Starting phenix.real_space_refine
on Wed Mar  4 03:31:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s9b_24931/03_2026/7s9b_24931.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s9b_24931/03_2026/7s9b_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s9b_24931/03_2026/7s9b_24931.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s9b_24931/03_2026/7s9b_24931.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s9b_24931/03_2026/7s9b_24931.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s9b_24931/03_2026/7s9b_24931.map"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.34, per 1000 atoms: 0.22
  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: 0.82
  Conformation dependent library (CDL) restraints added in 414.5 milliseconds
  

  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: 0.22
  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: 1.26

  Time building geometry restraints manager: 1.11 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: 0.02
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:             1.510
  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:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.520
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.510
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.007   0.001   ARG A 236 
 TYR   0.027   0.002   TYR A 123 
 PHE   0.025   0.002   PHE A 117 
 TRP   0.010   0.002   TRP A 472 
 HIS   0.010   0.002   HIS A  25 

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

*********************** 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  : 0.389 
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: 0.7947 (m-80)
  outliers start: 9
  outliers final: 7
  residues processed: 189
  average time/residue: 0.0765
  time to fit residues: 22.4791
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  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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  29 GLN ** 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  29 GLN ** 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 = 0.3481 r_free = 0.3481 target = 0.087976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.068726 restraints weight = 39693.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.070708 restraints weight = 21091.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.071994 restraints weight = 13601.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.072734 restraints weight = 10157.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.073284 restraints weight = 8495.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.1236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10694  Z= 0.139
  Angle     :  0.635   8.008  14540  Z= 0.326
  Chirality :  0.043   0.150   1728
  Planarity :  0.005   0.034   1814
  Dihedral  :  4.630  26.643   1450
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.09 %
    Favored  : 91.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.27 (0.24), residues: 1348
  helix:  0.99 (0.19), residues: 818
  sheet:  0.22 (0.87), residues: 32
  loop : -2.26 (0.29), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  20 
 TYR   0.030   0.002   TYR B 340 
 PHE   0.018   0.002   PHE A 111 
 TRP   0.008   0.001   TRP B 472 
 HIS   0.007   0.001   HIS A  25 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (10694)
  covalent geometry    : angle       0.63481 (14540)
  hydrogen bonds       : bond        0.04075 (  612)
  hydrogen bonds       : angle       4.32402 ( 1800)

*********************** 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
  194 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 GLN cc_start: 0.8429 (tp-100) cc_final: 0.8214 (tp40)
REVERT: A  266 LEU cc_start: 0.8654 (pp) cc_final: 0.8397 (pp)
REVERT: A  267 MET cc_start: 0.8303 (mmt) cc_final: 0.7950 (mmt)
REVERT: A  299 MET cc_start: 0.8714 (ppp) cc_final: 0.8316 (ppp)
REVERT: A  453 MET cc_start: 0.9140 (mmt) cc_final: 0.8905 (mmt)
REVERT: B   97 GLN cc_start: 0.9183 (tt0) cc_final: 0.8889 (tt0)
REVERT: B  266 LEU cc_start: 0.8649 (pp) cc_final: 0.8398 (pp)
REVERT: B  267 MET cc_start: 0.8380 (mmt) cc_final: 0.7976 (mmt)
REVERT: B  299 MET cc_start: 0.8727 (ppp) cc_final: 0.8306 (ppp)
REVERT: B  566 PHE cc_start: 0.8153 (m-80) cc_final: 0.7657 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 194
  average time/residue: 0.0780
  time to fit residues: 23.4675
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  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 52 optimal weight:    0.6980
   chunk 42 optimal weight:    5.9990
   chunk 5 optimal weight:    8.9990
   chunk 53 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 39 optimal weight:   20.0000
   chunk 1 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 102 optimal weight:    0.4980
   chunk 122 optimal weight:    4.9990
   overall best weight:    1.6184

-------------------------------------------------------------------------------
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 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.088622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.069140 restraints weight = 40102.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.071128 restraints weight = 21390.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.072424 restraints weight = 13905.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.073266 restraints weight = 10435.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.073705 restraints weight = 8630.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.1572

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= 0.134
  Angle     :  0.612   8.000  14540  Z= 0.312
  Chirality :  0.043   0.195   1728
  Planarity :  0.004   0.035   1814
  Dihedral  :  4.430  26.870   1450
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.60 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.24), residues: 1348
  helix:  1.21 (0.19), residues: 824
  sheet:  0.46 (0.89), residues: 32
  loop : -2.18 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 399 
 TYR   0.022   0.001   TYR A 123 
 PHE   0.017   0.001   PHE B 111 
 TRP   0.009   0.001   TRP A 472 
 HIS   0.006   0.001   HIS A  25 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (10694)
  covalent geometry    : angle       0.61158 (14540)
  hydrogen bonds       : bond        0.03760 (  612)
  hydrogen bonds       : angle       4.06473 ( 1800)

*********************** 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
  191 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  198 PHE cc_start: 0.8171 (m-10) cc_final: 0.7890 (m-10)
REVERT: A  207 GLU cc_start: 0.8246 (tt0) cc_final: 0.7794 (tm-30)
REVERT: A  236 ARG cc_start: 0.8194 (tmm160) cc_final: 0.7981 (tmm160)
REVERT: A  267 MET cc_start: 0.8282 (mmt) cc_final: 0.7919 (mmt)
REVERT: A  299 MET cc_start: 0.8816 (ppp) cc_final: 0.8521 (ppp)
REVERT: A  469 LEU cc_start: 0.9084 (tp) cc_final: 0.8810 (tp)
REVERT: A  566 PHE cc_start: 0.8320 (m-80) cc_final: 0.8110 (m-80)
REVERT: A  689 GLN cc_start: 0.8897 (mt0) cc_final: 0.8664 (mt0)
REVERT: B   94 GLN cc_start: 0.8548 (tp40) cc_final: 0.8312 (tp40)
REVERT: B  140 ILE cc_start: 0.7986 (mm) cc_final: 0.7728 (mm)
REVERT: B  198 PHE cc_start: 0.8407 (m-10) cc_final: 0.7981 (m-10)
REVERT: B  207 GLU cc_start: 0.8164 (tt0) cc_final: 0.7488 (tm-30)
REVERT: B  267 MET cc_start: 0.8394 (mmt) cc_final: 0.8040 (mmt)
REVERT: B  299 MET cc_start: 0.8783 (ppp) cc_final: 0.8501 (ppp)
REVERT: B  469 LEU cc_start: 0.9043 (tp) cc_final: 0.8780 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 191
  average time/residue: 0.0791
  time to fit residues: 23.3698
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  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 62 optimal weight:   10.0000
   chunk 68 optimal weight:    1.9990
   chunk 106 optimal weight:    7.9990
   chunk 43 optimal weight:    7.9990
   chunk 71 optimal weight:    3.9990
   chunk 73 optimal weight:    9.9990
   chunk 67 optimal weight:   10.0000
   chunk 64 optimal weight:    0.0470
   chunk 54 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 129 optimal weight:    2.9990
   overall best weight:    2.6086

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

Flipped N/Q/H residues before XYZ refinement:
A 363 ASN
** A 365 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 = 0.3476 r_free = 0.3476 target = 0.087806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.068239 restraints weight = 40417.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.070229 restraints weight = 21736.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.071533 restraints weight = 14196.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.072358 restraints weight = 10633.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.072851 restraints weight = 8826.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.1665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10694  Z= 0.163
  Angle     :  0.609   8.552  14540  Z= 0.311
  Chirality :  0.043   0.160   1728
  Planarity :  0.004   0.031   1814
  Dihedral  :  4.355  26.526   1450
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.72 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.09 (0.24), residues: 1348
  helix:  1.21 (0.19), residues: 830
  sheet:  0.36 (0.89), residues: 32
  loop : -2.08 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 399 
 TYR   0.021   0.001   TYR A 340 
 PHE   0.014   0.001   PHE A 191 
 TRP   0.006   0.001   TRP A 472 
 HIS   0.004   0.001   HIS B 704 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (10694)
  covalent geometry    : angle       0.60917 (14540)
  hydrogen bonds       : bond        0.03670 (  612)
  hydrogen bonds       : angle       4.05074 ( 1800)

*********************** 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
  188 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  207 GLU cc_start: 0.8251 (tt0) cc_final: 0.7771 (tm-30)
REVERT: A  226 LEU cc_start: 0.9394 (mt) cc_final: 0.9183 (mt)
REVERT: A  267 MET cc_start: 0.8373 (mmt) cc_final: 0.8004 (mmt)
REVERT: A  299 MET cc_start: 0.8810 (ppp) cc_final: 0.8503 (ppp)
REVERT: A  469 LEU cc_start: 0.9127 (tp) cc_final: 0.8867 (tp)
REVERT: B  198 PHE cc_start: 0.8366 (m-10) cc_final: 0.8126 (m-10)
REVERT: B  207 GLU cc_start: 0.8210 (tt0) cc_final: 0.7591 (tm-30)
REVERT: B  236 ARG cc_start: 0.8195 (tmm160) cc_final: 0.7841 (tmm160)
REVERT: B  267 MET cc_start: 0.8356 (mmt) cc_final: 0.7983 (mmt)
REVERT: B  299 MET cc_start: 0.8834 (ppp) cc_final: 0.8533 (ppp)
REVERT: B  420 MET cc_start: 0.8855 (tmm) cc_final: 0.8511 (ptp)
REVERT: B  469 LEU cc_start: 0.9099 (tp) cc_final: 0.8841 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 188
  average time/residue: 0.0928
  time to fit residues: 25.9845
Evaluate side-chains
  151 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 99 optimal weight:    8.9990
   chunk 58 optimal weight:    8.9990
   chunk 79 optimal weight:    8.9990
   chunk 27 optimal weight:    0.4980
   chunk 25 optimal weight:    0.8980
   chunk 132 optimal weight:    5.9990
   chunk 92 optimal weight:    0.9990
   chunk 129 optimal weight:    7.9990
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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**
** 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 = 0.3513 r_free = 0.3513 target = 0.090131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.070606 restraints weight = 39411.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.072681 restraints weight = 21001.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.074032 restraints weight = 13606.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.074884 restraints weight = 10101.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.075362 restraints weight = 8354.013|
|-----------------------------------------------------------------------------|
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  10694  Z= 0.114
  Angle     :  0.607   8.664  14540  Z= 0.305
  Chirality :  0.043   0.179   1728
  Planarity :  0.004   0.033   1814
  Dihedral  :  4.315  28.242   1450
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.42 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.24), residues: 1348
  helix:  1.32 (0.19), residues: 830
  sheet:  0.79 (0.88), residues: 32
  loop : -2.00 (0.29), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 236 
 TYR   0.044   0.001   TYR A 123 
 PHE   0.012   0.001   PHE A 198 
 TRP   0.005   0.001   TRP A 472 
 HIS   0.002   0.001   HIS A 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (10694)
  covalent geometry    : angle       0.60698 (14540)
  hydrogen bonds       : bond        0.03465 (  612)
  hydrogen bonds       : angle       3.89299 ( 1800)

*********************** 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
  196 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 GLN cc_start: 0.9353 (tt0) cc_final: 0.8733 (tt0)
REVERT: A  101 PHE cc_start: 0.8165 (m-80) cc_final: 0.7641 (m-80)
REVERT: A  198 PHE cc_start: 0.8107 (m-10) cc_final: 0.7863 (m-10)
REVERT: A  207 GLU cc_start: 0.8087 (tt0) cc_final: 0.7646 (tm-30)
REVERT: A  267 MET cc_start: 0.8336 (mmt) cc_final: 0.7946 (mmt)
REVERT: A  299 MET cc_start: 0.8877 (ppp) cc_final: 0.8546 (ppp)
REVERT: A  420 MET cc_start: 0.8806 (tmm) cc_final: 0.8497 (ptp)
REVERT: B  198 PHE cc_start: 0.8321 (m-10) cc_final: 0.8040 (m-10)
REVERT: B  207 GLU cc_start: 0.8133 (tt0) cc_final: 0.7545 (tm-30)
REVERT: B  266 LEU cc_start: 0.8606 (pp) cc_final: 0.8402 (pp)
REVERT: B  267 MET cc_start: 0.8370 (mmt) cc_final: 0.8006 (mmt)
REVERT: B  299 MET cc_start: 0.8855 (ppp) cc_final: 0.8555 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 196
  average time/residue: 0.0904
  time to fit residues: 26.4130
Evaluate side-chains
  151 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 81 optimal weight:    8.9990
   chunk 107 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0000
   chunk 112 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9990
   chunk 106 optimal weight:    8.9990
   chunk 6 optimal weight:    5.9990
   chunk 15 optimal weight:    0.0870
   chunk 38 optimal weight:   10.0000
   overall best weight:    1.2168

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN
** A 365 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 = 0.3509 r_free = 0.3509 target = 0.090004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.070664 restraints weight = 39941.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.072736 restraints weight = 21203.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.074028 restraints weight = 13663.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.074862 restraints weight = 10220.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.075285 restraints weight = 8439.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10694  Z= 0.117
  Angle     :  0.580   7.895  14540  Z= 0.293
  Chirality :  0.042   0.140   1728
  Planarity :  0.004   0.032   1814
  Dihedral  :  4.279  27.303   1450
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.12 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.24), residues: 1348
  helix:  1.31 (0.19), residues: 832
  sheet:  1.00 (0.85), residues: 32
  loop : -1.90 (0.30), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 236 
 TYR   0.035   0.001   TYR A 123 
 PHE   0.012   0.001   PHE B 566 
 TRP   0.004   0.001   TRP A 472 
 HIS   0.002   0.001   HIS A 704 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (10694)
  covalent geometry    : angle       0.57975 (14540)
  hydrogen bonds       : bond        0.03331 (  612)
  hydrogen bonds       : angle       3.84346 ( 1800)

*********************** 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
  186 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.9012 (mmm) cc_final: 0.8594 (tpp)
REVERT: A  198 PHE cc_start: 0.8151 (m-10) cc_final: 0.7874 (m-10)
REVERT: A  207 GLU cc_start: 0.8117 (tt0) cc_final: 0.7631 (tm-30)
REVERT: A  266 LEU cc_start: 0.8604 (pp) cc_final: 0.8398 (pp)
REVERT: A  267 MET cc_start: 0.8385 (mmt) cc_final: 0.7977 (mmt)
REVERT: A  299 MET cc_start: 0.8905 (ppp) cc_final: 0.8584 (ppp)
REVERT: A  469 LEU cc_start: 0.9080 (tp) cc_final: 0.8876 (tp)
REVERT: B   94 GLN cc_start: 0.8368 (mm-40) cc_final: 0.8093 (tp40)
REVERT: B  198 PHE cc_start: 0.8335 (m-10) cc_final: 0.8087 (m-10)
REVERT: B  207 GLU cc_start: 0.8121 (tt0) cc_final: 0.7523 (tm-30)
REVERT: B  267 MET cc_start: 0.8404 (mmt) cc_final: 0.7997 (mmt)
REVERT: B  299 MET cc_start: 0.8892 (ppp) cc_final: 0.8583 (ppp)
REVERT: B  420 MET cc_start: 0.8796 (tmm) cc_final: 0.8499 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 186
  average time/residue: 0.0868
  time to fit residues: 24.3581
Evaluate side-chains
  152 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 12 optimal weight:    0.0170
   chunk 77 optimal weight:   10.0000
   chunk 124 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 39 optimal weight:    9.9990
   chunk 28 optimal weight:    5.9990
   chunk 107 optimal weight:    0.8980
   chunk 93 optimal weight:    6.9990
   chunk 119 optimal weight:    3.9990
   chunk 99 optimal weight:    4.9990
   chunk 25 optimal weight:   10.0000
   overall best weight:    1.7422

-------------------------------------------------------------------------------
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**
** 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 = 0.3504 r_free = 0.3504 target = 0.089603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.070470 restraints weight = 39282.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.072481 restraints weight = 20894.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.073759 restraints weight = 13504.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.074588 restraints weight = 10099.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.075070 restraints weight = 8327.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.2210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10694  Z= 0.128
  Angle     :  0.596   8.711  14540  Z= 0.300
  Chirality :  0.042   0.180   1728
  Planarity :  0.004   0.060   1814
  Dihedral  :  4.234  26.921   1450
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.27 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.24), residues: 1348
  helix:  1.35 (0.19), residues: 834
  sheet:  1.05 (0.83), residues: 32
  loop : -1.88 (0.30), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 399 
 TYR   0.032   0.001   TYR A 123 
 PHE   0.007   0.001   PHE B 391 
 TRP   0.004   0.001   TRP A 472 
 HIS   0.002   0.001   HIS B 704 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (10694)
  covalent geometry    : angle       0.59598 (14540)
  hydrogen bonds       : bond        0.03315 (  612)
  hydrogen bonds       : angle       3.86436 ( 1800)

*********************** 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
  181 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.9030 (mmm) cc_final: 0.8643 (tpp)
REVERT: A  198 PHE cc_start: 0.8094 (m-10) cc_final: 0.7797 (m-10)
REVERT: A  207 GLU cc_start: 0.8100 (tt0) cc_final: 0.7654 (tm-30)
REVERT: A  267 MET cc_start: 0.8327 (mmt) cc_final: 0.7944 (mmt)
REVERT: A  299 MET cc_start: 0.8877 (ppp) cc_final: 0.8566 (ppp)
REVERT: A  382 ASN cc_start: 0.8916 (t0) cc_final: 0.8606 (t0)
REVERT: A  669 ASP cc_start: 0.8262 (m-30) cc_final: 0.8061 (m-30)
REVERT: B  198 PHE cc_start: 0.8257 (m-10) cc_final: 0.7997 (m-10)
REVERT: B  207 GLU cc_start: 0.8111 (tt0) cc_final: 0.7524 (tm-30)
REVERT: B  266 LEU cc_start: 0.8583 (pp) cc_final: 0.8375 (pp)
REVERT: B  267 MET cc_start: 0.8419 (mmt) cc_final: 0.8000 (mmt)
REVERT: B  299 MET cc_start: 0.8900 (ppp) cc_final: 0.8596 (ppp)
REVERT: B  382 ASN cc_start: 0.8952 (t0) cc_final: 0.8672 (t0)
REVERT: B  420 MET cc_start: 0.8837 (tmm) cc_final: 0.8494 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 181
  average time/residue: 0.0832
  time to fit residues: 23.0231
Evaluate side-chains
  156 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 120 optimal weight:    4.9990
   chunk 17 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 7 optimal weight:    5.9990
   chunk 129 optimal weight:    8.9990
   chunk 56 optimal weight:    5.9990
   chunk 26 optimal weight:    8.9990
   chunk 66 optimal weight:    4.9990
   chunk 114 optimal weight:    7.9990
   chunk 25 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    2.7786

-------------------------------------------------------------------------------
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**
** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  29 GLN
B 363 ASN
** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.088202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.069076 restraints weight = 40350.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.070944 restraints weight = 21950.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.072187 restraints weight = 14439.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.072944 restraints weight = 10913.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.073310 restraints weight = 9145.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.2175

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= 0.168
  Angle     :  0.632   9.078  14540  Z= 0.318
  Chirality :  0.044   0.243   1728
  Planarity :  0.004   0.038   1814
  Dihedral  :  4.298  25.969   1450
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.42 %
    Favored  : 92.43 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.24), residues: 1348
  helix:  1.37 (0.19), residues: 830
  sheet:  0.89 (0.82), residues: 32
  loop : -1.87 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 236 
 TYR   0.030   0.002   TYR A 123 
 PHE   0.013   0.001   PHE B  64 
 TRP   0.004   0.001   TRP A 472 
 HIS   0.004   0.001   HIS B 704 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (10694)
  covalent geometry    : angle       0.63173 (14540)
  hydrogen bonds       : bond        0.03561 (  612)
  hydrogen bonds       : angle       3.97770 ( 1800)

*********************** 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
  186 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.9055 (mmm) cc_final: 0.8732 (tpp)
REVERT: A  198 PHE cc_start: 0.8064 (m-10) cc_final: 0.7764 (m-10)
REVERT: A  207 GLU cc_start: 0.8055 (tt0) cc_final: 0.7681 (tm-30)
REVERT: A  267 MET cc_start: 0.8281 (mmt) cc_final: 0.7889 (mmt)
REVERT: A  299 MET cc_start: 0.8930 (ppp) cc_final: 0.8596 (ppp)
REVERT: A  378 LEU cc_start: 0.9406 (tp) cc_final: 0.9030 (tp)
REVERT: A  382 ASN cc_start: 0.8879 (t0) cc_final: 0.8607 (t0)
REVERT: A  469 LEU cc_start: 0.9140 (tp) cc_final: 0.8875 (tp)
REVERT: B  198 PHE cc_start: 0.8114 (m-10) cc_final: 0.7849 (m-10)
REVERT: B  207 GLU cc_start: 0.8107 (tt0) cc_final: 0.7506 (tm-30)
REVERT: B  266 LEU cc_start: 0.8588 (pp) cc_final: 0.8373 (pp)
REVERT: B  267 MET cc_start: 0.8302 (mmt) cc_final: 0.7926 (mmt)
REVERT: B  299 MET cc_start: 0.8922 (ppp) cc_final: 0.8611 (ppp)
REVERT: B  378 LEU cc_start: 0.9404 (tp) cc_final: 0.9023 (tp)
REVERT: B  382 ASN cc_start: 0.8924 (t0) cc_final: 0.8642 (t0)
REVERT: B  469 LEU cc_start: 0.9138 (tp) cc_final: 0.8892 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 186
  average time/residue: 0.0832
  time to fit residues: 23.5335
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  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 56 optimal weight:    7.9990
   chunk 129 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 42 optimal weight:    8.9990
   chunk 18 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 84 optimal weight:    0.0770
   chunk 30 optimal weight:   10.0000
   chunk 17 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.7140

-------------------------------------------------------------------------------
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**
** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  29 GLN
B  59 ASN
** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.090265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.071104 restraints weight = 39404.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.073120 restraints weight = 20864.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.074396 restraints weight = 13458.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.075197 restraints weight = 10064.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.075692 restraints weight = 8328.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.2413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10694  Z= 0.113
  Angle     :  0.605   8.498  14540  Z= 0.303
  Chirality :  0.043   0.230   1728
  Planarity :  0.004   0.035   1814
  Dihedral  :  4.297  27.728   1450
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.24), residues: 1348
  helix:  1.43 (0.19), residues: 830
  sheet:  1.34 (0.83), residues: 32
  loop : -1.85 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 236 
 TYR   0.028   0.001   TYR A 123 
 PHE   0.015   0.001   PHE B 566 
 TRP   0.003   0.000   TRP A 472 
 HIS   0.002   0.001   HIS B 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 (10694)
  covalent geometry    : angle       0.60473 (14540)
  hydrogen bonds       : bond        0.03301 (  612)
  hydrogen bonds       : angle       3.82395 ( 1800)

*********************** 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
  188 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.506 
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: 0.9013 (mmm) cc_final: 0.8686 (tpp)
REVERT: A  198 PHE cc_start: 0.8087 (m-10) cc_final: 0.7761 (m-10)
REVERT: A  207 GLU cc_start: 0.7992 (tt0) cc_final: 0.7575 (tm-30)
REVERT: A  266 LEU cc_start: 0.8616 (pp) cc_final: 0.8415 (pp)
REVERT: A  267 MET cc_start: 0.8286 (mmt) cc_final: 0.7870 (mmt)
REVERT: A  299 MET cc_start: 0.8869 (ppp) cc_final: 0.8559 (ppp)
REVERT: A  378 LEU cc_start: 0.9384 (tp) cc_final: 0.8941 (tp)
REVERT: A  382 ASN cc_start: 0.8927 (t0) cc_final: 0.8681 (t0)
REVERT: A  469 LEU cc_start: 0.9054 (tp) cc_final: 0.8852 (tp)
REVERT: A  508 TYR cc_start: 0.8573 (m-80) cc_final: 0.8334 (m-80)
REVERT: B  207 GLU cc_start: 0.8009 (tt0) cc_final: 0.7385 (tm-30)
REVERT: B  267 MET cc_start: 0.8323 (mmt) cc_final: 0.7925 (mmt)
REVERT: B  299 MET cc_start: 0.8891 (ppp) cc_final: 0.8563 (ppp)
REVERT: B  382 ASN cc_start: 0.8941 (t0) cc_final: 0.8668 (t0)
REVERT: B  420 MET cc_start: 0.8873 (tmm) cc_final: 0.8525 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 188
  average time/residue: 0.0834
  time to fit residues: 24.1685
Evaluate side-chains
  166 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 67 optimal weight:    6.9990
   chunk 133 optimal weight:    0.9980
   chunk 124 optimal weight:    3.9990
   chunk 117 optimal weight:    2.9990
   chunk 82 optimal weight:    0.1980
   chunk 63 optimal weight:   10.0000
   chunk 2 optimal weight:   20.0000
   chunk 13 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 21 optimal weight:    7.9990
   overall best weight:    1.3984

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.090005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.070710 restraints weight = 39354.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.072714 restraints weight = 20992.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.074013 restraints weight = 13608.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.074801 restraints weight = 10159.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.075134 restraints weight = 8431.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.2478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10694  Z= 0.121
  Angle     :  0.598   7.681  14540  Z= 0.300
  Chirality :  0.043   0.241   1728
  Planarity :  0.004   0.032   1814
  Dihedral  :  4.265  26.921   1450
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.46 (0.24), residues: 1348
  helix:  1.38 (0.19), residues: 832
  sheet:  1.40 (0.83), residues: 32
  loop : -1.74 (0.30), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 236 
 TYR   0.027   0.001   TYR A 123 
 PHE   0.016   0.001   PHE A  23 
 TRP   0.004   0.001   TRP A 472 
 HIS   0.002   0.001   HIS B 704 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (10694)
  covalent geometry    : angle       0.59834 (14540)
  hydrogen bonds       : bond        0.03275 (  612)
  hydrogen bonds       : angle       3.82698 ( 1800)

********************** 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  : 0.408 
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: 0.9029 (mmm) cc_final: 0.8693 (tpp)
REVERT: A  186 THR cc_start: 0.9359 (m) cc_final: 0.9102 (p)
REVERT: A  198 PHE cc_start: 0.8102 (m-10) cc_final: 0.7811 (m-10)
REVERT: A  207 GLU cc_start: 0.8063 (tt0) cc_final: 0.7604 (tm-30)
REVERT: A  266 LEU cc_start: 0.8626 (pp) cc_final: 0.8333 (pp)
REVERT: A  267 MET cc_start: 0.8294 (mmt) cc_final: 0.7880 (mmt)
REVERT: A  299 MET cc_start: 0.8878 (ppp) cc_final: 0.8571 (ppp)
REVERT: A  378 LEU cc_start: 0.9362 (tp) cc_final: 0.8936 (tp)
REVERT: A  382 ASN cc_start: 0.8904 (t0) cc_final: 0.8538 (t0)
REVERT: A  508 TYR cc_start: 0.8600 (m-80) cc_final: 0.8377 (m-80)
REVERT: B  207 GLU cc_start: 0.8089 (tt0) cc_final: 0.7412 (tm-30)
REVERT: B  266 LEU cc_start: 0.8588 (pp) cc_final: 0.8386 (pp)
REVERT: B  267 MET cc_start: 0.8319 (mmt) cc_final: 0.7927 (mmt)
REVERT: B  299 MET cc_start: 0.8871 (ppp) cc_final: 0.8564 (ppp)
REVERT: B  382 ASN cc_start: 0.8916 (t0) cc_final: 0.8660 (t0)
REVERT: B  420 MET cc_start: 0.8893 (tmm) cc_final: 0.8517 (ptp)
REVERT: B  686 ASP cc_start: 0.8747 (m-30) cc_final: 0.8454 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 186
  average time/residue: 0.0793
  time to fit residues: 22.9363
Evaluate side-chains
  159 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 72 optimal weight:    6.9990
   chunk 117 optimal weight:    2.9990
   chunk 2 optimal weight:   20.0000
   chunk 85 optimal weight:   10.0000
   chunk 94 optimal weight:    5.9990
   chunk 87 optimal weight:    0.8980
   chunk 82 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 131 optimal weight:    0.3980
   chunk 97 optimal weight:    7.9990
   chunk 1 optimal weight:    0.0470
   overall best weight:    0.6080

-------------------------------------------------------------------------------
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
** 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 = 0.3535 r_free = 0.3535 target = 0.091419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.072089 restraints weight = 39048.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.074117 restraints weight = 20923.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.075451 restraints weight = 13566.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.076265 restraints weight = 10086.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.076716 restraints weight = 8332.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.2617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  10694  Z= 0.111
  Angle     :  0.605   8.839  14540  Z= 0.300
  Chirality :  0.043   0.226   1728
  Planarity :  0.004   0.033   1814
  Dihedral  :  4.250  28.918   1450
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.51 (0.24), residues: 1348
  helix:  1.44 (0.19), residues: 830
  sheet:  1.61 (0.83), residues: 32
  loop : -1.76 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 236 
 TYR   0.029   0.001   TYR A 114 
 PHE   0.014   0.001   PHE B 191 
 TRP   0.003   0.001   TRP A 472 
 HIS   0.002   0.000   HIS B 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 (10694)
  covalent geometry    : angle       0.60540 (14540)
  hydrogen bonds       : bond        0.03100 (  612)
  hydrogen bonds       : angle       3.80779 ( 1800)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1610.79 seconds
wall clock time: 28 minutes 46.48 seconds (1726.48 seconds total)