Starting phenix.real_space_refine
on Mon Jul 28 19:30:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kcl_22812/07_2025/7kcl_22812.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kcl_22812/07_2025/7kcl_22812.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kcl_22812/07_2025/7kcl_22812.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kcl_22812/07_2025/7kcl_22812.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kcl_22812/07_2025/7kcl_22812.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kcl_22812/07_2025/7kcl_22812.cif"
  }
  resolution = 3.14
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 522 atoms to isotropic.
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: 7
    Type Number    sf(0)   Gaussians
     K       2      8.98       5
     P       6      5.49       5
     Mg      2      5.21       5
     S      44      5.16       5
     C    6358      2.51       5
     N    1742      2.21       5
     O    1903      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 63 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10057
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4890
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 612, 4890
          Classifications: {'peptide': 612}
          Link IDs: {'PTRANS': 18, 'TRANS': 593}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "B"
      Number of atoms: 4915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 614, 4915
          Classifications: {'peptide': 614}
          Link IDs: {'PTRANS': 18, 'TRANS': 595}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "C"
      Number of atoms: 186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 186
          Classifications: {'peptide': 23}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 20}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {'  K': 1, ' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {'  K': 1, ' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 6.55, per 1000 atoms: 0.65
  Number of scatterers: 10057
  At special positions: 0
  Unit cell: (92.796, 91.982, 132.682, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     K       2     19.00
     S      44     16.00
     P       6     15.00
     Mg      2     11.99
     O    1903      8.00
     N    1742      7.00
     C    6358      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.37
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2384

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 12 sheets defined
      47.3% alpha, 17.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 93 through 103
    Processing helix  chain 'A' and resid 110 through 135
      removed outlier: 4.461A  pdb=" N   ARG A 114 " --> pdb=" O   GLU A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 173
    Processing helix  chain 'A' and resid 178 through 186
      removed outlier: 3.749A  pdb=" N   ALA A 182 " --> pdb=" O   SER A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 210
    Processing helix  chain 'A' and resid 261 through 265
      removed outlier: 3.812A  pdb=" N   PHE A 264 " --> pdb=" O   CYS A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 278
    Processing helix  chain 'A' and resid 307 through 320
    Processing helix  chain 'A' and resid 382 through 386
      removed outlier: 4.255A  pdb=" N   PHE A 386 " --> pdb=" O   TRP A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 433
    Processing helix  chain 'A' and resid 433 through 455
      removed outlier: 6.299A  pdb=" N   LEU A 446 " --> pdb=" O   GLU A 442 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   PHE A 447 " --> pdb=" O   ASP A 443 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   MET A 448 " --> pdb=" O   TYR A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 466
    Processing helix  chain 'A' and resid 482 through 489
      removed outlier: 3.550A  pdb=" N   ARG A 489 " --> pdb=" O   GLU A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 510
    Processing helix  chain 'A' and resid 511 through 517
    Processing helix  chain 'A' and resid 518 through 520
      No H-bonds generated for 'chain 'A' and resid 518 through 520'
    Processing helix  chain 'A' and resid 531 through 540
    Processing helix  chain 'A' and resid 550 through 557
    Processing helix  chain 'A' and resid 575 through 590
      removed outlier: 3.509A  pdb=" N   TRP A 585 " --> pdb=" O   GLU A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 614 through 628
      removed outlier: 3.638A  pdb=" N   HIS A 620 " --> pdb=" O   GLY A 616 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ARG A 623 " --> pdb=" O   ARG A 619 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 653
    Processing helix  chain 'A' and resid 653 through 659
      removed outlier: 3.703A  pdb=" N   ALA A 659 " --> pdb=" O   ASN A 655 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 661 through 680
    Processing helix  chain 'A' and resid 686 through 701
      removed outlier: 3.794A  pdb=" N   VAL A 690 " --> pdb=" O   PRO A 686 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   GLY A 691 " --> pdb=" O   ARG A 687 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   ARG A 692 " --> pdb=" O   ALA A 688 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   LYS A 699 " --> pdb=" O   GLU A 695 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   LEU A 701 " --> pdb=" O   LEU A 697 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 104
    Processing helix  chain 'B' and resid 110 through 131
      removed outlier: 4.278A  pdb=" N   ARG B 114 " --> pdb=" O   GLU B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 172
    Processing helix  chain 'B' and resid 178 through 186
      removed outlier: 3.902A  pdb=" N   ALA B 182 " --> pdb=" O   SER B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 210
    Processing helix  chain 'B' and resid 261 through 265
    Processing helix  chain 'B' and resid 266 through 278
    Processing helix  chain 'B' and resid 302 through 306
      removed outlier: 3.533A  pdb=" N   VAL B 306 " --> pdb=" O   PRO B 303 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 320
    Processing helix  chain 'B' and resid 351 through 356
      removed outlier: 3.600A  pdb=" N   VAL B 355 " --> pdb=" O   SER B 351 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   SER B 356 " --> pdb=" O   MET B 352 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 351 through 356'
    Processing helix  chain 'B' and resid 381 through 387
      removed outlier: 4.399A  pdb=" N   PHE B 386 " --> pdb=" O   TRP B 383 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ILE B 387 " --> pdb=" O   LEU B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 408 through 433
    Processing helix  chain 'B' and resid 433 through 455
      removed outlier: 6.812A  pdb=" N   LEU B 446 " --> pdb=" O   GLU B 442 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   PHE B 447 " --> pdb=" O   ASP B 443 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   MET B 448 " --> pdb=" O   TYR B 444 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 457 through 466
    Processing helix  chain 'B' and resid 482 through 488
    Processing helix  chain 'B' and resid 504 through 510
    Processing helix  chain 'B' and resid 511 through 518
    Processing helix  chain 'B' and resid 531 through 540
    Processing helix  chain 'B' and resid 550 through 557
    Processing helix  chain 'B' and resid 575 through 590
    Processing helix  chain 'B' and resid 614 through 625
      removed outlier: 3.504A  pdb=" N   HIS B 620 " --> pdb=" O   GLY B 616 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ARG B 623 " --> pdb=" O   ARG B 619 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 631 through 639
      removed outlier: 3.964A  pdb=" N   LEU B 637 " --> pdb=" O   GLU B 633 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 648 through 658
      removed outlier: 3.886A  pdb=" N   ASN B 655 " --> pdb=" O   ILE B 651 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   GLN B 656 " --> pdb=" O   LYS B 652 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 661 through 681
      removed outlier: 3.512A  pdb=" N   GLN B 666 " --> pdb=" O   PRO B 662 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LEU B 667 " --> pdb=" O   GLY B 663 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 688 through 701
      removed outlier: 4.586A  pdb=" N   ARG B 692 " --> pdb=" O   ALA B 688 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   LYS B 699 " --> pdb=" O   GLU B 695 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 136 through 140
      removed outlier: 4.058A  pdb=" N   VAL C 140 " --> pdb=" O   LYS C 137 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 145 through 157
      removed outlier: 3.755A  pdb=" N   GLN C 149 " --> pdb=" O   ASN C 145 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   TYR C 150 " --> pdb=" O   PHE C 146 " (cutoff:3.500A)
      Proline residue:  C 155  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81
    Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81
      removed outlier: 3.899A  pdb=" N   ARG B 214 " --> pdb=" O   HIS B 256 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   ILE B 143 " --> pdb=" O   TYR B 286 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92
      removed outlier: 7.219A  pdb=" N   GLN A  91 " --> pdb=" O   ILE B 175 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 291
      removed outlier: 6.331A  pdb=" N   ILE A 143 " --> pdb=" O   TYR A 286 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ARG A 214 " --> pdb=" O   HIS A 256 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 291
      removed outlier: 6.331A  pdb=" N   ILE A 143 " --> pdb=" O   TYR A 286 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ARG A 214 " --> pdb=" O   HIS A 256 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 174 through 175
    Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 333
      removed outlier: 6.448A  pdb=" N   VAL A 345 " --> pdb=" O   ARG A 326 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   THR A 328 " --> pdb=" O   PHE A 343 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   PHE A 343 " --> pdb=" O   THR A 328 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   HIS A 330 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   SER A 341 " --> pdb=" O   HIS A 330 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   LYS A 332 " --> pdb=" O   ILE A 339 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   ILE A 339 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 471 through 472
      removed outlier: 3.941A  pdb=" N   GLU A 471 " --> pdb=" O   PHE A 526 " (cutoff:3.500A)
      removed outlier: 8.877A  pdb=" N   LEU A 525 " --> pdb=" O   ASN A 496 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   TYR A 498 " --> pdb=" O   LEU A 525 " (cutoff:3.500A)
      removed outlier: 7.873A  pdb=" N   CYS A 527 " --> pdb=" O   TYR A 498 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   LEU A 500 " --> pdb=" O   CYS A 527 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   TYR A 499 " --> pdb=" O   ILE A 548 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 596 through 599
    Processing sheet with id=AB1, first strand: chain 'B' and resid 325 through 333
    Processing sheet with id=AB2, first strand: chain 'B' and resid 524 through 527
      removed outlier: 8.769A  pdb=" N   LEU B 525 " --> pdb=" O   ASN B 496 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   TYR B 498 " --> pdb=" O   LEU B 525 " (cutoff:3.500A)
      removed outlier: 7.919A  pdb=" N   CYS B 527 " --> pdb=" O   TYR B 498 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   LEU B 500 " --> pdb=" O   CYS B 527 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   TYR B 499 " --> pdb=" O   ILE B 548 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 596 through 599
      removed outlier: 6.385A  pdb=" N   ASN B 596 " --> pdb=" O   LEU B 642 " (cutoff:3.500A)
      removed outlier: 7.980A  pdb=" N   ILE B 644 " --> pdb=" O   ASN B 596 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   LYS B 598 " --> pdb=" O   ILE B 644 " (cutoff:3.500A)

    503 hydrogen bonds defined for protein.
    1389 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: 3.67

  Time building geometry restraints manager: 2.85 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3313
        1.34 -     1.46: 2175
        1.46 -     1.58: 4658
        1.58 -     1.70: 8
        1.70 -     1.81: 80
  Bond restraints: 10234
  Sorted by residual:
  bond pdb=" O3A ANP A 801 "
       pdb=" PB  ANP A 801 "
    ideal  model  delta    sigma   weight residual
    1.700  1.556  0.144 2.00e-02 2.50e+03 5.18e+01
  bond pdb=" O3A ANP B 801 "
       pdb=" PB  ANP B 801 "
    ideal  model  delta    sigma   weight residual
    1.700  1.556  0.144 2.00e-02 2.50e+03 5.17e+01
  bond pdb=" N3B ANP B 801 "
       pdb=" PG  ANP B 801 "
    ideal  model  delta    sigma   weight residual
    1.795  1.691  0.104 2.00e-02 2.50e+03 2.71e+01
  bond pdb=" N3B ANP A 801 "
       pdb=" PG  ANP A 801 "
    ideal  model  delta    sigma   weight residual
    1.795  1.692  0.103 2.00e-02 2.50e+03 2.66e+01
  bond pdb=" O5' ANP A 801 "
       pdb=" PA  ANP A 801 "
    ideal  model  delta    sigma   weight residual
    1.655  1.577  0.078 2.00e-02 2.50e+03 1.52e+01
  ... (remaining 10229 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.26: 13746
        3.26 -     6.52: 55
        6.52 -     9.78: 8
        9.78 -    13.04: 2
       13.04 -    16.30: 2
  Bond angle restraints: 13813
  Sorted by residual:
  angle pdb=" PB  ANP A 801 "
        pdb=" N3B ANP A 801 "
        pdb=" PG  ANP A 801 "
      ideal   model   delta    sigma   weight residual
     126.95  110.65   16.30 3.00e+00 1.11e-01 2.95e+01
  angle pdb=" PB  ANP B 801 "
        pdb=" N3B ANP B 801 "
        pdb=" PG  ANP B 801 "
      ideal   model   delta    sigma   weight residual
     126.95  110.80   16.15 3.00e+00 1.11e-01 2.90e+01
  angle pdb=" O1B ANP B 801 "
        pdb=" PB  ANP B 801 "
        pdb=" O2B ANP B 801 "
      ideal   model   delta    sigma   weight residual
     120.08  108.92   11.16 3.00e+00 1.11e-01 1.38e+01
  angle pdb=" O1B ANP A 801 "
        pdb=" PB  ANP A 801 "
        pdb=" O2B ANP A 801 "
      ideal   model   delta    sigma   weight residual
     120.08  109.00   11.08 3.00e+00 1.11e-01 1.36e+01
  angle pdb=" N3B ANP A 801 "
        pdb=" PG  ANP A 801 "
        pdb=" O2G ANP A 801 "
      ideal   model   delta    sigma   weight residual
     101.05  109.79   -8.74 3.00e+00 1.11e-01 8.48e+00
  ... (remaining 13808 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 5587
       17.96 -    35.92: 547
       35.92 -    53.87: 114
       53.87 -    71.83: 31
       71.83 -    89.79: 17
  Dihedral angle restraints: 6296
    sinusoidal: 2627
      harmonic: 3669
  Sorted by residual:
  dihedral pdb=" CB  GLU A 216 "
           pdb=" CG  GLU A 216 "
           pdb=" CD  GLU A 216 "
           pdb=" OE1 GLU A 216 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.79  -89.79     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CG  ARG A 415 "
           pdb=" CD  ARG A 415 "
           pdb=" NE  ARG A 415 "
           pdb=" CZ  ARG A 415 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.20  -44.20     2      1.50e+01 4.44e-03 1.04e+01
  dihedral pdb=" CB  GLU A 578 "
           pdb=" CG  GLU A 578 "
           pdb=" CD  GLU A 578 "
           pdb=" OE1 GLU A 578 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.66   87.66     1      3.00e+01 1.11e-03 1.02e+01
  ... (remaining 6293 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1304
       0.055 -    0.109: 227
       0.109 -    0.164: 23
       0.164 -    0.219: 1
       0.219 -    0.274: 2
  Chirality restraints: 1557
  Sorted by residual:
  chirality pdb=" C3' ANP B 801 "
            pdb=" C2' ANP B 801 "
            pdb=" C4' ANP B 801 "
            pdb=" O3' ANP B 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.63    0.27 2.00e-01 2.50e+01 1.87e+00
  chirality pdb=" C3' ANP A 801 "
            pdb=" C2' ANP A 801 "
            pdb=" C4' ANP A 801 "
            pdb=" O3' ANP A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.63    0.27 2.00e-01 2.50e+01 1.85e+00
  chirality pdb=" CB  ILE B 156 "
            pdb=" CA  ILE B 156 "
            pdb=" CG1 ILE B 156 "
            pdb=" CG2 ILE B 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.21 2.00e-01 2.50e+01 1.06e+00
  ... (remaining 1554 not shown)

  Planarity restraints: 1752
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 639 "    0.035 5.00e-02 4.00e+02   5.32e-02 4.53e+00
        pdb=" N   PRO B 640 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO B 640 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 640 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 123 "   -0.007 2.00e-02 2.50e+03   1.35e-02 1.82e+00
        pdb=" C   ALA A 123 "    0.023 2.00e-02 2.50e+03
        pdb=" O   ALA A 123 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   LEU A 124 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 121 "    0.006 2.00e-02 2.50e+03   1.28e-02 1.63e+00
        pdb=" C   SER A 121 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   SER A 121 "    0.008 2.00e-02 2.50e+03
        pdb=" N   ASP A 122 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1749 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.63: 158
        2.63 -     3.26: 10413
        3.26 -     3.89: 20514
        3.89 -     4.51: 28111
        4.51 -     5.14: 43557
  Nonbonded interactions: 102753
  Sorted by model distance:
  nonbonded pdb=" O3G ANP B 801 "
            pdb="MG    MG B 802 "
     model   vdw
     2.009 2.170
  nonbonded pdb=" O3G ANP A 801 "
            pdb="MG    MG A 802 "
     model   vdw
     2.011 2.170
  nonbonded pdb=" OD1 ASN B 119 "
            pdb="MG    MG B 802 "
     model   vdw
     2.029 2.170
  nonbonded pdb=" OD1 ASN A 119 "
            pdb="MG    MG A 802 "
     model   vdw
     2.061 2.170
  nonbonded pdb=" O1B ANP B 801 "
            pdb="MG    MG B 802 "
     model   vdw
     2.089 2.170
  ... (remaining 102748 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 70 through 355 or resid 361 through 626 or resid 631 throu \ 
gh 704 or resid 801 through 803))
  selection = (chain 'B' and (resid 70 through 355 or resid 361 through 625 or resid 631 or re \ 
sid 636 through 704 or resid 801 through 803))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.080
  Set scattering table:                    0.080
  Process input model:                     26.960
  Find NCS groups from input model:        0.530
  Set up NCS constraints:                  0.050
  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:3.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
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      :  0.004   0.144  10234  Z= 0.194
  Angle     :  0.621  16.305  13813  Z= 0.306
  Chirality :  0.042   0.274   1557
  Planarity :  0.003   0.053   1752
  Dihedral  : 15.769  89.789   3912
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.24), residues: 1231
  helix:  0.53 (0.23), residues: 531
  sheet:  0.60 (0.41), residues: 175
  loop : -0.82 (0.27), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 231 
 HIS   0.004   0.001   HIS A 311 
 PHE   0.019   0.001   PHE C 146 
 TYR   0.010   0.001   TYR A 317 
 ARG   0.006   0.000   ARG A 692 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12679 (  470)
  hydrogen bonds       : angle       6.11222 ( 1389)
  covalent geometry    : bond        0.00394 (10234)
  covalent geometry    : angle       0.62119 (13813)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 1.172 
Fit side-chains
REVERT: A  643 GLU cc_start: 0.7549 (mp0) cc_final: 0.7133 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.2289
  time to fit residues: 48.1187
Evaluate side-chains
  128 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    4.9990
   chunk 93 optimal weight:    2.9990
   chunk 52 optimal weight:    5.9990
   chunk 32 optimal weight:    0.7980
   chunk 63 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 97 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 112 optimal weight:    6.9990
   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 230 GLN
A 506 HIS
B  72 HIS
B 288 ASN
B 406 GLN
B 510 HIS
B 648 HIS
B 655 ASN
** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.133930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.104870 restraints weight = 14126.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 2.55
r_work: 0.3140 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.1301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  10234  Z= 0.209
  Angle     :  0.575   8.118  13813  Z= 0.296
  Chirality :  0.044   0.199   1557
  Planarity :  0.004   0.042   1752
  Dihedral  :  5.725  56.074   1427
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 11.00 %
    Favored  : 88.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.25), residues: 1231
  helix:  1.15 (0.23), residues: 518
  sheet:  0.44 (0.39), residues: 180
  loop : -0.75 (0.28), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 231 
 HIS   0.004   0.001   HIS A 606 
 PHE   0.011   0.002   PHE B 264 
 TYR   0.020   0.002   TYR B 218 
 ARG   0.005   0.001   ARG A 402 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03521 (  470)
  hydrogen bonds       : angle       4.83378 ( 1389)
  covalent geometry    : bond        0.00487 (10234)
  covalent geometry    : angle       0.57528 (13813)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 137
  time to evaluate  : 1.094 
Fit side-chains
REVERT: A  317 TYR cc_start: 0.8133 (t80) cc_final: 0.7900 (t80)
  outliers start: 6
  outliers final: 4
  residues processed: 140
  average time/residue: 0.2304
  time to fit residues: 46.0245
Evaluate side-chains
  130 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 126
  time to evaluate  : 1.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain B residue  108 GLU
Chi-restraints excluded: chain B residue  379 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 76 optimal weight:    6.9990
   chunk 72 optimal weight:    5.9990
   chunk 50 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 65 optimal weight:    0.7980
   chunk 82 optimal weight:    0.6980
   chunk 81 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 101 optimal weight:    7.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 200 GLN
A 279 ASN
B 146 GLN
B 504 ASN
B 671 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.136175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.108075 restraints weight = 14146.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 2.43
r_work: 0.3186 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.1387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10234  Z= 0.127
  Angle     :  0.504   7.461  13813  Z= 0.261
  Chirality :  0.041   0.173   1557
  Planarity :  0.003   0.031   1752
  Dihedral  :  5.377  53.200   1427
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  : 13.57 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.25), residues: 1231
  helix:  1.13 (0.23), residues: 526
  sheet:  0.41 (0.38), residues: 185
  loop : -0.75 (0.28), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 585 
 HIS   0.003   0.001   HIS A 538 
 PHE   0.008   0.001   PHE C 146 
 TYR   0.011   0.001   TYR A 437 
 ARG   0.003   0.000   ARG A 692 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03113 (  470)
  hydrogen bonds       : angle       4.59085 ( 1389)
  covalent geometry    : bond        0.00292 (10234)
  covalent geometry    : angle       0.50419 (13813)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 138
  time to evaluate  : 1.111 
Fit side-chains
   revert: symmetry clash
REVERT: A  317 TYR cc_start: 0.8134 (t80) cc_final: 0.7833 (t80)
REVERT: A  614 GLU cc_start: 0.7256 (pt0) cc_final: 0.7053 (pt0)
REVERT: B   75 ILE cc_start: 0.6922 (mm) cc_final: 0.6704 (mm)
REVERT: B  141 MET cc_start: 0.8723 (mmm) cc_final: 0.8519 (mtp)
REVERT: B  156 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8518 (mt)
  outliers start: 8
  outliers final: 6
  residues processed: 142
  average time/residue: 0.2428
  time to fit residues: 48.8479
Evaluate side-chains
  138 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 131
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain B residue  108 GLU
Chi-restraints excluded: chain B residue  113 ILE
Chi-restraints excluded: chain B residue  156 ILE
Chi-restraints excluded: chain B residue  379 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 60 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
B 256 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.132525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.104176 restraints weight = 14284.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 2.46
r_work: 0.3138 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.1758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10234  Z= 0.177
  Angle     :  0.540   6.958  13813  Z= 0.279
  Chirality :  0.042   0.178   1557
  Planarity :  0.003   0.044   1752
  Dihedral  :  5.512  54.642   1427
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 14.57 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.24), residues: 1231
  helix:  1.08 (0.23), residues: 524
  sheet:  0.25 (0.37), residues: 187
  loop : -0.80 (0.28), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 231 
 HIS   0.004   0.001   HIS A 538 
 PHE   0.009   0.001   PHE B 264 
 TYR   0.013   0.001   TYR A 206 
 ARG   0.004   0.000   ARG A 495 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03263 (  470)
  hydrogen bonds       : angle       4.65178 ( 1389)
  covalent geometry    : bond        0.00412 (10234)
  covalent geometry    : angle       0.54035 (13813)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 1.184 
Fit side-chains
   revert: symmetry clash
REVERT: A  620 HIS cc_start: 0.8103 (t-170) cc_final: 0.7638 (t-170)
REVERT: B  301 MET cc_start: 0.7531 (pmm) cc_final: 0.7237 (ptt)
REVERT: B  637 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8449 (pp)
REVERT: B  693 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8382 (tt)
  outliers start: 17
  outliers final: 10
  residues processed: 142
  average time/residue: 0.2403
  time to fit residues: 48.0141
Evaluate side-chains
  139 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 127
  time to evaluate  : 1.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain B residue  108 GLU
Chi-restraints excluded: chain B residue  113 ILE
Chi-restraints excluded: chain B residue  156 ILE
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  637 LEU
Chi-restraints excluded: chain B residue  693 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 68 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   chunk 83 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0980
   chunk 29 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    1.0186

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

Flipped N/Q/H residues before XYZ refinement:
B 230 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.133671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.105596 restraints weight = 14108.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 2.44
r_work: 0.3155 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.1821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10234  Z= 0.142
  Angle     :  0.515   7.070  13813  Z= 0.267
  Chirality :  0.041   0.220   1557
  Planarity :  0.003   0.034   1752
  Dihedral  :  5.367  50.933   1427
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 15.77 %
    Favored  : 82.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.24), residues: 1231
  helix:  1.10 (0.23), residues: 531
  sheet:  0.25 (0.37), residues: 185
  loop : -0.85 (0.28), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 231 
 HIS   0.004   0.001   HIS A 538 
 PHE   0.009   0.001   PHE A 112 
 TYR   0.012   0.001   TYR B 437 
 ARG   0.004   0.000   ARG A 495 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03123 (  470)
  hydrogen bonds       : angle       4.56262 ( 1389)
  covalent geometry    : bond        0.00330 (10234)
  covalent geometry    : angle       0.51467 (13813)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 141
  time to evaluate  : 1.215 
Fit side-chains
   revert: symmetry clash
REVERT: A  317 TYR cc_start: 0.7953 (t80) cc_final: 0.7744 (t80)
REVERT: A  620 HIS cc_start: 0.8116 (t-170) cc_final: 0.7609 (t-170)
REVERT: B  693 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8394 (tt)
  outliers start: 24
  outliers final: 14
  residues processed: 158
  average time/residue: 0.2288
  time to fit residues: 50.7972
Evaluate side-chains
  144 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 129
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain B residue  108 GLU
Chi-restraints excluded: chain B residue  113 ILE
Chi-restraints excluded: chain B residue  156 ILE
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  494 THR
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  693 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   chunk 30 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 73 optimal weight:    0.0980
   chunk 38 optimal weight:    1.9990
   chunk 120 optimal weight:    0.0670
   chunk 61 optimal weight:    0.0980
   chunk 64 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.3718

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

Flipped N/Q/H residues before XYZ refinement:
B 230 GLN
** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.136736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.109454 restraints weight = 14099.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 2.35
r_work: 0.3209 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.1845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  10234  Z= 0.097
  Angle     :  0.501   7.636  13813  Z= 0.256
  Chirality :  0.040   0.200   1557
  Planarity :  0.003   0.029   1752
  Dihedral  :  5.055  43.806   1427
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 16.41 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.24), residues: 1231
  helix:  1.19 (0.23), residues: 530
  sheet:  0.35 (0.38), residues: 185
  loop : -0.83 (0.28), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 231 
 HIS   0.004   0.001   HIS A 538 
 PHE   0.008   0.001   PHE A 112 
 TYR   0.011   0.001   TYR A 437 
 ARG   0.004   0.000   ARG A 495 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02901 (  470)
  hydrogen bonds       : angle       4.37475 ( 1389)
  covalent geometry    : bond        0.00215 (10234)
  covalent geometry    : angle       0.50101 (13813)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 139
  time to evaluate  : 1.171 
Fit side-chains
   revert: symmetry clash
REVERT: A   99 ASP cc_start: 0.8338 (t0) cc_final: 0.8095 (t0)
REVERT: A  312 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7904 (mt-10)
REVERT: A  317 TYR cc_start: 0.7984 (t80) cc_final: 0.7774 (t80)
REVERT: B  156 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8435 (mt)
REVERT: B  340 ARG cc_start: 0.8665 (mmt-90) cc_final: 0.8352 (mmt-90)
REVERT: B  352 MET cc_start: 0.8031 (tpp) cc_final: 0.7703 (tpt)
REVERT: B  585 TRP cc_start: 0.8180 (t60) cc_final: 0.7932 (t60)
REVERT: B  693 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8376 (tt)
  outliers start: 12
  outliers final: 5
  residues processed: 148
  average time/residue: 0.2266
  time to fit residues: 47.3247
Evaluate side-chains
  131 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 124
  time to evaluate  : 1.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain B residue  108 GLU
Chi-restraints excluded: chain B residue  156 ILE
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  494 THR
Chi-restraints excluded: chain B residue  693 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 47 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 116 optimal weight:    7.9990
   chunk 34 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 86 optimal weight:    6.9990
   chunk 54 optimal weight:    0.0010
   chunk 48 optimal weight:    7.9990
   chunk 79 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    1.3388

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

Flipped N/Q/H residues before XYZ refinement:
** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 GLN
** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.133010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.104717 restraints weight = 14321.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 2.47
r_work: 0.3140 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.2025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10234  Z= 0.172
  Angle     :  0.552   8.215  13813  Z= 0.282
  Chirality :  0.042   0.228   1557
  Planarity :  0.003   0.052   1752
  Dihedral  :  5.387  51.029   1427
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 16.59 %
    Favored  : 81.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.24), residues: 1231
  helix:  1.19 (0.23), residues: 525
  sheet:  0.24 (0.37), residues: 185
  loop : -0.81 (0.28), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 231 
 HIS   0.011   0.001   HIS A 620 
 PHE   0.016   0.001   PHE A 112 
 TYR   0.013   0.001   TYR B 437 
 ARG   0.004   0.000   ARG A 495 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03183 (  470)
  hydrogen bonds       : angle       4.56478 ( 1389)
  covalent geometry    : bond        0.00406 (10234)
  covalent geometry    : angle       0.55209 (13813)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 134
  time to evaluate  : 1.175 
Fit side-chains
   revert: symmetry clash
REVERT: A   99 ASP cc_start: 0.8359 (t0) cc_final: 0.8068 (t0)
REVERT: A  295 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8350 (tt)
REVERT: B  340 ARG cc_start: 0.8678 (mmt-90) cc_final: 0.8243 (mmt-90)
REVERT: B  693 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8437 (tt)
  outliers start: 21
  outliers final: 15
  residues processed: 149
  average time/residue: 0.2387
  time to fit residues: 50.0661
Evaluate side-chains
  144 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 1.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  517 MET
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain B residue  108 GLU
Chi-restraints excluded: chain B residue  113 ILE
Chi-restraints excluded: chain B residue  156 ILE
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  230 GLN
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  494 THR
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  693 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 48 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 29 optimal weight:    0.5980
   chunk 45 optimal weight:    4.9990
   chunk 100 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9990
   chunk 119 optimal weight:    2.9990
   chunk 118 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 114 optimal weight:    5.9990
   overall best weight:    1.5188

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

Flipped N/Q/H residues before XYZ refinement:
** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.132332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.104441 restraints weight = 14207.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.25
r_work: 0.3155 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2988 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8527
moved from start:          0.2177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10234  Z= 0.188
  Angle     :  0.580  10.219  13813  Z= 0.294
  Chirality :  0.043   0.235   1557
  Planarity :  0.003   0.046   1752
  Dihedral  :  5.481  51.879   1427
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 16.87 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.24), residues: 1231
  helix:  1.13 (0.23), residues: 525
  sheet:  0.16 (0.37), residues: 185
  loop : -0.79 (0.28), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 231 
 HIS   0.013   0.001   HIS A 620 
 PHE   0.011   0.001   PHE A 112 
 TYR   0.013   0.001   TYR A 317 
 ARG   0.004   0.000   ARG A 495 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03246 (  470)
  hydrogen bonds       : angle       4.62109 ( 1389)
  covalent geometry    : bond        0.00444 (10234)
  covalent geometry    : angle       0.58019 (13813)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 129
  time to evaluate  : 1.175 
Fit side-chains
   revert: symmetry clash
REVERT: A   99 ASP cc_start: 0.8597 (t0) cc_final: 0.8256 (t0)
REVERT: A  295 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8398 (tt)
REVERT: A  312 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8190 (mt-10)
REVERT: B  192 GLU cc_start: 0.6590 (tp30) cc_final: 0.6345 (tp30)
REVERT: B  585 TRP cc_start: 0.8490 (t60) cc_final: 0.8284 (t60)
REVERT: B  636 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7800 (pp30)
REVERT: B  693 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8490 (tt)
  outliers start: 23
  outliers final: 17
  residues processed: 145
  average time/residue: 0.2319
  time to fit residues: 47.9038
Evaluate side-chains
  145 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 125
  time to evaluate  : 1.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  517 MET
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  108 GLU
Chi-restraints excluded: chain B residue  113 ILE
Chi-restraints excluded: chain B residue  156 ILE
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  230 GLN
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  494 THR
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  636 GLN
Chi-restraints excluded: chain B residue  693 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 79 optimal weight:    4.9990
   chunk 108 optimal weight:    0.1980
   chunk 74 optimal weight:    0.9990
   chunk 1 optimal weight:    9.9990
   chunk 73 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 111 optimal weight:    7.9990
   chunk 63 optimal weight:    3.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
B 230 GLN
B 655 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.133006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.105526 restraints weight = 14178.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 2.35
r_work: 0.3134 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.2226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10234  Z= 0.160
  Angle     :  0.577  10.854  13813  Z= 0.290
  Chirality :  0.042   0.230   1557
  Planarity :  0.003   0.043   1752
  Dihedral  :  5.423  50.237   1427
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 17.51 %
    Favored  : 80.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.24), residues: 1231
  helix:  1.13 (0.23), residues: 521
  sheet:  0.16 (0.37), residues: 185
  loop : -0.73 (0.28), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 231 
 HIS   0.011   0.001   HIS A 620 
 PHE   0.011   0.001   PHE A 112 
 TYR   0.012   0.001   TYR B 437 
 ARG   0.003   0.000   ARG A 495 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03205 (  470)
  hydrogen bonds       : angle       4.60724 ( 1389)
  covalent geometry    : bond        0.00376 (10234)
  covalent geometry    : angle       0.57688 (13813)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 1.135 
Fit side-chains
   revert: symmetry clash
REVERT: A   99 ASP cc_start: 0.8342 (t0) cc_final: 0.8043 (t0)
REVERT: A  290 ARG cc_start: 0.7978 (ptm160) cc_final: 0.7694 (ptm-80)
REVERT: A  295 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8393 (tt)
REVERT: A  312 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7918 (mt-10)
REVERT: A  643 GLU cc_start: 0.7868 (mp0) cc_final: 0.7621 (mp0)
REVERT: B  141 MET cc_start: 0.8763 (mmm) cc_final: 0.8555 (mtp)
REVERT: B  340 ARG cc_start: 0.8678 (mmt-90) cc_final: 0.8250 (mmt-90)
REVERT: B  636 GLN cc_start: 0.8131 (pt0) cc_final: 0.7881 (pp30)
REVERT: B  655 ASN cc_start: 0.7507 (t0) cc_final: 0.7197 (t0)
REVERT: B  693 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8410 (tt)
  outliers start: 20
  outliers final: 18
  residues processed: 148
  average time/residue: 0.2381
  time to fit residues: 49.3136
Evaluate side-chains
  145 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 125
  time to evaluate  : 1.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  517 MET
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  108 GLU
Chi-restraints excluded: chain B residue  113 ILE
Chi-restraints excluded: chain B residue  156 ILE
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  230 GLN
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  494 THR
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  693 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 111 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 56 optimal weight:    5.9990
   chunk 115 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9980
   chunk 107 optimal weight:    3.9990
   chunk 117 optimal weight:    3.9990
   chunk 83 optimal weight:    3.9990
   chunk 82 optimal weight:    0.6980
   chunk 119 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 230 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.134217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.106568 restraints weight = 14190.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 2.39
r_work: 0.3159 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.2245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10234  Z= 0.135
  Angle     :  0.573  10.804  13813  Z= 0.286
  Chirality :  0.041   0.219   1557
  Planarity :  0.003   0.042   1752
  Dihedral  :  5.307  47.959   1427
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 17.05 %
    Favored  : 81.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.24), residues: 1231
  helix:  1.18 (0.23), residues: 520
  sheet:  0.22 (0.37), residues: 185
  loop : -0.70 (0.28), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 585 
 HIS   0.010   0.001   HIS A 620 
 PHE   0.012   0.001   PHE A 112 
 TYR   0.012   0.001   TYR B 437 
 ARG   0.003   0.000   ARG A 495 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03128 (  470)
  hydrogen bonds       : angle       4.54566 ( 1389)
  covalent geometry    : bond        0.00313 (10234)
  covalent geometry    : angle       0.57274 (13813)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 130
  time to evaluate  : 1.076 
Fit side-chains
   revert: symmetry clash
REVERT: A   99 ASP cc_start: 0.8348 (t0) cc_final: 0.8072 (t0)
REVERT: A  290 ARG cc_start: 0.7966 (ptm160) cc_final: 0.7677 (ptm-80)
REVERT: A  295 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8424 (tt)
REVERT: A  643 GLU cc_start: 0.7866 (mp0) cc_final: 0.7573 (mp0)
REVERT: B  340 ARG cc_start: 0.8679 (mmt-90) cc_final: 0.8271 (mmt-90)
REVERT: B  354 ASP cc_start: 0.6182 (m-30) cc_final: 0.5970 (m-30)
REVERT: B  636 GLN cc_start: 0.8084 (pt0) cc_final: 0.7880 (pp30)
REVERT: B  693 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8434 (tt)
  outliers start: 20
  outliers final: 18
  residues processed: 145
  average time/residue: 0.2194
  time to fit residues: 44.9956
Evaluate side-chains
  148 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 128
  time to evaluate  : 1.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  517 MET
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  108 GLU
Chi-restraints excluded: chain B residue  113 ILE
Chi-restraints excluded: chain B residue  156 ILE
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  230 GLN
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  446 LEU
Chi-restraints excluded: chain B residue  494 THR
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain B residue  693 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 79 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 83 optimal weight:    2.9990
   chunk 64 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 123 optimal weight:   10.0000
   chunk 106 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
B 230 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.134020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.106683 restraints weight = 14173.045|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 2.34
r_work: 0.3159 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10234  Z= 0.140
  Angle     :  0.573  10.533  13813  Z= 0.287
  Chirality :  0.042   0.218   1557
  Planarity :  0.003   0.041   1752
  Dihedral  :  5.306  48.080   1427
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 16.96 %
    Favored  : 80.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.24), residues: 1231
  helix:  1.17 (0.23), residues: 520
  sheet:  0.23 (0.37), residues: 185
  loop : -0.68 (0.28), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 585 
 HIS   0.009   0.001   HIS A 620 
 PHE   0.012   0.001   PHE A 112 
 TYR   0.012   0.001   TYR B 437 
 ARG   0.003   0.000   ARG A 495 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03146 (  470)
  hydrogen bonds       : angle       4.54490 ( 1389)
  covalent geometry    : bond        0.00329 (10234)
  covalent geometry    : angle       0.57335 (13813)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5008.01 seconds
wall clock time: 86 minutes 49.95 seconds (5209.95 seconds total)