evaluate  : 0.374 
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    1 MET cc_start: 0.6381 (ppp) cc_final: 0.6054 (tmm)
REVERT: A  258 LYS cc_start: 0.7222 (tppt) cc_final: 0.6501 (tptt)
REVERT: A  326 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8012 (tt)
REVERT: A  368 TYR cc_start: 0.7469 (p90) cc_final: 0.7126 (p90)
REVERT: B    1 MET cc_start: 0.7011 (ppp) cc_final: 0.5229 (tmm)
REVERT: B  157 ARG cc_start: 0.8432 (ptp-110) cc_final: 0.7958 (ptp-110)
REVERT: B  258 LYS cc_start: 0.6802 (mmtm) cc_final: 0.6491 (tptt)
REVERT: B  355 MET cc_start: 0.8286 (mtt) cc_final: 0.8066 (mtt)
REVERT: B  457 TRP cc_start: 0.8263 (t-100) cc_final: 0.7938 (t60)
REVERT: B  518 TYR cc_start: 0.7894 (t80) cc_final: 0.7638 (t80)
  outliers start: 20
  outliers final: 8
  residues processed: 176
  average time/residue: 0.1006
  time to fit residues: 24.8427
Evaluate side-chains
  150 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 141
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
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 65 optimal weight:   20.0000
   chunk 91 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 48 optimal weight:    8.9990
   chunk 56 optimal weight:    0.2980
   chunk 13 optimal weight:    3.9990
   chunk 72 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 83 optimal weight:    0.9980
   chunk 96 optimal weight:    6.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
A  92 GLN
** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 476 HIS
B   6 HIS
B  81 GLN
B  92 GLN
** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 248 ASN
** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4685 r_free = 0.4685 target = 0.229087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.170108 restraints weight = 14685.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.169791 restraints weight = 15908.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.171719 restraints weight = 12281.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.172679 restraints weight = 8182.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.172961 restraints weight = 7708.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.4133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10666  Z= 0.190
  Angle     :  0.654  10.028  14432  Z= 0.327
  Chirality :  0.043   0.271   1554
  Planarity :  0.005   0.047   1670
  Dihedral  : 15.484 128.414   2488
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 22.93 %
    Favored  : 73.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.08 (0.25), residues: 1120
  helix:  0.48 (0.18), residues: 832
  sheet:  None (None), residues: 0
  loop : -0.93 (0.38), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 157 
 TYR   0.048   0.002   TYR A 512 
 PHE   0.041   0.002   PHE A 372 
 TRP   0.013   0.001   TRP B 607 
 HIS   0.007   0.001   HIS B 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 (10664)
  covalent geometry    : angle       0.65436 (14428)
  SS BOND              : bond        0.00158 (    2)
  SS BOND              : angle       0.76158 (    4)
  hydrogen bonds       : bond        0.06055 (  611)
  hydrogen bonds       : angle       4.92901 ( 1809)

*********************** 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
  188 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 152
  time to evaluate  : 0.337 
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    1 MET cc_start: 0.6170 (ppp) cc_final: 0.5934 (tmm)
REVERT: A   54 PHE cc_start: 0.6929 (t80) cc_final: 0.6639 (t80)
REVERT: A  258 LYS cc_start: 0.7312 (tppt) cc_final: 0.6637 (tptt)
REVERT: A  326 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8101 (tt)
REVERT: B    1 MET cc_start: 0.6640 (ppp) cc_final: 0.5381 (tmm)
REVERT: B  132 LYS cc_start: 0.7455 (mtpt) cc_final: 0.7183 (mmtt)
REVERT: B  195 ILE cc_start: 0.5301 (OUTLIER) cc_final: 0.4932 (mp)
REVERT: B  237 VAL cc_start: 0.8104 (OUTLIER) cc_final: 0.7329 (m)
REVERT: B  326 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8344 (tt)
REVERT: B  379 PHE cc_start: 0.6592 (t80) cc_final: 0.6281 (t80)
REVERT: B  457 TRP cc_start: 0.8209 (t-100) cc_final: 0.7790 (t60)
REVERT: B  489 MET cc_start: 0.8069 (tpt) cc_final: 0.7799 (tpt)
REVERT: B  511 PHE cc_start: 0.8245 (t80) cc_final: 0.8000 (t80)
  outliers start: 36
  outliers final: 12
  residues processed: 181
  average time/residue: 0.1058
  time to fit residues: 26.8509
Evaluate side-chains
  155 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 139
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
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  326 LEU
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  530 LEU
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  237 VAL
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  519 ILE
Chi-restraints excluded: chain B residue  530 LEU
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 81 optimal weight:    0.9990
   chunk 1 optimal weight:    6.9990
   chunk 6 optimal weight:    6.9990
   chunk 112 optimal weight:    1.9990
   chunk 64 optimal weight:    9.9990
   chunk 87 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 79 optimal weight:    0.6980
   chunk 68 optimal weight:   10.0000
   chunk 38 optimal weight:   10.0000
   chunk 14 optimal weight:   10.0000
   overall best weight:    1.1388

-------------------------------------------------------------------------------
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  92 GLN
B 119 HIS
** 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 = 0.4676 r_free = 0.4676 target = 0.228226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.169518 restraints weight = 14594.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.170281 restraints weight = 12686.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.171918 restraints weight = 10173.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.172335 restraints weight = 7624.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.172691 restraints weight = 7176.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.4133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.2234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10666  Z= 0.162
  Angle     :  0.611   9.468  14432  Z= 0.313
  Chirality :  0.042   0.259   1554
  Planarity :  0.005   0.088   1670
  Dihedral  : 15.167 124.390   2488
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 23.52 %
    Favored  : 73.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.15 (0.25), residues: 1120
  helix:  0.57 (0.18), residues: 838
  sheet:  None (None), residues: 0
  loop : -1.08 (0.37), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 308 
 TYR   0.050   0.002   TYR A 512 
 PHE   0.040   0.002   PHE A 372 
 TRP   0.013   0.001   TRP B 607 
 HIS   0.007   0.001   HIS B 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (10664)
  covalent geometry    : angle       0.61066 (14428)
  SS BOND              : bond        0.00150 (    2)
  SS BOND              : angle       0.67147 (    4)
  hydrogen bonds       : bond        0.05529 (  611)
  hydrogen bonds       : angle       4.75735 ( 1809)

*********************** 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
  180 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 152
  time to evaluate  : 0.351 
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: 0.7295 (tppt) cc_final: 0.6667 (tptt)
REVERT: A  326 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8100 (tt)
REVERT: B  146 GLN cc_start: 0.8435 (pm20) cc_final: 0.8010 (pm20)
REVERT: B  326 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8315 (tt)
REVERT: B  379 PHE cc_start: 0.6510 (t80) cc_final: 0.6077 (t80)
REVERT: B  457 TRP cc_start: 0.8208 (t-100) cc_final: 0.7773 (t60)
REVERT: B  511 PHE cc_start: 0.8360 (t80) cc_final: 0.8006 (t80)
REVERT: B  615 GLU cc_start: 0.8121 (tp30) cc_final: 0.7591 (tp30)
  outliers start: 28
  outliers final: 16
  residues processed: 173
  average time/residue: 0.1024
  time to fit residues: 24.9625
Evaluate side-chains
  156 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 138
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
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  346 VAL
Chi-restraints excluded: chain A residue  530 LEU
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  297 VAL
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  519 ILE
Chi-restraints excluded: chain B residue  530 LEU
Chi-restraints excluded: chain B residue  579 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 71 optimal weight:    9.9990
   chunk 47 optimal weight:    2.9990
   chunk 16 optimal weight:   10.0000
   chunk 49 optimal weight:    0.3980
   chunk 36 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 14 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9980
   chunk 66 optimal weight:   20.0000
   chunk 12 optimal weight:    1.9990
   overall best weight:    1.0786

-------------------------------------------------------------------------------
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  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 = 0.4678 r_free = 0.4678 target = 0.228561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.169205 restraints weight = 14711.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.168388 restraints weight = 13003.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.170205 restraints weight = 10502.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.171084 restraints weight = 7395.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.171267 restraints weight = 6957.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.4129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.2527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10666  Z= 0.159
  Angle     :  0.608  10.897  14432  Z= 0.311
  Chirality :  0.040   0.198   1554
  Planarity :  0.004   0.041   1670
  Dihedral  : 15.042 121.830   2488
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 23.62 %
    Favored  : 73.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.25 (0.25), residues: 1120
  helix:  0.64 (0.18), residues: 848
  sheet:  None (None), residues: 0
  loop : -1.12 (0.38), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 157 
 TYR   0.050   0.002   TYR A 512 
 PHE   0.022   0.002   PHE A 153 
 TRP   0.013   0.001   TRP A 175 
 HIS   0.007   0.001   HIS B 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (10664)
  covalent geometry    : angle       0.60846 (14428)
  SS BOND              : bond        0.00148 (    2)
  SS BOND              : angle       0.63142 (    4)
  hydrogen bonds       : bond        0.05330 (  611)
  hydrogen bonds       : angle       4.67982 ( 1809)

*********************** 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
  182 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 148
  time to evaluate  : 0.386 
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: 0.7313 (tppt) cc_final: 0.6734 (tptt)
REVERT: A  326 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8104 (tt)
REVERT: B  237 VAL cc_start: 0.8019 (OUTLIER) cc_final: 0.7300 (m)
REVERT: B  326 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8337 (tt)
REVERT: B  457 TRP cc_start: 0.8206 (t-100) cc_final: 0.7771 (t60)
REVERT: B  482 LYS cc_start: 0.8969 (tmmt) cc_final: 0.8562 (tmmt)
REVERT: B  615 GLU cc_start: 0.7990 (tp30) cc_final: 0.7501 (tp30)
  outliers start: 34
  outliers final: 17
  residues processed: 175
  average time/residue: 0.1064
  time to fit residues: 26.0454
Evaluate side-chains
  159 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 139
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
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  346 VAL
Chi-restraints excluded: chain A residue  530 LEU
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  297 VAL
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  519 ILE
Chi-restraints excluded: chain B residue  530 LEU
Chi-restraints excluded: chain B residue  575 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 14 optimal weight:    9.9990
   chunk 98 optimal weight:    0.8980
   chunk 6 optimal weight:    5.9990
   chunk 62 optimal weight:   20.0000
   chunk 58 optimal weight:   10.0000
   chunk 86 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 21 optimal weight:    0.2980
   chunk 51 optimal weight:    2.9990
   chunk 95 optimal weight:   10.0000
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 540 ASN
B  10 HIS
B  92 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 = 0.4708 r_free = 0.4708 target = 0.232115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.174166 restraints weight = 14886.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.171820 restraints weight = 14601.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.175488 restraints weight = 11547.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.175111 restraints weight = 7647.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.176065 restraints weight = 6937.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.4165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.2756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10666  Z= 0.137
  Angle     :  0.610   8.659  14432  Z= 0.313
  Chirality :  0.040   0.158   1554
  Planarity :  0.004   0.042   1670
  Dihedral  : 14.770 119.707   2488
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 24.80 %
    Favored  : 72.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.25), residues: 1120
  helix:  0.81 (0.18), residues: 846
  sheet:  None (None), residues: 0
  loop : -1.04 (0.38), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 157 
 TYR   0.048   0.002   TYR A 512 
 PHE   0.026   0.001   PHE A 153 
 TRP   0.018   0.001   TRP A 175 
 HIS   0.007   0.001   HIS B 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (10664)
  covalent geometry    : angle       0.60973 (14428)
  SS BOND              : bond        0.00163 (    2)
  SS BOND              : angle       0.57298 (    4)
  hydrogen bonds       : bond        0.04942 (  611)
  hydrogen bonds       : angle       4.52984 ( 1809)

*********************** 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
  169 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 146
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  158 LYS cc_start: 0.9128 (mmmt) cc_final: 0.8863 (mmtt)
REVERT: A  258 LYS cc_start: 0.7347 (tppt) cc_final: 0.6766 (tptt)
REVERT: A  326 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7855 (tt)
REVERT: B  457 TRP cc_start: 0.8187 (t-100) cc_final: 0.7744 (t60)
REVERT: B  482 LYS cc_start: 0.8897 (tmmt) cc_final: 0.8502 (tmmt)
REVERT: B  489 MET cc_start: 0.7993 (tpt) cc_final: 0.7658 (tpt)
REVERT: B  615 GLU cc_start: 0.7928 (tp30) cc_final: 0.7470 (tp30)
  outliers start: 23
  outliers final: 14
  residues processed: 161
  average time/residue: 0.1037
  time to fit residues: 23.5652
Evaluate side-chains
  149 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 134
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
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  297 VAL
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  478 VAL
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 23 optimal weight:    0.5980
   chunk 55 optimal weight:    0.5980
   chunk 111 optimal weight:    0.3980
   chunk 40 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 20 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   chunk 11 optimal weight:    5.9990
   chunk 58 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9980
   chunk 95 optimal weight:    6.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A  60 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 540 ASN
B  92 GLN
** 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 = 0.4704 r_free = 0.4704 target = 0.231599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.175131 restraints weight = 14678.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.172394 restraints weight = 15640.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.175616 restraints weight = 11587.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.176306 restraints weight = 7559.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.176766 restraints weight = 7263.509|
|-----------------------------------------------------------------------------|
r_work (final): 0.4168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.3002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10666  Z= 0.132
  Angle     :  0.601   8.464  14432  Z= 0.313
  Chirality :  0.039   0.147   1554
  Planarity :  0.004   0.042   1670
  Dihedral  : 14.542 117.870   2488
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 25.59 %
    Favored  : 71.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.25), residues: 1120
  helix:  0.92 (0.18), residues: 846
  sheet:  None (None), residues: 0
  loop : -1.03 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 308 
 TYR   0.047   0.002   TYR A 512 
 PHE   0.016   0.001   PHE A 153 
 TRP   0.028   0.001   TRP B 175 
 HIS   0.007   0.001   HIS B 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (10664)
  covalent geometry    : angle       0.60151 (14428)
  SS BOND              : bond        0.00161 (    2)
  SS BOND              : angle       0.55403 (    4)
  hydrogen bonds       : bond        0.04768 (  611)
  hydrogen bonds       : angle       4.47998 ( 1809)

*********************** 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
  178 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 153
  time to evaluate  : 0.277 
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  258 LYS cc_start: 0.7329 (tppt) cc_final: 0.6785 (tptt)
REVERT: A  326 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7843 (tt)
REVERT: A  482 LYS cc_start: 0.8856 (tmmt) cc_final: 0.8492 (tmmt)
REVERT: B  157 ARG cc_start: 0.8358 (ptp-110) cc_final: 0.8015 (ptp-170)
REVERT: B  457 TRP cc_start: 0.8149 (t-100) cc_final: 0.7679 (t60)
REVERT: B  508 MET cc_start: 0.7493 (ptp) cc_final: 0.7267 (ptp)
REVERT: B  613 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7422 (mm-30)
REVERT: B  615 GLU cc_start: 0.7960 (tp30) cc_final: 0.7454 (tp30)
  outliers start: 25
  outliers final: 13
  residues processed: 171
  average time/residue: 0.0987
  time to fit residues: 23.7577
Evaluate side-chains
  158 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 144
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
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  300 VAL
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  328 CYS
Chi-restraints excluded: chain A residue  540 ASN
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   92 GLN
Chi-restraints excluded: chain B residue  326 LEU
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 67 optimal weight:    7.9990
   chunk 3 optimal weight:   10.0000
   chunk 109 optimal weight:    8.9990
   chunk 17 optimal weight:    6.9990
   chunk 43 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 68 optimal weight:    6.9990
   chunk 4 optimal weight:    0.7980
   chunk 75 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 5 optimal weight:    7.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 441 HIS
A 540 ASN
** 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 = 0.4640 r_free = 0.4640 target = 0.224658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.167479 restraints weight = 14681.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.165027 restraints weight = 15039.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.168053 restraints weight = 11662.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.168527 restraints weight = 7698.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.169082 restraints weight = 7370.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.4107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.3191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  10666  Z= 0.214
  Angle     :  0.672   8.950  14432  Z= 0.344
  Chirality :  0.043   0.272   1554
  Planarity :  0.004   0.045   1670
  Dihedral  : 14.878 117.079   2488
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 25.89 %
    Favored  : 71.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.25), residues: 1120
  helix:  0.74 (0.18), residues: 846
  sheet:  None (None), residues: 0
  loop : -1.09 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 308 
 TYR   0.048   0.002   TYR A 512 
 PHE   0.025   0.002   PHE A  59 
 TRP   0.029   0.002   TRP B 175 
 HIS   0.007   0.001   HIS B 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 (10664)
  covalent geometry    : angle       0.67220 (14428)
  SS BOND              : bond        0.00202 (    2)
  SS BOND              : angle       0.65899 (    4)
  hydrogen bonds       : bond        0.05474 (  611)
  hydrogen bonds       : angle       4.65970 ( 1809)

*********************** 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
  167 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 144
  time to evaluate  : 0.372 
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: 0.7427 (tppt) cc_final: 0.6843 (tptt)
REVERT: A  326 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7922 (tt)
REVERT: B  157 ARG cc_start: 0.8382 (ptp-110) cc_final: 0.8147 (ptp-170)
REVERT: B  165 LYS cc_start: 0.8728 (mtmm) cc_final: 0.8328 (mttt)
REVERT: B  193 GLN cc_start: 0.7184 (OUTLIER) cc_final: 0.6868 (pm20)
REVERT: B  326 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8416 (tt)
REVERT: B  457 TRP cc_start: 0.8178 (t-100) cc_final: 0.7749 (t60)
REVERT: B  508 MET cc_start: 0.7534 (ptp) cc_final: 0.7317 (ptp)
REVERT: B  615 GLU cc_start: 0.8070 (tp30) cc_final: 0.7587 (tp30)
  outliers start: 23
  outliers final: 13
  residues processed: 165
  average time/residue: 0.1076
  time to fit residues: 24.6871
Evaluate side-chains
  156 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 140
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
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  300 VAL
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  328 CYS
Chi-restraints excluded: chain A residue  530 LEU
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  193 GLN
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  530 LEU
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 32 optimal weight:    0.0370
   chunk 59 optimal weight:    0.7980
   chunk 34 optimal weight:    0.5980
   chunk 65 optimal weight:    6.9990
   chunk 102 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9990
   chunk 69 optimal weight:    0.8980
   chunk 90 optimal weight:    0.8980
   chunk 76 optimal weight:    0.3980
   chunk 106 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.5458

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

Flipped N/Q/H residues before XYZ refinement:
** A  60 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**
** B  92 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 = 0.4684 r_free = 0.4684 target = 0.229961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.171574 restraints weight = 14701.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.171355 restraints weight = 12084.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.173154 restraints weight = 9777.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.173764 restraints weight = 7053.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.174086 restraints weight = 6524.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.4152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.3397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10666  Z= 0.133
  Angle     :  0.637  10.459  14432  Z= 0.327
  Chirality :  0.041   0.291   1554
  Planarity :  0.004   0.043   1670
  Dihedral  : 14.344 115.276   2488
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 26.67 %
    Favored  : 71.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.25), residues: 1120
  helix:  0.92 (0.18), residues: 840
  sheet:  None (None), residues: 0
  loop : -1.03 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 308 
 TYR   0.045   0.002   TYR A 512 
 PHE   0.015   0.001   PHE A 138 
 TRP   0.042   0.002   TRP B 175 
 HIS   0.007   0.001   HIS B 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (10664)
  covalent geometry    : angle       0.63738 (14428)
  SS BOND              : bond        0.00229 (    2)
  SS BOND              : angle       0.61049 (    4)
  hydrogen bonds       : bond        0.04760 (  611)
  hydrogen bonds       : angle       4.45347 ( 1809)

*********************** 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
  159 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 143
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  258 LYS cc_start: 0.7422 (tppt) cc_final: 0.6803 (tptt)
REVERT: A  326 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8087 (tt)
REVERT: A  482 LYS cc_start: 0.8814 (tmmt) cc_final: 0.8375 (tmmt)
REVERT: B  146 GLN cc_start: 0.8474 (pm20) cc_final: 0.8137 (pm20)
REVERT: B  457 TRP cc_start: 0.8183 (t-100) cc_final: 0.7690 (t60)
REVERT: B  508 MET cc_start: 0.7560 (ptp) cc_final: 0.7330 (ptp)
REVERT: B  615 GLU cc_start: 0.7980 (tp30) cc_final: 0.7470 (tp30)
  outliers start: 16
  outliers final: 12
  residues processed: 155
  average time/residue: 0.1084
  time to fit residues: 23.6810
Evaluate side-chains
  148 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 135
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
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  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  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 43 optimal weight:    2.9990
   chunk 59 optimal weight:    8.9990
   chunk 29 optimal weight:    0.8980
   chunk 91 optimal weight:    0.8980
   chunk 109 optimal weight:    8.9990
   chunk 4 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 113 optimal weight:    2.9990
   chunk 12 optimal weight:    0.4980
   chunk 45 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 313 HIS ** 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 = 0.4659 r_free = 0.4659 target = 0.226661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.171779 restraints weight = 14714.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.169590 restraints weight = 17524.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.172180 restraints weight = 14033.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.172322 restraints weight = 9345.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.172933 restraints weight = 8945.556|
|-----------------------------------------------------------------------------|
r_work (final): 0.4133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.3548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  10666  Z= 0.195
  Angle     :  0.713  16.800  14432  Z= 0.361
  Chirality :  0.043   0.215   1554
  Planarity :  0.005   0.048   1670
  Dihedral  : 14.662 113.709   2488
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 26.57 %
    Favored  : 71.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.42 (0.25), residues: 1120
  helix:  0.78 (0.18), residues: 848
  sheet:  None (None), residues: 0
  loop : -1.10 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 308 
 TYR   0.048   0.002   TYR A 512 
 PHE   0.028   0.002   PHE A  59 
 TRP   0.030   0.002   TRP B 175 
 HIS   0.007   0.001   HIS B 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 (10664)
  covalent geometry    : angle       0.71294 (14428)
  SS BOND              : bond        0.00140 (    2)
  SS BOND              : angle       0.66053 (    4)
  hydrogen bonds       : bond        0.05519 (  611)
  hydrogen bonds       : angle       4.64577 ( 1809)

********************** 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
  157 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 142
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  258 LYS cc_start: 0.7516 (tppt) cc_final: 0.6957 (tptt)
REVERT: A  326 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8161 (tt)
REVERT: A  508 MET cc_start: 0.7215 (ptp) cc_final: 0.6972 (ptp)
REVERT: B  326 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8394 (tt)
REVERT: B  457 TRP cc_start: 0.8120 (t-100) cc_final: 0.7705 (t60)
REVERT: B  615 GLU cc_start: 0.8036 (tp30) cc_final: 0.7588 (tp30)
  outliers start: 15
  outliers final: 11
  residues processed: 154
  average time/residue: 0.1048
  time to fit residues: 22.8969
Evaluate side-chains
  145 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 132
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 GLU
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  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  530 LEU
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:    6.9990
   chunk 28 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0020
   chunk 83 optimal weight:    0.7980
   chunk 4 optimal weight:    8.9990
   chunk 69 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 23 optimal weight:    0.6980
   chunk 63 optimal weight:   10.0000
   chunk 99 optimal weight:    3.9990
   chunk 106 optimal weight:    0.2980
   overall best weight:    0.9590

-------------------------------------------------------------------------------
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**
** 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 = 0.4679 r_free = 0.4679 target = 0.229056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.175704 restraints weight = 14738.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.173797 restraints weight = 17078.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.175264 restraints weight = 14347.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.179703 restraints weight = 10272.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.179321 restraints weight = 8064.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.4193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.3658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10666  Z= 0.155
  Angle     :  0.680  14.166  14432  Z= 0.346
  Chirality :  0.042   0.185   1554
  Planarity :  0.004   0.043   1670
  Dihedral  : 14.350 112.083   2488
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 26.77 %
    Favored  : 72.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.25), residues: 1120
  helix:  0.85 (0.18), residues: 842
  sheet:  None (None), residues: 0
  loop : -1.09 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG A 157 
 TYR   0.054   0.002   TYR B 512 
 PHE   0.027   0.001   PHE B 511 
 TRP   0.028   0.002   TRP B 175 
 HIS   0.007   0.001   HIS B 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (10664)
  covalent geometry    : angle       0.68048 (14428)
  SS BOND              : bond        0.00168 (    2)
  SS BOND              : angle       0.63311 (    4)
  hydrogen bonds       : bond        0.05115 (  611)
  hydrogen bonds       : angle       4.52108 ( 1809)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1694.89 seconds
wall clock time: 30 minutes 8.82 seconds (1808.82 seconds total)