Starting phenix.real_space_refine
on Mon Jul 28 16:43:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s9b_24931/07_2025/7s9b_24931.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s9b_24931/07_2025/7s9b_24931.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s9b_24931/07_2025/7s9b_24931.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s9b_24931/07_2025/7s9b_24931.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s9b_24931/07_2025/7s9b_24931.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s9b_24931/07_2025/7s9b_24931.cif"
  }
  resolution = 4.2
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    6856      2.51       5
     N    1680      2.21       5
     O    1872      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10458
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 678, 5229
          Classifications: {'peptide': 678}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 33, 'TRANS': 644}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 5229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 678, 5229
          Classifications: {'peptide': 678}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 33, 'TRANS': 644}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
  Time building chain proxies: 6.27, per 1000 atoms: 0.60
  Number of scatterers: 10458
  At special positions: 0
  Unit cell: (115.867, 111.615, 117.993, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      50     16.00
     O    1872      8.00
     N    1680      7.00
     C    6856      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: 2.81
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2500

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 4 sheets defined
      64.3% alpha, 2.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 31
    Processing helix  chain 'A' and resid 44 through 48
      removed outlier: 3.519A  pdb=" N   LYS A  47 " --> pdb=" O   ASP A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 65
      removed outlier: 3.617A  pdb=" N   ILE A  57 " --> pdb=" O   THR A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 71
    Processing helix  chain 'A' and resid 78 through 105
      Proline residue:  A  96  - end of helix
    Processing helix  chain 'A' and resid 108 through 126
      removed outlier: 3.960A  pdb=" N   GLY A 112 " --> pdb=" O   PRO A 108 " (cutoff:3.500A)
      Proline residue:  A 119  - end of helix
    Processing helix  chain 'A' and resid 138 through 152
    Processing helix  chain 'A' and resid 168 through 195
    Processing helix  chain 'A' and resid 200 through 205
    Processing helix  chain 'A' and resid 206 through 231
      removed outlier: 4.203A  pdb=" N   LYS A 227 " --> pdb=" O   THR A 223 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   TYR A 228 " --> pdb=" O   SER A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 253
    Processing helix  chain 'A' and resid 258 through 282
      removed outlier: 3.539A  pdb=" N   PHE A 282 " --> pdb=" O   PHE A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 307
      removed outlier: 3.585A  pdb=" N   PHE A 295 " --> pdb=" O   PRO A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 363
      removed outlier: 3.724A  pdb=" N   ASP A 342 " --> pdb=" O   LEU A 338 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   ALA A 345 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
      removed outlier: 5.288A  pdb=" N   ILE A 346 " --> pdb=" O   ASP A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 388
      removed outlier: 3.526A  pdb=" N   GLU A 374 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 406
      removed outlier: 4.015A  pdb=" N   SER A 400 " --> pdb=" O   SER A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 427
      removed outlier: 4.226A  pdb=" N   SER A 418 " --> pdb=" O   GLY A 414 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   LEU A 419 " --> pdb=" O   CYS A 415 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   LEU A 423 " --> pdb=" O   LEU A 419 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   VAL A 424 " --> pdb=" O   MET A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 437 through 448
    Processing helix  chain 'A' and resid 448 through 454
    Processing helix  chain 'A' and resid 456 through 465
      removed outlier: 3.748A  pdb=" N   PHE A 460 " --> pdb=" O   SER A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 482
    Processing helix  chain 'A' and resid 483 through 505
      removed outlier: 4.043A  pdb=" N   VAL A 499 " --> pdb=" O   ALA A 495 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ILE A 500 " --> pdb=" O   LEU A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 561
    Processing helix  chain 'A' and resid 563 through 579
    Processing helix  chain 'A' and resid 653 through 671
    Processing helix  chain 'A' and resid 680 through 690
    Processing helix  chain 'A' and resid 697 through 702
      removed outlier: 4.010A  pdb=" N   LEU A 702 " --> pdb=" O   LEU A 699 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 721
      removed outlier: 3.644A  pdb=" N   GLU A 721 " --> pdb=" O   GLU A 717 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 31
    Processing helix  chain 'B' and resid 44 through 48
      removed outlier: 3.520A  pdb=" N   LYS B  47 " --> pdb=" O   ASP B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 65
      removed outlier: 3.616A  pdb=" N   ILE B  57 " --> pdb=" O   THR B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 71
    Processing helix  chain 'B' and resid 78 through 105
      Proline residue:  B  96  - end of helix
    Processing helix  chain 'B' and resid 108 through 126
      removed outlier: 3.959A  pdb=" N   GLY B 112 " --> pdb=" O   PRO B 108 " (cutoff:3.500A)
      Proline residue:  B 119  - end of helix
    Processing helix  chain 'B' and resid 138 through 152
    Processing helix  chain 'B' and resid 168 through 195
    Processing helix  chain 'B' and resid 200 through 205
    Processing helix  chain 'B' and resid 206 through 231
      removed outlier: 4.201A  pdb=" N   LYS B 227 " --> pdb=" O   THR B 223 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   TYR B 228 " --> pdb=" O   SER B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 253
    Processing helix  chain 'B' and resid 258 through 282
      removed outlier: 3.539A  pdb=" N   PHE B 282 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 307
      removed outlier: 3.584A  pdb=" N   PHE B 295 " --> pdb=" O   PRO B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 335 through 363
      removed outlier: 3.723A  pdb=" N   ASP B 342 " --> pdb=" O   LEU B 338 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   ALA B 345 " --> pdb=" O   VAL B 341 " (cutoff:3.500A)
      removed outlier: 5.288A  pdb=" N   ILE B 346 " --> pdb=" O   ASP B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 388
      removed outlier: 3.526A  pdb=" N   GLU B 374 " --> pdb=" O   ASP B 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 406
      removed outlier: 3.937A  pdb=" N   SER B 400 " --> pdb=" O   SER B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 427
      removed outlier: 4.226A  pdb=" N   SER B 418 " --> pdb=" O   GLY B 414 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   LEU B 419 " --> pdb=" O   CYS B 415 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   LEU B 423 " --> pdb=" O   LEU B 419 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   VAL B 424 " --> pdb=" O   MET B 420 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 437 through 448
    Processing helix  chain 'B' and resid 448 through 454
    Processing helix  chain 'B' and resid 456 through 465
      removed outlier: 3.749A  pdb=" N   PHE B 460 " --> pdb=" O   SER B 456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 466 through 482
    Processing helix  chain 'B' and resid 483 through 505
      removed outlier: 4.041A  pdb=" N   VAL B 499 " --> pdb=" O   ALA B 495 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ILE B 500 " --> pdb=" O   LEU B 496 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 549 through 561
    Processing helix  chain 'B' and resid 563 through 579
    Processing helix  chain 'B' and resid 653 through 671
    Processing helix  chain 'B' and resid 680 through 690
    Processing helix  chain 'B' and resid 697 through 702
      removed outlier: 4.011A  pdb=" N   LEU B 702 " --> pdb=" O   LEU B 699 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 705 through 721
      removed outlier: 3.643A  pdb=" N   GLU B 721 " --> pdb=" O   GLU B 717 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 511 through 513
    Processing sheet with id=AA2, first strand: chain 'A' and resid 535 through 539
      removed outlier: 6.622A  pdb=" N   LYS A 536 " --> pdb=" O   ILE A 643 " (cutoff:3.500A)
      removed outlier: 7.532A  pdb=" N   ASP A 645 " --> pdb=" O   LYS A 536 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   PHE A 538 " --> pdb=" O   ASP A 645 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 511 through 513
    Processing sheet with id=AA4, first strand: chain 'B' and resid 535 through 539
      removed outlier: 6.623A  pdb=" N   LYS B 536 " --> pdb=" O   ILE B 643 " (cutoff:3.500A)
      removed outlier: 7.532A  pdb=" N   ASP B 645 " --> pdb=" O   LYS B 536 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   PHE B 538 " --> pdb=" O   ASP B 645 " (cutoff:3.500A)

    612 hydrogen bonds defined for protein.
    1800 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.80

  Time building geometry restraints manager: 3.28 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2280
        1.33 -     1.45: 2325
        1.45 -     1.57: 6007
        1.57 -     1.70: 0
        1.70 -     1.82: 82
  Bond restraints: 10694
  Sorted by residual:
  bond pdb=" CB  PHE B 351 "
       pdb=" CG  PHE B 351 "
    ideal  model  delta    sigma   weight residual
    1.502  1.433  0.069 2.30e-02 1.89e+03 9.05e+00
  bond pdb=" CB  PHE A 351 "
       pdb=" CG  PHE A 351 "
    ideal  model  delta    sigma   weight residual
    1.502  1.434  0.068 2.30e-02 1.89e+03 8.87e+00
  bond pdb=" CA  SER B 400 "
       pdb=" CB  SER B 400 "
    ideal  model  delta    sigma   weight residual
    1.529  1.484  0.045 1.64e-02 3.72e+03 7.48e+00
  bond pdb=" CA  SER A 400 "
       pdb=" CB  SER A 400 "
    ideal  model  delta    sigma   weight residual
    1.528  1.486  0.043 1.66e-02 3.63e+03 6.56e+00
  bond pdb=" CD1 PHE A 351 "
       pdb=" CE1 PHE A 351 "
    ideal  model  delta    sigma   weight residual
    1.382  1.307  0.075 3.00e-02 1.11e+03 6.21e+00
  ... (remaining 10689 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 14109
        2.12 -     4.24: 374
        4.24 -     6.35: 49
        6.35 -     8.47: 4
        8.47 -    10.59: 4
  Bond angle restraints: 14540
  Sorted by residual:
  angle pdb=" C   PHE B  23 "
        pdb=" N   SER B  24 "
        pdb=" CA  SER B  24 "
      ideal   model   delta    sigma   weight residual
     121.54  112.27    9.27 1.91e+00 2.74e-01 2.35e+01
  angle pdb=" C   PHE A  23 "
        pdb=" N   SER A  24 "
        pdb=" CA  SER A  24 "
      ideal   model   delta    sigma   weight residual
     121.54  112.32    9.22 1.91e+00 2.74e-01 2.33e+01
  angle pdb=" C   GLU A 404 "
        pdb=" N   GLY A 405 "
        pdb=" CA  GLY A 405 "
      ideal   model   delta    sigma   weight residual
     120.14  114.65    5.49 1.25e+00 6.40e-01 1.93e+01
  angle pdb=" N   LEU A 401 "
        pdb=" CA  LEU A 401 "
        pdb=" C   LEU A 401 "
      ideal   model   delta    sigma   weight residual
     111.71  106.99    4.72 1.15e+00 7.56e-01 1.68e+01
  angle pdb=" N   LEU B 401 "
        pdb=" CA  LEU B 401 "
        pdb=" C   LEU B 401 "
      ideal   model   delta    sigma   weight residual
     111.71  107.33    4.38 1.15e+00 7.56e-01 1.45e+01
  ... (remaining 14535 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.04: 5865
       17.04 -    34.08: 399
       34.08 -    51.12: 42
       51.12 -    68.16: 13
       68.16 -    85.20: 7
  Dihedral angle restraints: 6326
    sinusoidal: 2418
      harmonic: 3908
  Sorted by residual:
  dihedral pdb=" CA  LYS B  77 "
           pdb=" C   LYS B  77 "
           pdb=" N   GLU B  78 "
           pdb=" CA  GLU B  78 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.08   26.92     0      5.00e+00 4.00e-02 2.90e+01
  dihedral pdb=" CA  LYS A  77 "
           pdb=" C   LYS A  77 "
           pdb=" N   GLU A  78 "
           pdb=" CA  GLU A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.13   26.87     0      5.00e+00 4.00e-02 2.89e+01
  dihedral pdb=" CA  SER A  24 "
           pdb=" C   SER A  24 "
           pdb=" N   HIS A  25 "
           pdb=" CA  HIS A  25 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.67   25.33     0      5.00e+00 4.00e-02 2.57e+01
  ... (remaining 6323 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1224
       0.047 -    0.093: 407
       0.093 -    0.140: 85
       0.140 -    0.186: 8
       0.186 -    0.233: 4
  Chirality restraints: 1728
  Sorted by residual:
  chirality pdb=" CB  THR A 390 "
            pdb=" CA  THR A 390 "
            pdb=" OG1 THR A 390 "
            pdb=" CG2 THR A 390 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CB  THR B 390 "
            pdb=" CA  THR B 390 "
            pdb=" OG1 THR B 390 "
            pdb=" CG2 THR B 390 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CB  ILE A 344 "
            pdb=" CA  ILE A 344 "
            pdb=" CG1 ILE A 344 "
            pdb=" CG2 ILE A 344 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.98e-01
  ... (remaining 1725 not shown)

  Planarity restraints: 1814
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 396 "    0.016 2.00e-02 2.50e+03   3.13e-02 9.77e+00
        pdb=" C   SER A 396 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   SER A 396 "    0.020 2.00e-02 2.50e+03
        pdb=" N   LEU A 397 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 396 "   -0.013 2.00e-02 2.50e+03   2.60e-02 6.77e+00
        pdb=" C   SER B 396 "    0.045 2.00e-02 2.50e+03
        pdb=" O   SER B 396 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   LEU B 397 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 330 "   -0.027 5.00e-02 4.00e+02   4.06e-02 2.63e+00
        pdb=" N   PRO B 331 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO B 331 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 331 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1811 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1744
        2.75 -     3.29: 11763
        3.29 -     3.83: 17894
        3.83 -     4.36: 19870
        4.36 -     4.90: 32512
  Nonbonded interactions: 83783
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 154 "
            pdb=" NZ  LYS B 235 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" OD2 ASP A 154 "
            pdb=" NZ  LYS A 235 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" OE2 GLU A 627 "
            pdb=" N   GLN A 630 "
     model   vdw
     2.222 3.120
  nonbonded pdb=" OE2 GLU B 627 "
            pdb=" N   GLN B 630 "
     model   vdw
     2.223 3.120
  nonbonded pdb=" O   HIS B 220 "
            pdb=" OG1 THR B 223 "
     model   vdw
     2.243 3.040
  ... (remaining 83778 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     25.860
  Find NCS groups from input model:        0.190
  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:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
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      :  0.006   0.075  10694  Z= 0.308
  Angle     :  0.824  10.589  14540  Z= 0.477
  Chirality :  0.047   0.233   1728
  Planarity :  0.005   0.041   1814
  Dihedral  : 11.725  85.201   3826
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 19.98
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  9.94 %
    Favored  : 89.76 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  1.05 %
    Favored  : 98.17 %
  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: -0.99 (0.23), residues: 1348
  helix:  0.41 (0.18), residues: 828
  sheet: -0.21 (0.90), residues: 32
  loop : -2.60 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 472 
 HIS   0.010   0.002   HIS A  25 
 PHE   0.025   0.002   PHE A 117 
 TYR   0.027   0.002   TYR A 123 
 ARG   0.007   0.001   ARG A 236 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11405 (  612)
  hydrogen bonds       : angle       5.39238 ( 1800)
  covalent geometry    : bond        0.00615 (10694)
  covalent geometry    : angle       0.82383 (14540)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 182
  time to evaluate  : 1.063 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  266 LEU cc_start: 0.8633 (pp) cc_final: 0.8334 (pp)
REVERT: A  267 MET cc_start: 0.8414 (mmt) cc_final: 0.7986 (mmt)
REVERT: A  299 MET cc_start: 0.8540 (ppp) cc_final: 0.8189 (ppp)
REVERT: A  566 PHE cc_start: 0.7957 (m-80) cc_final: 0.7717 (m-80)
REVERT: B  266 LEU cc_start: 0.8631 (pp) cc_final: 0.8397 (pp)
REVERT: B  267 MET cc_start: 0.8412 (mmt) cc_final: 0.8062 (mmt)
REVERT: B  299 MET cc_start: 0.8561 (ppp) cc_final: 0.8179 (ppp)
REVERT: B  566 PHE cc_start: 0.7848 (m-80) cc_final: 0.7620 (m-80)
REVERT: B  693 PHE cc_start: 0.8257 (m-10) cc_final: 0.7946 (m-80)
  outliers start: 9
  outliers final: 7
  residues processed: 189
  average time/residue: 0.1754
  time to fit residues: 50.6972
Evaluate side-chains
  150 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 143
  time to evaluate  : 1.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 113 optimal weight:    0.8980
   chunk 101 optimal weight:    1.9990
   chunk 56 optimal weight:    0.4980
   chunk 34 optimal weight:    2.9990
   chunk 68 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   chunk 105 optimal weight:    5.9990
   chunk 40 optimal weight:    9.9990
   chunk 63 optimal weight:    5.9990
   chunk 78 optimal weight:    9.9990
   chunk 121 optimal weight:    1.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
** A  25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 689 GLN
** B  25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 365 HIS ** 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 = 0.3474 r_free = 0.3474 target = 0.087628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.068274 restraints weight = 39757.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.070211 restraints weight = 21156.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.071479 restraints weight = 13743.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.1228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10694  Z= 0.146
  Angle     :  0.639   8.141  14540  Z= 0.329
  Chirality :  0.044   0.154   1728
  Planarity :  0.005   0.037   1814
  Dihedral  :  4.630  26.428   1450
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.38 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  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: -0.26 (0.24), residues: 1348
  helix:  0.98 (0.19), residues: 820
  sheet:  0.21 (0.87), residues: 32
  loop : -2.24 (0.29), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 472 
 HIS   0.008   0.001   HIS A  25 
 PHE   0.016   0.001   PHE A 117 
 TYR   0.030   0.002   TYR B 340 
 ARG   0.004   0.001   ARG A 236 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04038 (  612)
  hydrogen bonds       : angle       4.34757 ( 1800)
  covalent geometry    : bond        0.00316 (10694)
  covalent geometry    : angle       0.63925 (14540)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 1.086 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLN cc_start: 0.8495 (tp-100) cc_final: 0.8273 (tp40)
REVERT: A  266 LEU cc_start: 0.8672 (pp) cc_final: 0.8416 (pp)
REVERT: A  267 MET cc_start: 0.8293 (mmt) cc_final: 0.7957 (mmt)
REVERT: A  299 MET cc_start: 0.8719 (ppp) cc_final: 0.8355 (ppp)
REVERT: A  453 MET cc_start: 0.9150 (mmt) cc_final: 0.8926 (mmt)
REVERT: B   94 GLN cc_start: 0.8457 (tp-100) cc_final: 0.8209 (mm-40)
REVERT: B  266 LEU cc_start: 0.8668 (pp) cc_final: 0.8419 (pp)
REVERT: B  267 MET cc_start: 0.8431 (mmt) cc_final: 0.8027 (mmt)
REVERT: B  299 MET cc_start: 0.8708 (ppp) cc_final: 0.8287 (ppp)
REVERT: B  566 PHE cc_start: 0.8227 (m-80) cc_final: 0.7693 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 191
  average time/residue: 0.1742
  time to fit residues: 51.0523
Evaluate side-chains
  154 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 96 optimal weight:   20.0000
   chunk 36 optimal weight:    2.9990
   chunk 123 optimal weight:    6.9990
   chunk 88 optimal weight:    6.9990
   chunk 118 optimal weight:    8.9990
   chunk 13 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A  25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.087559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.068228 restraints weight = 40188.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.070193 restraints weight = 21495.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.071465 restraints weight = 13967.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10694  Z= 0.160
  Angle     :  0.625   8.503  14540  Z= 0.320
  Chirality :  0.044   0.185   1728
  Planarity :  0.004   0.032   1814
  Dihedral  :  4.463  26.190   1450
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.82 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  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: -0.06 (0.24), residues: 1348
  helix:  1.14 (0.19), residues: 826
  sheet:  0.30 (0.89), residues: 32
  loop : -2.18 (0.30), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 472 
 HIS   0.007   0.002   HIS A  25 
 PHE   0.012   0.001   PHE B 693 
 TYR   0.022   0.001   TYR A 123 
 ARG   0.005   0.001   ARG A 236 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03894 (  612)
  hydrogen bonds       : angle       4.16270 ( 1800)
  covalent geometry    : bond        0.00353 (10694)
  covalent geometry    : angle       0.62485 (14540)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 1.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  198 PHE cc_start: 0.8196 (m-10) cc_final: 0.7914 (m-10)
REVERT: A  207 GLU cc_start: 0.8278 (tt0) cc_final: 0.7826 (tm-30)
REVERT: A  236 ARG cc_start: 0.8202 (tmm160) cc_final: 0.7872 (tmm160)
REVERT: A  267 MET cc_start: 0.8339 (mmt) cc_final: 0.7991 (mmt)
REVERT: A  299 MET cc_start: 0.8814 (ppp) cc_final: 0.8524 (ppp)
REVERT: A  382 ASN cc_start: 0.8808 (t0) cc_final: 0.8602 (t0)
REVERT: A  469 LEU cc_start: 0.9112 (tp) cc_final: 0.8845 (tp)
REVERT: B   94 GLN cc_start: 0.8426 (tp-100) cc_final: 0.8158 (tp40)
REVERT: B  198 PHE cc_start: 0.8467 (m-10) cc_final: 0.8044 (m-10)
REVERT: B  267 MET cc_start: 0.8414 (mmt) cc_final: 0.8058 (mmt)
REVERT: B  299 MET cc_start: 0.8809 (ppp) cc_final: 0.8477 (ppp)
REVERT: B  469 LEU cc_start: 0.9076 (tp) cc_final: 0.8817 (tp)
REVERT: B  689 GLN cc_start: 0.8933 (mt0) cc_final: 0.8693 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 183
  average time/residue: 0.1792
  time to fit residues: 49.5818
Evaluate side-chains
  147 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 1.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 29 optimal weight:   20.0000
   chunk 24 optimal weight:    0.9980
   chunk 25 optimal weight:    6.9990
   chunk 127 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   chunk 108 optimal weight:    0.9990
   chunk 31 optimal weight:   10.0000
   chunk 79 optimal weight:    0.8980
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
A  25 HIS
A  29 GLN
A 363 ASN
** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  25 HIS
B  29 GLN
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.088872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.069207 restraints weight = 39518.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.071218 restraints weight = 21321.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.072517 restraints weight = 13953.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10694  Z= 0.128
  Angle     :  0.593   8.200  14540  Z= 0.301
  Chirality :  0.043   0.162   1728
  Planarity :  0.004   0.031   1814
  Dihedral  :  4.356  27.458   1450
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.42 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  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:  0.10 (0.24), residues: 1348
  helix:  1.23 (0.19), residues: 828
  sheet:  0.57 (0.91), residues: 32
  loop : -2.09 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 472 
 HIS   0.005   0.001   HIS B  25 
 PHE   0.016   0.001   PHE A 191 
 TYR   0.020   0.001   TYR A 340 
 ARG   0.004   0.000   ARG A 236 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03553 (  612)
  hydrogen bonds       : angle       3.99366 ( 1800)
  covalent geometry    : bond        0.00280 (10694)
  covalent geometry    : angle       0.59305 (14540)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 1.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 ILE cc_start: 0.7967 (mm) cc_final: 0.7751 (mm)
REVERT: A  207 GLU cc_start: 0.8205 (tt0) cc_final: 0.7763 (tm-30)
REVERT: A  267 MET cc_start: 0.8394 (mmt) cc_final: 0.8032 (mmt)
REVERT: A  299 MET cc_start: 0.8840 (ppp) cc_final: 0.8529 (ppp)
REVERT: A  469 LEU cc_start: 0.9111 (tp) cc_final: 0.8868 (tp)
REVERT: B   94 GLN cc_start: 0.8343 (tp-100) cc_final: 0.8072 (tp40)
REVERT: B  198 PHE cc_start: 0.8373 (m-10) cc_final: 0.8121 (m-10)
REVERT: B  267 MET cc_start: 0.8393 (mmt) cc_final: 0.8017 (mmt)
REVERT: B  299 MET cc_start: 0.8828 (ppp) cc_final: 0.8538 (ppp)
REVERT: B  420 MET cc_start: 0.8829 (tmm) cc_final: 0.8485 (ptp)
REVERT: B  469 LEU cc_start: 0.9046 (tp) cc_final: 0.8800 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 195
  average time/residue: 0.1963
  time to fit residues: 56.8072
Evaluate side-chains
  149 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 1.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 118 optimal weight:    0.7980
   chunk 62 optimal weight:    5.9990
   chunk 59 optimal weight:    0.6980
   chunk 108 optimal weight:    9.9990
   chunk 24 optimal weight:    5.9990
   chunk 46 optimal weight:    7.9990
   chunk 10 optimal weight:    7.9990
   chunk 27 optimal weight:    7.9990
   chunk 112 optimal weight:    7.9990
   chunk 7 optimal weight:    6.9990
   overall best weight:    4.0986

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  29 GLN
B 363 ASN
** B 365 HIS ** 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 = 0.3449 r_free = 0.3449 target = 0.086373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.067036 restraints weight = 40598.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.068932 restraints weight = 21858.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.070175 restraints weight = 14309.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.1682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  10694  Z= 0.230
  Angle     :  0.675   8.903  14540  Z= 0.347
  Chirality :  0.045   0.203   1728
  Planarity :  0.004   0.035   1814
  Dihedral  :  4.441  25.615   1450
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 14.80
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.79 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  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: -0.00 (0.24), residues: 1348
  helix:  1.09 (0.19), residues: 830
  sheet:  0.52 (0.87), residues: 32
  loop : -2.03 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 472 
 HIS   0.005   0.002   HIS B 704 
 PHE   0.021   0.002   PHE A 538 
 TYR   0.017   0.002   TYR A 123 
 ARG   0.006   0.001   ARG A 236 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03964 (  612)
  hydrogen bonds       : angle       4.24493 ( 1800)
  covalent geometry    : bond        0.00510 (10694)
  covalent geometry    : angle       0.67504 (14540)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 1.692 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  207 GLU cc_start: 0.8183 (tt0) cc_final: 0.7798 (tm-30)
REVERT: A  267 MET cc_start: 0.8439 (mmt) cc_final: 0.8028 (mmt)
REVERT: A  299 MET cc_start: 0.8837 (ppp) cc_final: 0.8527 (ppp)
REVERT: A  469 LEU cc_start: 0.9182 (tp) cc_final: 0.8917 (tp)
REVERT: B   94 GLN cc_start: 0.8353 (tp-100) cc_final: 0.8082 (tp40)
REVERT: B  198 PHE cc_start: 0.8370 (m-10) cc_final: 0.8133 (m-10)
REVERT: B  266 LEU cc_start: 0.8638 (pp) cc_final: 0.8437 (pp)
REVERT: B  267 MET cc_start: 0.8385 (mmt) cc_final: 0.8018 (mmt)
REVERT: B  299 MET cc_start: 0.8883 (ppp) cc_final: 0.8534 (ppp)
REVERT: B  469 LEU cc_start: 0.9170 (tp) cc_final: 0.8905 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.2186
  time to fit residues: 57.4311
Evaluate side-chains
  145 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 1.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 28 optimal weight:    7.9990
   chunk 76 optimal weight:    0.0070
   chunk 5 optimal weight:    6.9990
   chunk 90 optimal weight:    1.9990
   chunk 68 optimal weight:    5.9990
   chunk 104 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9990
   chunk 56 optimal weight:    6.9990
   chunk 82 optimal weight:    9.9990
   chunk 67 optimal weight:    6.9990
   overall best weight:    3.0006

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

Flipped N/Q/H residues before XYZ refinement:
** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 382 ASN ** 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 = 0.3465 r_free = 0.3465 target = 0.087270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.067947 restraints weight = 40208.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.069919 restraints weight = 21338.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.071176 restraints weight = 13769.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027  10694  Z= 0.178
  Angle     :  0.631   8.598  14540  Z= 0.324
  Chirality :  0.044   0.167   1728
  Planarity :  0.004   0.054   1814
  Dihedral  :  4.505  26.596   1450
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.42 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  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:  0.14 (0.24), residues: 1348
  helix:  1.21 (0.19), residues: 828
  sheet:  0.46 (0.84), residues: 32
  loop : -1.97 (0.30), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 472 
 HIS   0.004   0.001   HIS B 704 
 PHE   0.012   0.002   PHE A 566 
 TYR   0.045   0.002   TYR A 123 
 ARG   0.005   0.001   ARG B 399 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03799 (  612)
  hydrogen bonds       : angle       4.15986 ( 1800)
  covalent geometry    : bond        0.00392 (10694)
  covalent geometry    : angle       0.63091 (14540)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 1.490 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  207 GLU cc_start: 0.8170 (tt0) cc_final: 0.7718 (tm-30)
REVERT: A  266 LEU cc_start: 0.8667 (pp) cc_final: 0.8451 (pp)
REVERT: A  267 MET cc_start: 0.8408 (mmt) cc_final: 0.8002 (mmt)
REVERT: A  299 MET cc_start: 0.8842 (ppp) cc_final: 0.8535 (ppp)
REVERT: A  378 LEU cc_start: 0.9362 (tp) cc_final: 0.9110 (tp)
REVERT: A  382 ASN cc_start: 0.8970 (t0) cc_final: 0.8620 (t0)
REVERT: A  469 LEU cc_start: 0.9153 (tp) cc_final: 0.8904 (tp)
REVERT: A  669 ASP cc_start: 0.8401 (m-30) cc_final: 0.8198 (m-30)
REVERT: B  198 PHE cc_start: 0.8330 (m-10) cc_final: 0.8097 (m-10)
REVERT: B  266 LEU cc_start: 0.8642 (pp) cc_final: 0.8438 (pp)
REVERT: B  267 MET cc_start: 0.8448 (mmt) cc_final: 0.8045 (mmt)
REVERT: B  299 MET cc_start: 0.8889 (ppp) cc_final: 0.8541 (ppp)
REVERT: B  378 LEU cc_start: 0.9377 (tp) cc_final: 0.9126 (tp)
REVERT: B  382 ASN cc_start: 0.8941 (t0) cc_final: 0.8602 (t0)
REVERT: B  420 MET cc_start: 0.8823 (tmm) cc_final: 0.8475 (ptp)
REVERT: B  469 LEU cc_start: 0.9145 (tp) cc_final: 0.8889 (tp)
REVERT: B  669 ASP cc_start: 0.8345 (m-30) cc_final: 0.8140 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 0.2553
  time to fit residues: 70.0203
Evaluate side-chains
  150 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 1.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 40 optimal weight:    6.9990
   chunk 47 optimal weight:    4.9990
   chunk 15 optimal weight:    0.0020
   chunk 132 optimal weight:    0.0470
   chunk 112 optimal weight:    1.9990
   chunk 101 optimal weight:    7.9990
   chunk 9 optimal weight:    9.9990
   chunk 25 optimal weight:    2.9990
   chunk 59 optimal weight:    0.2980
   chunk 98 optimal weight:    6.9990
   chunk 43 optimal weight:    6.9990
   overall best weight:    1.0690

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  29 GLN
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.089284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.070200 restraints weight = 40261.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.072167 restraints weight = 21556.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.073463 restraints weight = 14005.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.2105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10694  Z= 0.119
  Angle     :  0.621   9.425  14540  Z= 0.312
  Chirality :  0.043   0.197   1728
  Planarity :  0.004   0.035   1814
  Dihedral  :  4.425  30.057   1450
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.49 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.24), residues: 1348
  helix:  1.30 (0.19), residues: 830
  sheet:  0.84 (0.85), residues: 32
  loop : -1.95 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 472 
 HIS   0.002   0.001   HIS B  25 
 PHE   0.023   0.001   PHE A 351 
 TYR   0.038   0.001   TYR A 123 
 ARG   0.005   0.000   ARG A 236 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03504 (  612)
  hydrogen bonds       : angle       3.97382 ( 1800)
  covalent geometry    : bond        0.00256 (10694)
  covalent geometry    : angle       0.62077 (14540)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 1.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.9043 (mmm) cc_final: 0.8631 (tpp)
REVERT: A  186 THR cc_start: 0.9360 (m) cc_final: 0.9141 (m)
REVERT: A  198 PHE cc_start: 0.8021 (m-10) cc_final: 0.7682 (m-10)
REVERT: A  207 GLU cc_start: 0.8157 (tt0) cc_final: 0.7704 (tm-30)
REVERT: A  267 MET cc_start: 0.8314 (mmt) cc_final: 0.7922 (mmt)
REVERT: A  299 MET cc_start: 0.8848 (ppp) cc_final: 0.8537 (ppp)
REVERT: A  382 ASN cc_start: 0.8967 (t0) cc_final: 0.8636 (t0)
REVERT: A  469 LEU cc_start: 0.9134 (tp) cc_final: 0.8920 (tp)
REVERT: B   94 GLN cc_start: 0.8498 (tp-100) cc_final: 0.8133 (mm-40)
REVERT: B  198 PHE cc_start: 0.8316 (m-10) cc_final: 0.8054 (m-10)
REVERT: B  236 ARG cc_start: 0.8112 (tmm160) cc_final: 0.7759 (tmm160)
REVERT: B  266 LEU cc_start: 0.8616 (pp) cc_final: 0.8402 (pp)
REVERT: B  267 MET cc_start: 0.8418 (mmt) cc_final: 0.7996 (mmt)
REVERT: B  299 MET cc_start: 0.8839 (ppp) cc_final: 0.8530 (ppp)
REVERT: B  354 THR cc_start: 0.9262 (p) cc_final: 0.9058 (t)
REVERT: B  382 ASN cc_start: 0.9009 (t0) cc_final: 0.8663 (t0)
REVERT: B  469 LEU cc_start: 0.9110 (tp) cc_final: 0.8896 (tp)
REVERT: B  669 ASP cc_start: 0.8219 (m-30) cc_final: 0.8018 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.3308
  time to fit residues: 99.2988
Evaluate side-chains
  161 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 1.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 42 optimal weight:    9.9990
   chunk 89 optimal weight:    6.9990
   chunk 105 optimal weight:    8.9990
   chunk 124 optimal weight:    0.0870
   chunk 118 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 77 optimal weight:    9.9990
   chunk 34 optimal weight:    0.9990
   chunk 44 optimal weight:    0.5980
   overall best weight:    0.7362

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

Flipped N/Q/H residues before XYZ refinement:
A  94 GLN
** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 382 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 = 0.3518 r_free = 0.3518 target = 0.090303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.070980 restraints weight = 39278.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.073015 restraints weight = 20910.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.074319 restraints weight = 13598.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.2320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  10694  Z= 0.113
  Angle     :  0.597   7.979  14540  Z= 0.301
  Chirality :  0.043   0.230   1728
  Planarity :  0.004   0.042   1814
  Dihedral  :  4.373  28.309   1450
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.53 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  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:  0.31 (0.24), residues: 1348
  helix:  1.29 (0.19), residues: 832
  sheet:  1.19 (0.85), residues: 32
  loop : -1.84 (0.30), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 472 
 HIS   0.002   0.001   HIS B 310 
 PHE   0.017   0.001   PHE A 191 
 TYR   0.032   0.001   TYR A 123 
 ARG   0.008   0.000   ARG B 399 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03326 (  612)
  hydrogen bonds       : angle       3.86760 ( 1800)
  covalent geometry    : bond        0.00239 (10694)
  covalent geometry    : angle       0.59707 (14540)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 2.335 
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  122 MET cc_start: 0.9038 (mmm) cc_final: 0.8593 (tpp)
REVERT: A  186 THR cc_start: 0.9339 (m) cc_final: 0.9003 (p)
REVERT: A  198 PHE cc_start: 0.8029 (m-10) cc_final: 0.7805 (m-10)
REVERT: A  207 GLU cc_start: 0.8048 (tt0) cc_final: 0.7591 (tm-30)
REVERT: A  266 LEU cc_start: 0.8633 (pp) cc_final: 0.8426 (pp)
REVERT: A  267 MET cc_start: 0.8314 (mmt) cc_final: 0.7910 (mmt)
REVERT: A  299 MET cc_start: 0.8888 (ppp) cc_final: 0.8567 (ppp)
REVERT: A  382 ASN cc_start: 0.9029 (t0) cc_final: 0.8648 (t0)
REVERT: A  420 MET cc_start: 0.8909 (tmm) cc_final: 0.8559 (ptp)
REVERT: B  186 THR cc_start: 0.9348 (m) cc_final: 0.9015 (p)
REVERT: B  198 PHE cc_start: 0.8201 (m-10) cc_final: 0.7934 (m-10)
REVERT: B  266 LEU cc_start: 0.8608 (pp) cc_final: 0.8394 (pp)
REVERT: B  267 MET cc_start: 0.8367 (mmt) cc_final: 0.7974 (mmt)
REVERT: B  299 MET cc_start: 0.8885 (ppp) cc_final: 0.8567 (ppp)
REVERT: B  382 ASN cc_start: 0.8979 (t0) cc_final: 0.8628 (t0)
REVERT: B  669 ASP cc_start: 0.8216 (m-30) cc_final: 0.8012 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.3089
  time to fit residues: 87.0264
Evaluate side-chains
  165 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 1.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 76 optimal weight:   10.0000
   chunk 5 optimal weight:    4.9990
   chunk 3 optimal weight:    0.6980
   chunk 131 optimal weight:    0.5980
   chunk 58 optimal weight:    2.9990
   chunk 89 optimal weight:    7.9990
   chunk 38 optimal weight:    6.9990
   chunk 130 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   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 365 HIS
** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 689 GLN
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.089789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.070723 restraints weight = 40028.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.072714 restraints weight = 21569.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.074000 restraints weight = 14006.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.2405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10694  Z= 0.122
  Angle     :  0.603   8.897  14540  Z= 0.303
  Chirality :  0.043   0.238   1728
  Planarity :  0.004   0.039   1814
  Dihedral  :  4.258  27.497   1450
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.49 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  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:  0.37 (0.24), residues: 1348
  helix:  1.33 (0.19), residues: 832
  sheet:  1.34 (0.85), residues: 32
  loop : -1.82 (0.30), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 472 
 HIS   0.002   0.001   HIS A 704 
 PHE   0.014   0.001   PHE B 191 
 TYR   0.031   0.001   TYR A 123 
 ARG   0.004   0.000   ARG B 236 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03316 (  612)
  hydrogen bonds       : angle       3.86046 ( 1800)
  covalent geometry    : bond        0.00269 (10694)
  covalent geometry    : angle       0.60294 (14540)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 1.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.9020 (mmm) cc_final: 0.8594 (tpp)
REVERT: A  186 THR cc_start: 0.9341 (m) cc_final: 0.9004 (p)
REVERT: A  198 PHE cc_start: 0.7993 (m-10) cc_final: 0.7760 (m-10)
REVERT: A  207 GLU cc_start: 0.8019 (tt0) cc_final: 0.7604 (tm-30)
REVERT: A  266 LEU cc_start: 0.8644 (pp) cc_final: 0.8439 (pp)
REVERT: A  267 MET cc_start: 0.8324 (mmt) cc_final: 0.7901 (mmt)
REVERT: A  299 MET cc_start: 0.8890 (ppp) cc_final: 0.8561 (ppp)
REVERT: A  382 ASN cc_start: 0.8949 (t0) cc_final: 0.8624 (t0)
REVERT: A  420 MET cc_start: 0.8909 (tmm) cc_final: 0.8590 (ptp)
REVERT: B  186 THR cc_start: 0.9346 (m) cc_final: 0.9011 (p)
REVERT: B  198 PHE cc_start: 0.8161 (m-10) cc_final: 0.7901 (m-10)
REVERT: B  266 LEU cc_start: 0.8594 (pp) cc_final: 0.8377 (pp)
REVERT: B  267 MET cc_start: 0.8353 (mmt) cc_final: 0.7954 (mmt)
REVERT: B  299 MET cc_start: 0.8887 (ppp) cc_final: 0.8558 (ppp)
REVERT: B  382 ASN cc_start: 0.8978 (t0) cc_final: 0.8640 (t0)
REVERT: B  420 MET cc_start: 0.8835 (tmm) cc_final: 0.8528 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 183
  average time/residue: 0.1948
  time to fit residues: 53.3766
Evaluate side-chains
  161 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 70 optimal weight:    6.9990
   chunk 109 optimal weight:    0.9990
   chunk 116 optimal weight:    4.9990
   chunk 131 optimal weight:    0.8980
   chunk 89 optimal weight:    0.0270
   chunk 122 optimal weight:    0.9990
   chunk 27 optimal weight:    9.9990
   chunk 130 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.7040

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN
A  94 GLN
A 689 GLN
B 365 HIS
** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 689 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.091022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.071727 restraints weight = 39463.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.073786 restraints weight = 21073.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.075095 restraints weight = 13604.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.2591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10694  Z= 0.114
  Angle     :  0.616   8.470  14540  Z= 0.309
  Chirality :  0.043   0.233   1728
  Planarity :  0.005   0.074   1814
  Dihedral  :  4.312  27.974   1450
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  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:  0.40 (0.24), residues: 1348
  helix:  1.38 (0.19), residues: 830
  sheet:  1.55 (0.84), residues: 32
  loop : -1.87 (0.29), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 472 
 HIS   0.002   0.001   HIS A 310 
 PHE   0.011   0.001   PHE A  23 
 TYR   0.028   0.001   TYR A 123 
 ARG   0.004   0.000   ARG A  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03250 (  612)
  hydrogen bonds       : angle       3.82715 ( 1800)
  covalent geometry    : bond        0.00244 (10694)
  covalent geometry    : angle       0.61606 (14540)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 1.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.9032 (mmm) cc_final: 0.8589 (tpp)
REVERT: A  186 THR cc_start: 0.9344 (m) cc_final: 0.8987 (p)
REVERT: A  198 PHE cc_start: 0.8052 (m-10) cc_final: 0.7808 (m-10)
REVERT: A  207 GLU cc_start: 0.8017 (tt0) cc_final: 0.7610 (tm-30)
REVERT: A  236 ARG cc_start: 0.8212 (tmm160) cc_final: 0.7854 (tmm160)
REVERT: A  266 LEU cc_start: 0.8638 (pp) cc_final: 0.8429 (pp)
REVERT: A  267 MET cc_start: 0.8332 (mmt) cc_final: 0.7886 (mmt)
REVERT: A  299 MET cc_start: 0.8893 (ppp) cc_final: 0.8587 (ppp)
REVERT: A  382 ASN cc_start: 0.8984 (t0) cc_final: 0.8647 (t0)
REVERT: A  420 MET cc_start: 0.8913 (tmm) cc_final: 0.8559 (ptp)
REVERT: A  508 TYR cc_start: 0.8492 (m-80) cc_final: 0.8048 (m-80)
REVERT: B  186 THR cc_start: 0.9348 (m) cc_final: 0.8987 (p)
REVERT: B  266 LEU cc_start: 0.8607 (pp) cc_final: 0.8394 (pp)
REVERT: B  267 MET cc_start: 0.8369 (mmt) cc_final: 0.7964 (mmt)
REVERT: B  299 MET cc_start: 0.8887 (ppp) cc_final: 0.8576 (ppp)
REVERT: B  382 ASN cc_start: 0.8966 (t0) cc_final: 0.8619 (t0)
REVERT: B  508 TYR cc_start: 0.8500 (m-80) cc_final: 0.8092 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 186
  average time/residue: 0.1819
  time to fit residues: 50.2308
Evaluate side-chains
  161 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 128 optimal weight:    1.9990
   chunk 29 optimal weight:    9.9990
   chunk 60 optimal weight:    4.9990
   chunk 43 optimal weight:    5.9990
   chunk 56 optimal weight:    7.9990
   chunk 121 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9990
   chunk 69 optimal weight:    9.9990
   chunk 8 optimal weight:    0.8980
   chunk 112 optimal weight:    0.8980
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 689 GLN
B 689 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.090343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.071327 restraints weight = 39426.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.073262 restraints weight = 21359.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.074544 restraints weight = 14053.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.2604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10694  Z= 0.124
  Angle     :  0.611   8.857  14540  Z= 0.306
  Chirality :  0.043   0.224   1728
  Planarity :  0.004   0.068   1814
  Dihedral  :  4.264  28.097   1450
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.97 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  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:  0.43 (0.24), residues: 1348
  helix:  1.40 (0.19), residues: 830
  sheet:  1.55 (0.83), residues: 32
  loop : -1.86 (0.29), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 472 
 HIS   0.002   0.001   HIS B 704 
 PHE   0.016   0.001   PHE B  23 
 TYR   0.029   0.001   TYR A 123 
 ARG   0.005   0.000   ARG B  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03239 (  612)
  hydrogen bonds       : angle       3.83645 ( 1800)
  covalent geometry    : bond        0.00276 (10694)
  covalent geometry    : angle       0.61127 (14540)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3377.79 seconds
wall clock time: 62 minutes 17.51 seconds (3737.51 seconds total)