Starting phenix.real_space_refine
on Mon Jun  9 03:34:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fmv_50571/06_2025/9fmv_50571.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fmv_50571/06_2025/9fmv_50571.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.43
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fmv_50571/06_2025/9fmv_50571.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fmv_50571/06_2025/9fmv_50571.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fmv_50571/06_2025/9fmv_50571.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fmv_50571/06_2025/9fmv_50571.cif"
  }
  resolution = 3.43
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.012
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      43      5.16       5
     C    6848      2.51       5
     N    1740      2.21       5
     O    1641      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 10272
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 6272
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 777, 6272
          Classifications: {'peptide': 777}
          Link IDs: {'PTRANS': 39, 'TRANS': 737}
          Chain breaks: 6
    Chain: "B"
      Number of atoms: 1205
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1205
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 6, 'TRANS': 137}
    Chain: "C"
      Number of atoms: 1205
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1205
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 6, 'TRANS': 137}
    Chain: "D"
      Number of atoms: 1205
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1205
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 6, 'TRANS': 137}
    Chain: "E"
      Number of atoms: 385
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 385
          Classifications: {'peptide': 45}
          Link IDs: {'PTRANS': 1, 'TRANS': 43}
  Time building chain proxies: 8.27, per 1000 atoms: 0.81
  Number of scatterers: 10272
  At special positions: 0
  Unit cell: (107.392, 119.138, 153.537, 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      43     16.00
     O    1641      8.00
     N    1740      7.00
     C    6848      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.47
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2356

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 2 sheets defined
      73.9% alpha, 5.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.92
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 9
      removed outlier: 3.650A  pdb=" N   THR A   5 " --> pdb=" O   MET A   1 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 10 through 27
      removed outlier: 3.803A  pdb=" N   HIS A  27 " --> pdb=" O   ASP A  23 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 30 through 48
    Processing helix  chain 'A' and resid 52 through 61
      removed outlier: 3.889A  pdb=" N   GLU A  61 " --> pdb=" O   ARG A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 66
    Processing helix  chain 'A' and resid 77 through 92
    Processing helix  chain 'A' and resid 106 through 134
      Proline residue:  A 124  - end of helix
    Processing helix  chain 'A' and resid 144 through 168
    Processing helix  chain 'A' and resid 172 through 193
      removed outlier: 3.555A  pdb=" N   ARG A 192 " --> pdb=" O   LEU A 188 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   MET A 193 " --> pdb=" O   ILE A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 221
      removed outlier: 3.534A  pdb=" N   THR A 221 " --> pdb=" O   ARG A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 254
    Processing helix  chain 'A' and resid 268 through 272
    Processing helix  chain 'A' and resid 285 through 298
      removed outlier: 3.901A  pdb=" N   ASN A 291 " --> pdb=" O   ASN A 287 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   THR A 292 " --> pdb=" O   VAL A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 304
      No H-bonds generated for 'chain 'A' and resid 302 through 304'
    Processing helix  chain 'A' and resid 316 through 327
    Processing helix  chain 'A' and resid 338 through 349
      removed outlier: 3.663A  pdb=" N   LYS A 349 " --> pdb=" O   ASN A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 374
      removed outlier: 3.532A  pdb=" N   MET A 372 " --> pdb=" O   SER A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 380
    Processing helix  chain 'A' and resid 418 through 426
      removed outlier: 3.577A  pdb=" N   MET A 425 " --> pdb=" O   ASP A 421 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   TRP A 426 " --> pdb=" O   GLY A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 446
    Processing helix  chain 'A' and resid 455 through 467
    Processing helix  chain 'A' and resid 486 through 508
    Processing helix  chain 'A' and resid 517 through 531
    Processing helix  chain 'A' and resid 534 through 549
      Proline residue:  A 544  - end of helix
    Processing helix  chain 'A' and resid 558 through 582
      Proline residue:  A 568  - end of helix
    Processing helix  chain 'A' and resid 587 through 600
      removed outlier: 3.622A  pdb=" N   TYR A 600 " --> pdb=" O   VAL A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 601 through 609
      removed outlier: 3.578A  pdb=" N   LEU A 609 " --> pdb=" O   THR A 605 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 636 through 660
      removed outlier: 3.520A  pdb=" N   ILE A 640 " --> pdb=" O   SER A 636 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   LEU A 642 " --> pdb=" O   PRO A 638 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   VAL A 650 " --> pdb=" O   ASN A 646 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 661 through 663
      No H-bonds generated for 'chain 'A' and resid 661 through 663'
    Processing helix  chain 'A' and resid 664 through 692
    Processing helix  chain 'A' and resid 778 through 790
    Processing helix  chain 'A' and resid 810 through 830
    Processing helix  chain 'A' and resid 831 through 850
      removed outlier: 4.626A  pdb=" N   ILE A 837 " --> pdb=" O   SER A 833 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 14 through 18
    Processing helix  chain 'B' and resid 22 through 37
      removed outlier: 4.063A  pdb=" N   PHE B  26 " --> pdb=" O   SER B  22 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   TYR B  27 " --> pdb=" O   GLY B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 56
    Processing helix  chain 'B' and resid 60 through 83
      Proline residue:  B  73  - end of helix
    Processing helix  chain 'B' and resid 87 through 101
      removed outlier: 5.047A  pdb=" N   SER B  96 " --> pdb=" O   MET B  92 " (cutoff:3.500A)
      removed outlier: 5.544A  pdb=" N   GLN B  97 " --> pdb=" O   SER B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 114
    Processing helix  chain 'B' and resid 115 through 133
    Processing helix  chain 'B' and resid 137 through 155
      removed outlier: 4.113A  pdb=" N   PHE B 141 " --> pdb=" O   ARG B 137 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 13 through 18
    Processing helix  chain 'C' and resid 23 through 37
      removed outlier: 3.702A  pdb=" N   TYR C  27 " --> pdb=" O   GLY C  23 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 43 through 56
    Processing helix  chain 'C' and resid 60 through 83
      Proline residue:  C  73  - end of helix
    Processing helix  chain 'C' and resid 87 through 101
      removed outlier: 5.280A  pdb=" N   SER C  96 " --> pdb=" O   MET C  92 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   GLN C  97 " --> pdb=" O   SER C  93 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   PHE C 101 " --> pdb=" O   GLN C  97 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 114
    Processing helix  chain 'C' and resid 115 through 133
    Processing helix  chain 'C' and resid 137 through 155
    Processing helix  chain 'D' and resid 22 through 38
      removed outlier: 4.216A  pdb=" N   PHE D  26 " --> pdb=" O   SER D  22 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   TYR D  27 " --> pdb=" O   GLY D  23 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 43 through 55
    Processing helix  chain 'D' and resid 60 through 83
      Proline residue:  D  73  - end of helix
    Processing helix  chain 'D' and resid 87 through 101
      removed outlier: 4.354A  pdb=" N   SER D  96 " --> pdb=" O   MET D  92 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   GLN D  97 " --> pdb=" O   SER D  93 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 102 through 114
    Processing helix  chain 'D' and resid 115 through 136
    Processing helix  chain 'D' and resid 138 through 155
    Processing helix  chain 'E' and resid 27 through 36
      removed outlier: 3.946A  pdb=" N   LEU E  31 " --> pdb=" O   TRP E  27 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   TRP E  32 " --> pdb=" O   PHE E  28 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 38 through 70
    Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 331
      removed outlier: 8.798A  pdb=" N   LYS A 329 " --> pdb=" O   LEU A 306 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   ILE A 308 " --> pdb=" O   LYS A 329 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   ILE A 331 " --> pdb=" O   ILE A 308 " (cutoff:3.500A)
      removed outlier: 5.949A  pdb=" N   ILE A 310 " --> pdb=" O   ILE A 331 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   VAL A 275 " --> pdb=" O   ASN A 307 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   TRP A 309 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   ILE A 277 " --> pdb=" O   TRP A 309 " (cutoff:3.500A)
      removed outlier: 7.530A  pdb=" N   LEU A 311 " --> pdb=" O   ILE A 277 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   VAL A 279 " --> pdb=" O   LEU A 311 " (cutoff:3.500A)
      removed outlier: 6.120A  pdb=" N   ASP A 276 " --> pdb=" O   SER A 357 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ALA A 436 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   ALA A 384 " --> pdb=" O   ARG A 439 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   ALA A 472 " --> pdb=" O   ALA A 384 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   MET A 386 " --> pdb=" O   ALA A 472 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 706 through 710
      removed outlier: 6.791A  pdb=" N   GLY A 730 " --> pdb=" O   GLN A 722 " (cutoff:3.500A)
      removed outlier: 4.760A  pdb=" N   PHE A 724 " --> pdb=" O   GLY A 728 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   GLY A 728 " --> pdb=" O   PHE A 724 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   LYS A 773 " --> pdb=" O   VAL A 762 " (cutoff:3.500A)
      removed outlier: 5.474A  pdb=" N   VAL A 762 " --> pdb=" O   LYS A 773 " (cutoff:3.500A)
      removed outlier: 5.060A  pdb=" N   LYS A 750 " --> pdb=" O   PRO A 706 " (cutoff:3.500A)

    683 hydrogen bonds defined for protein.
    2022 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.25

  Time building geometry restraints manager: 2.97 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3112
        1.34 -     1.46: 2867
        1.46 -     1.58: 4549
        1.58 -     1.70: 0
        1.70 -     1.82: 75
  Bond restraints: 10603
  Sorted by residual:
  bond pdb=" CB  PRO A 604 "
       pdb=" CG  PRO A 604 "
    ideal  model  delta    sigma   weight residual
    1.492  1.401  0.091 5.00e-02 4.00e+02 3.34e+00
  bond pdb=" CG1 ILE A 815 "
       pdb=" CD1 ILE A 815 "
    ideal  model  delta    sigma   weight residual
    1.513  1.455  0.058 3.90e-02 6.57e+02 2.20e+00
  bond pdb=" CA  PRO A 603 "
       pdb=" C   PRO A 603 "
    ideal  model  delta    sigma   weight residual
    1.517  1.530 -0.013 9.30e-03 1.16e+04 1.98e+00
  bond pdb=" CG  LEU E  52 "
       pdb=" CD2 LEU E  52 "
    ideal  model  delta    sigma   weight residual
    1.521  1.480  0.041 3.30e-02 9.18e+02 1.55e+00
  bond pdb=" C   PRO A 603 "
       pdb=" N   PRO A 604 "
    ideal  model  delta    sigma   weight residual
    1.335  1.351 -0.016 1.30e-02 5.92e+03 1.51e+00
  ... (remaining 10598 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.31: 14261
        2.31 -     4.62: 162
        4.62 -     6.93: 28
        6.93 -     9.24: 9
        9.24 -    11.55: 3
  Bond angle restraints: 14463
  Sorted by residual:
  angle pdb=" N   PRO A 603 "
        pdb=" CA  PRO A 603 "
        pdb=" C   PRO A 603 "
      ideal   model   delta    sigma   weight residual
     110.70  118.59   -7.89 1.22e+00 6.72e-01 4.18e+01
  angle pdb=" CA  PRO A 603 "
        pdb=" C   PRO A 603 "
        pdb=" N   PRO A 604 "
      ideal   model   delta    sigma   weight residual
     117.93  124.45   -6.52 1.20e+00 6.94e-01 2.95e+01
  angle pdb=" C   SER D  22 "
        pdb=" CA  SER D  22 "
        pdb=" CB  SER D  22 "
      ideal   model   delta    sigma   weight residual
     117.23  110.25    6.98 1.36e+00 5.41e-01 2.64e+01
  angle pdb=" C   SER B  22 "
        pdb=" CA  SER B  22 "
        pdb=" CB  SER B  22 "
      ideal   model   delta    sigma   weight residual
     117.23  110.41    6.82 1.36e+00 5.41e-01 2.51e+01
  angle pdb=" N   ILE A 592 "
        pdb=" CA  ILE A 592 "
        pdb=" C   ILE A 592 "
      ideal   model   delta    sigma   weight residual
     110.62  106.44    4.18 1.02e+00 9.61e-01 1.68e+01
  ... (remaining 14458 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 5317
       17.88 -    35.76: 582
       35.76 -    53.65: 117
       53.65 -    71.53: 17
       71.53 -    89.41: 7
  Dihedral angle restraints: 6040
    sinusoidal: 2398
      harmonic: 3642
  Sorted by residual:
  dihedral pdb=" CA  THR A 373 "
           pdb=" C   THR A 373 "
           pdb=" N   MET A 374 "
           pdb=" CA  MET A 374 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.77  -19.23     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  ARG A 711 "
           pdb=" C   ARG A 711 "
           pdb=" N   GLU A 712 "
           pdb=" CA  GLU A 712 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.01   18.99     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CA  PRO A 603 "
           pdb=" C   PRO A 603 "
           pdb=" N   PRO A 604 "
           pdb=" CA  PRO A 604 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.97   16.03     0      5.00e+00 4.00e-02 1.03e+01
  ... (remaining 6037 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 1448
       0.067 -    0.134: 148
       0.134 -    0.201: 9
       0.201 -    0.268: 1
       0.268 -    0.335: 2
  Chirality restraints: 1608
  Sorted by residual:
  chirality pdb=" CG  LEU D 147 "
            pdb=" CB  LEU D 147 "
            pdb=" CD1 LEU D 147 "
            pdb=" CD2 LEU D 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.25   -0.34 2.00e-01 2.50e+01 2.81e+00
  chirality pdb=" CA  PRO A 603 "
            pdb=" N   PRO A 603 "
            pdb=" C   PRO A 603 "
            pdb=" CB  PRO A 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.39    0.33 2.00e-01 2.50e+01 2.77e+00
  chirality pdb=" CB  ILE A 155 "
            pdb=" CA  ILE A 155 "
            pdb=" CG1 ILE A 155 "
            pdb=" CG2 ILE A 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.24 2.00e-01 2.50e+01 1.45e+00
  ... (remaining 1605 not shown)

  Planarity restraints: 1756
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 567 "    0.058 5.00e-02 4.00e+02   8.66e-02 1.20e+01
        pdb=" N   PRO A 568 "   -0.150 5.00e-02 4.00e+02
        pdb=" CA  PRO A 568 "    0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A 568 "    0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 263 "    0.045 5.00e-02 4.00e+02   6.78e-02 7.35e+00
        pdb=" N   PRO A 264 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO A 264 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 264 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 172 "   -0.043 5.00e-02 4.00e+02   6.47e-02 6.71e+00
        pdb=" N   PRO A 173 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO A 173 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 173 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 1753 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1001
        2.74 -     3.28: 10328
        3.28 -     3.82: 17501
        3.82 -     4.36: 18879
        4.36 -     4.90: 32868
  Nonbonded interactions: 80577
  Sorted by model distance:
  nonbonded pdb=" O   MET D  56 "
            pdb=" NH1 ARG D  67 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" O   LEU A 348 "
            pdb=" NH2 ARG A 440 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" O   LEU A 143 "
            pdb=" NH1 ARG A 148 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" OH  TYR C  27 "
            pdb=" O   GLY C  75 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" NH2 ARG A  54 "
            pdb=" OE1 GLN D  16 "
     model   vdw
     2.267 3.120
  ... (remaining 80572 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             30.810
  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:          0.420
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     27.370
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   61.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7059
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.091  10603  Z= 0.159
  Angle     :  0.645  11.549  14463  Z= 0.345
  Chirality :  0.043   0.335   1608
  Planarity :  0.006   0.087   1756
  Dihedral  : 15.229  89.412   3684
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 18.99 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.24), residues: 1232
  helix:  1.77 (0.17), residues: 853
  sheet: -0.11 (0.59), residues: 67
  loop : -0.59 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A 633 
 HIS   0.009   0.001   HIS A 569 
 PHE   0.033   0.001   PHE A 171 
 TYR   0.022   0.001   TYR D  27 
 ARG   0.009   0.001   ARG E  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14814 (  683)
  hydrogen bonds       : angle       5.77401 ( 2022)
  covalent geometry    : bond        0.00364 (10603)
  covalent geometry    : angle       0.64521 (14463)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 170
  time to evaluate  : 1.110 
Fit side-chains
REVERT: A  374 MET cc_start: 0.8637 (mmm) cc_final: 0.7876 (mmm)
REVERT: A  594 GLU cc_start: 0.7087 (mp0) cc_final: 0.6751 (mp0)
REVERT: A  603 PRO cc_start: 0.8835 (Cg_endo) cc_final: 0.8577 (Cg_exo)
  outliers start: 6
  outliers final: 2
  residues processed: 171
  average time/residue: 0.2750
  time to fit residues: 62.5763
Evaluate side-chains
  166 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 164
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  691 GLU
Chi-restraints excluded: chain D residue  147 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 103 optimal weight:    0.4980
   chunk 93 optimal weight:    0.3980
   chunk 51 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 96 optimal weight:    0.3980
   chunk 37 optimal weight:    0.9980
   chunk 58 optimal weight:    0.0980
   chunk 71 optimal weight:    0.9980
   chunk 111 optimal weight:    0.4980
   overall best weight:    0.3780

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

Flipped N/Q/H residues before XYZ refinement:
** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 142 HIS
A 371 GLN
A 569 HIS
** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.173697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.147269 restraints weight = 15233.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.3854 rms_B_bonded: 1.93
r_work: 0.3727 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3572 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7183
moved from start:          0.0895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  10603  Z= 0.165
  Angle     :  0.577   8.818  14463  Z= 0.299
  Chirality :  0.041   0.209   1608
  Planarity :  0.005   0.063   1756
  Dihedral  :  4.665  58.817   1369
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 17.14 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.24), residues: 1232
  helix:  2.03 (0.17), residues: 864
  sheet: -0.33 (0.57), residues: 68
  loop : -0.50 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 633 
 HIS   0.012   0.001   HIS A 133 
 PHE   0.013   0.001   PHE A 369 
 TYR   0.026   0.001   TYR D  27 
 ARG   0.006   0.000   ARG D  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04789 (  683)
  hydrogen bonds       : angle       4.30539 ( 2022)
  covalent geometry    : bond        0.00378 (10603)
  covalent geometry    : angle       0.57677 (14463)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 170
  time to evaluate  : 0.990 
Fit side-chains
REVERT: A    1 MET cc_start: 0.3908 (mmm) cc_final: 0.3686 (mmm)
REVERT: A  193 MET cc_start: 0.7871 (ppp) cc_final: 0.7394 (ppp)
REVERT: A  272 TRP cc_start: 0.6950 (m-10) cc_final: 0.6743 (m-10)
REVERT: A  366 THR cc_start: 0.7836 (m) cc_final: 0.7531 (t)
REVERT: A  565 PHE cc_start: 0.7879 (m-80) cc_final: 0.7666 (m-80)
REVERT: A  570 MET cc_start: 0.7742 (mpp) cc_final: 0.7411 (mtt)
REVERT: A  594 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7390 (mp0)
REVERT: A  633 TRP cc_start: 0.7207 (p-90) cc_final: 0.6823 (p-90)
REVERT: B   68 HIS cc_start: 0.1971 (OUTLIER) cc_final: 0.1393 (m90)
REVERT: C   92 MET cc_start: 0.8122 (mtt) cc_final: 0.7899 (mtm)
  outliers start: 31
  outliers final: 14
  residues processed: 183
  average time/residue: 0.2672
  time to fit residues: 65.7224
Evaluate side-chains
  176 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 161
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  686 VAL
Chi-restraints excluded: chain A residue  691 GLU
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  813 LEU
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   68 HIS
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain D residue  118 MET
Chi-restraints excluded: chain D residue  147 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 104 optimal weight:    0.0970
   chunk 56 optimal weight:    0.0970
   chunk 73 optimal weight:    0.9990
   chunk 118 optimal weight:    0.2980
   chunk 111 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 81 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 34 optimal weight:    0.3980
   overall best weight:    0.3176

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

Flipped N/Q/H residues before XYZ refinement:
** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 142 HIS
A 223 ASN
A 371 GLN
A 569 HIS
** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 825 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 = 0.4175 r_free = 0.4175 target = 0.173851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.147381 restraints weight = 15499.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.3812 rms_B_bonded: 1.95
r_work: 0.3681 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3525 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7185
moved from start:          0.1153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  10603  Z= 0.144
  Angle     :  0.554  12.326  14463  Z= 0.283
  Chirality :  0.040   0.219   1608
  Planarity :  0.005   0.062   1756
  Dihedral  :  4.628  59.185   1369
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 18.34 %
    Favored  : 79.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.95 (0.24), residues: 1232
  helix:  2.08 (0.17), residues: 865
  sheet: -0.32 (0.60), residues: 68
  loop : -0.63 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E  58 
 HIS   0.010   0.001   HIS A 133 
 PHE   0.015   0.001   PHE A 171 
 TYR   0.023   0.001   TYR D  27 
 ARG   0.010   0.000   ARG A 463 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04350 (  683)
  hydrogen bonds       : angle       4.14090 ( 2022)
  covalent geometry    : bond        0.00333 (10603)
  covalent geometry    : angle       0.55366 (14463)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 163
  time to evaluate  : 1.086 
Fit side-chains
REVERT: A    1 MET cc_start: 0.3805 (mmm) cc_final: 0.3589 (mmm)
REVERT: A  193 MET cc_start: 0.7919 (ppp) cc_final: 0.7459 (ppp)
REVERT: A  594 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7400 (mt-10)
REVERT: A  633 TRP cc_start: 0.7161 (p-90) cc_final: 0.6802 (p-90)
REVERT: A  817 LYS cc_start: 0.8060 (mttm) cc_final: 0.7757 (mtmm)
REVERT: B   68 HIS cc_start: 0.1940 (OUTLIER) cc_final: 0.1379 (m90)
  outliers start: 28
  outliers final: 16
  residues processed: 173
  average time/residue: 0.3007
  time to fit residues: 69.7356
Evaluate side-chains
  177 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 160
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  529 PHE
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  813 LEU
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   68 HIS
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain C residue  118 MET
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue  118 MET
Chi-restraints excluded: chain D residue  119 ILE
Chi-restraints excluded: chain D residue  147 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 83 optimal weight:    0.8980
   chunk 90 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 95 optimal weight:    0.0570
   chunk 46 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0870
   chunk 28 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.4876

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

Flipped N/Q/H residues before XYZ refinement:
** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 336 HIS
A 371 GLN
** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 743 GLN
** A 825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.172579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.146159 restraints weight = 15236.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.3785 rms_B_bonded: 1.93
r_work: 0.3656 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3502 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7212
moved from start:          0.1426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  10603  Z= 0.188
  Angle     :  0.581  12.991  14463  Z= 0.297
  Chirality :  0.042   0.221   1608
  Planarity :  0.005   0.061   1756
  Dihedral  :  4.485  57.642   1366
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 18.53 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.24), residues: 1232
  helix:  1.96 (0.17), residues: 865
  sheet: -0.37 (0.61), residues: 68
  loop : -0.69 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D  24 
 HIS   0.009   0.001   HIS A 133 
 PHE   0.014   0.001   PHE A 369 
 TYR   0.030   0.001   TYR D  27 
 ARG   0.009   0.001   ARG A 463 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04548 (  683)
  hydrogen bonds       : angle       4.18316 ( 2022)
  covalent geometry    : bond        0.00443 (10603)
  covalent geometry    : angle       0.58133 (14463)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 171
  time to evaluate  : 1.003 
Fit side-chains
REVERT: A    1 MET cc_start: 0.3861 (mmm) cc_final: 0.3642 (mmm)
REVERT: A  155 ILE cc_start: 0.7274 (OUTLIER) cc_final: 0.6865 (mt)
REVERT: A  193 MET cc_start: 0.7950 (ppp) cc_final: 0.7527 (ppp)
REVERT: A  594 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7377 (mt-10)
REVERT: A  703 MET cc_start: 0.5210 (ppp) cc_final: 0.5003 (ppp)
REVERT: A  817 LYS cc_start: 0.8179 (mttm) cc_final: 0.7868 (mtmm)
REVERT: B   68 HIS cc_start: 0.1842 (OUTLIER) cc_final: 0.1260 (m90)
REVERT: E   59 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7609 (ttt90)
  outliers start: 39
  outliers final: 20
  residues processed: 193
  average time/residue: 0.2925
  time to fit residues: 75.4703
Evaluate side-chains
  190 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 167
  time to evaluate  : 1.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  149 ARG
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  529 PHE
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  665 MET
Chi-restraints excluded: chain A residue  686 VAL
Chi-restraints excluded: chain A residue  691 GLU
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain B residue   68 HIS
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain C residue  118 MET
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue   85 LEU
Chi-restraints excluded: chain D residue  118 MET
Chi-restraints excluded: chain D residue  119 ILE
Chi-restraints excluded: chain D residue  147 LEU
Chi-restraints excluded: chain E residue   59 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 115 optimal weight:    0.6980
   chunk 94 optimal weight:    0.6980
   chunk 54 optimal weight:    0.6980
   chunk 66 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 56 optimal weight:    0.0570
   chunk 58 optimal weight:    0.3980
   chunk 100 optimal weight:    0.3980
   chunk 95 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.4298

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

Flipped N/Q/H residues before XYZ refinement:
** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 142 HIS
A 371 GLN
** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 761 GLN
** A 825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.172790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.146235 restraints weight = 15204.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.3799 rms_B_bonded: 1.93
r_work: 0.3670 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3515 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7213
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  10603  Z= 0.170
  Angle     :  0.573  13.821  14463  Z= 0.290
  Chirality :  0.041   0.227   1608
  Planarity :  0.005   0.062   1756
  Dihedral  :  4.467  56.866   1366
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 18.80 %
    Favored  : 77.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.24), residues: 1232
  helix:  1.98 (0.17), residues: 865
  sheet: -0.37 (0.62), residues: 68
  loop : -0.69 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 633 
 HIS   0.008   0.001   HIS A 133 
 PHE   0.013   0.001   PHE A 369 
 TYR   0.026   0.001   TYR D  27 
 ARG   0.009   0.001   ARG A 463 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04405 (  683)
  hydrogen bonds       : angle       4.11691 ( 2022)
  covalent geometry    : bond        0.00399 (10603)
  covalent geometry    : angle       0.57324 (14463)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 169
  time to evaluate  : 1.089 
Fit side-chains
REVERT: A    1 MET cc_start: 0.3880 (mmm) cc_final: 0.3669 (mmm)
REVERT: A   61 GLU cc_start: 0.7624 (mp0) cc_final: 0.7289 (mp0)
REVERT: A  155 ILE cc_start: 0.7285 (OUTLIER) cc_final: 0.6870 (mt)
REVERT: A  193 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7570 (ppp)
REVERT: A  446 ILE cc_start: 0.8610 (pt) cc_final: 0.8399 (mt)
REVERT: A  594 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7408 (mt-10)
REVERT: B   68 HIS cc_start: 0.1784 (OUTLIER) cc_final: 0.1521 (m170)
REVERT: C   92 MET cc_start: 0.8292 (mtm) cc_final: 0.8081 (mtm)
REVERT: E   59 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7565 (ttt90)
  outliers start: 43
  outliers final: 24
  residues processed: 191
  average time/residue: 0.3108
  time to fit residues: 79.6745
Evaluate side-chains
  195 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 167
  time to evaluate  : 1.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  149 ARG
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  193 MET
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  529 PHE
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  665 MET
Chi-restraints excluded: chain A residue  686 VAL
Chi-restraints excluded: chain A residue  691 GLU
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  813 LEU
Chi-restraints excluded: chain A residue  829 PHE
Chi-restraints excluded: chain B residue   56 MET
Chi-restraints excluded: chain B residue   68 HIS
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain C residue  118 MET
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  118 MET
Chi-restraints excluded: chain D residue  119 ILE
Chi-restraints excluded: chain D residue  147 LEU
Chi-restraints excluded: chain E residue   56 VAL
Chi-restraints excluded: chain E residue   59 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 55 optimal weight:    0.5980
   chunk 103 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 88 optimal weight:    0.5980
   chunk 40 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   chunk 118 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 113 optimal weight:    1.9990
   chunk 106 optimal weight:    0.2980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 223 ASN
A 371 GLN
A 569 HIS
** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 825 HIS
B 134 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.171018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.144536 restraints weight = 15223.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.3792 rms_B_bonded: 1.94
r_work: 0.3659 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3502 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7250
moved from start:          0.1852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074  10603  Z= 0.230
  Angle     :  0.636  15.551  14463  Z= 0.320
  Chirality :  0.044   0.239   1608
  Planarity :  0.005   0.063   1756
  Dihedral  :  4.610  54.831   1366
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 18.62 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.24), residues: 1232
  helix:  1.80 (0.17), residues: 861
  sheet: -0.57 (0.61), residues: 68
  loop : -0.76 (0.35), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 633 
 HIS   0.007   0.001   HIS A 133 
 PHE   0.015   0.002   PHE A 758 
 TYR   0.032   0.002   TYR D  27 
 ARG   0.015   0.001   ARG E  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04870 (  683)
  hydrogen bonds       : angle       4.27518 ( 2022)
  covalent geometry    : bond        0.00543 (10603)
  covalent geometry    : angle       0.63622 (14463)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 171
  time to evaluate  : 1.183 
Fit side-chains
REVERT: A    1 MET cc_start: 0.3954 (mmm) cc_final: 0.3721 (mmm)
REVERT: A   51 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6513 (pm20)
REVERT: A   61 GLU cc_start: 0.7654 (mp0) cc_final: 0.7314 (mp0)
REVERT: A   75 ARG cc_start: 0.7626 (tmt170) cc_final: 0.6849 (tmt-80)
REVERT: A  133 HIS cc_start: 0.6981 (OUTLIER) cc_final: 0.6528 (p90)
REVERT: A  155 ILE cc_start: 0.7425 (OUTLIER) cc_final: 0.7030 (mt)
REVERT: A  193 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7646 (ppp)
REVERT: A  463 ARG cc_start: 0.8131 (mpt-90) cc_final: 0.7893 (mtt-85)
REVERT: A  570 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7304 (mtp)
REVERT: A  594 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7409 (mt-10)
REVERT: A  821 ARG cc_start: 0.7139 (ptm-80) cc_final: 0.6793 (ttt-90)
REVERT: C   92 MET cc_start: 0.8350 (mtm) cc_final: 0.8147 (mtm)
REVERT: E   59 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7593 (ttt90)
  outliers start: 51
  outliers final: 32
  residues processed: 199
  average time/residue: 0.2942
  time to fit residues: 78.7298
Evaluate side-chains
  206 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 168
  time to evaluate  : 1.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   51 GLU
Chi-restraints excluded: chain A residue  133 HIS
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  149 ARG
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  193 MET
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  277 ILE
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  529 PHE
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  570 MET
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  665 MET
Chi-restraints excluded: chain A residue  686 VAL
Chi-restraints excluded: chain A residue  691 GLU
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  813 LEU
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain C residue  118 MET
Chi-restraints excluded: chain D residue   36 TRP
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  118 MET
Chi-restraints excluded: chain D residue  119 ILE
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain D residue  147 LEU
Chi-restraints excluded: chain E residue   56 VAL
Chi-restraints excluded: chain E residue   59 ARG
Chi-restraints excluded: chain E residue   60 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0670
   chunk 113 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0670
   chunk 10 optimal weight:    4.9990
   chunk 114 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 36 optimal weight:    0.2980
   chunk 119 optimal weight:    0.0870
   chunk 96 optimal weight:    0.2980
   overall best weight:    0.1634

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

Flipped N/Q/H residues before XYZ refinement:
** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 142 HIS
A 223 ASN
A 646 ASN
** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 134 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.174331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.147804 restraints weight = 15420.330|
|-----------------------------------------------------------------------------|
r_work (start): 0.3830 rms_B_bonded: 1.95
r_work: 0.3701 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3546 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7181
moved from start:          0.1855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  10603  Z= 0.115
  Angle     :  0.553  14.044  14463  Z= 0.277
  Chirality :  0.040   0.245   1608
  Planarity :  0.005   0.061   1756
  Dihedral  :  4.369  53.435   1366
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 20.09 %
    Favored  : 77.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.98 (0.24), residues: 1232
  helix:  2.12 (0.17), residues: 865
  sheet: -0.47 (0.59), residues: 68
  loop : -0.63 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 633 
 HIS   0.006   0.001   HIS A 133 
 PHE   0.009   0.001   PHE A 547 
 TYR   0.014   0.001   TYR C  27 
 ARG   0.014   0.000   ARG E  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03892 (  683)
  hydrogen bonds       : angle       4.00113 ( 2022)
  covalent geometry    : bond        0.00258 (10603)
  covalent geometry    : angle       0.55339 (14463)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 174
  time to evaluate  : 1.506 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 GLU cc_start: 0.7651 (mp0) cc_final: 0.7285 (mp0)
REVERT: A   75 ARG cc_start: 0.7520 (tmt170) cc_final: 0.6825 (tmt170)
REVERT: A  133 HIS cc_start: 0.6943 (OUTLIER) cc_final: 0.6509 (p90)
REVERT: A  193 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7659 (ppp)
REVERT: A  196 ARG cc_start: 0.7143 (mtt180) cc_final: 0.6931 (mtt180)
REVERT: A  594 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7374 (mt-10)
REVERT: A  633 TRP cc_start: 0.6972 (p-90) cc_final: 0.6736 (p-90)
REVERT: A  817 LYS cc_start: 0.8073 (mttm) cc_final: 0.7760 (mtmm)
  outliers start: 31
  outliers final: 18
  residues processed: 189
  average time/residue: 0.3328
  time to fit residues: 85.4980
Evaluate side-chains
  185 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 165
  time to evaluate  : 1.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue  133 HIS
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  193 MET
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  529 PHE
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  665 MET
Chi-restraints excluded: chain A residue  691 GLU
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  813 LEU
Chi-restraints excluded: chain A residue  833 SER
Chi-restraints excluded: chain B residue   56 MET
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  118 MET
Chi-restraints excluded: chain D residue  119 ILE
Chi-restraints excluded: chain D residue  147 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 104 optimal weight:    0.1980
   chunk 79 optimal weight:    0.8980
   chunk 91 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 120 optimal weight:    0.4980
   chunk 98 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 113 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0050
   chunk 77 optimal weight:    0.4980
   overall best weight:    0.4194

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

Flipped N/Q/H residues before XYZ refinement:
** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 142 HIS
** A 678 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 = 0.4165 r_free = 0.4165 target = 0.172920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.146436 restraints weight = 15393.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3791 rms_B_bonded: 1.94
r_work: 0.3662 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3506 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7215
moved from start:          0.1931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  10603  Z= 0.169
  Angle     :  0.609  15.466  14463  Z= 0.303
  Chirality :  0.041   0.236   1608
  Planarity :  0.005   0.062   1756
  Dihedral  :  4.399  51.786   1366
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 20.46 %
    Favored  : 76.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.24), residues: 1232
  helix:  1.95 (0.17), residues: 871
  sheet: -0.47 (0.60), residues: 68
  loop : -0.62 (0.37), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D  80 
 HIS   0.006   0.001   HIS A 133 
 PHE   0.016   0.001   PHE A 171 
 TYR   0.025   0.001   TYR D  27 
 ARG   0.014   0.000   ARG E  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04300 (  683)
  hydrogen bonds       : angle       4.12316 ( 2022)
  covalent geometry    : bond        0.00402 (10603)
  covalent geometry    : angle       0.60903 (14463)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 167
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6518 (pm20)
REVERT: A   61 GLU cc_start: 0.7647 (mp0) cc_final: 0.7306 (mp0)
REVERT: A   75 ARG cc_start: 0.7560 (tmt170) cc_final: 0.6766 (tmt170)
REVERT: A  133 HIS cc_start: 0.6954 (OUTLIER) cc_final: 0.6528 (p90)
REVERT: A  155 ILE cc_start: 0.7260 (OUTLIER) cc_final: 0.6834 (mt)
REVERT: A  193 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7667 (ppp)
REVERT: A  570 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7257 (mtp)
REVERT: A  594 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7470 (mt-10)
REVERT: A  633 TRP cc_start: 0.7068 (p-90) cc_final: 0.6784 (p-90)
REVERT: A  817 LYS cc_start: 0.8172 (mttm) cc_final: 0.7862 (mtmm)
  outliers start: 34
  outliers final: 20
  residues processed: 187
  average time/residue: 0.2747
  time to fit residues: 69.2809
Evaluate side-chains
  190 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 165
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   51 GLU
Chi-restraints excluded: chain A residue  133 HIS
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  193 MET
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  529 PHE
Chi-restraints excluded: chain A residue  570 MET
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  665 MET
Chi-restraints excluded: chain A residue  691 GLU
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  833 SER
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain C residue  118 MET
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  118 MET
Chi-restraints excluded: chain D residue  119 ILE
Chi-restraints excluded: chain D residue  147 LEU
Chi-restraints excluded: chain E residue   60 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9990
   chunk 114 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9980
   chunk 18 optimal weight:    0.3980
   chunk 111 optimal weight:    0.4980
   chunk 51 optimal weight:    0.0060
   chunk 5 optimal weight:    1.9990
   chunk 83 optimal weight:    0.6980
   chunk 95 optimal weight:    0.0980
   overall best weight:    0.3396

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

Flipped N/Q/H residues before XYZ refinement:
** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 142 HIS
A 223 ASN
** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.173340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.146900 restraints weight = 15366.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3802 rms_B_bonded: 1.94
r_work: 0.3672 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3518 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7204
moved from start:          0.2018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  10603  Z= 0.149
  Angle     :  0.595  15.069  14463  Z= 0.297
  Chirality :  0.041   0.242   1608
  Planarity :  0.005   0.061   1756
  Dihedral  :  4.353  48.950   1366
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 20.46 %
    Favored  : 76.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.24), residues: 1232
  helix:  1.97 (0.17), residues: 871
  sheet: -0.41 (0.60), residues: 68
  loop : -0.60 (0.37), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D  80 
 HIS   0.006   0.001   HIS A 133 
 PHE   0.017   0.001   PHE A 171 
 TYR   0.021   0.001   TYR D  27 
 ARG   0.016   0.000   ARG E  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04144 (  683)
  hydrogen bonds       : angle       4.10079 ( 2022)
  covalent geometry    : bond        0.00351 (10603)
  covalent geometry    : angle       0.59539 (14463)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 166
  time to evaluate  : 0.980 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 GLU cc_start: 0.7653 (mp0) cc_final: 0.7301 (mp0)
REVERT: A   75 ARG cc_start: 0.7506 (tmt170) cc_final: 0.6676 (tmt170)
REVERT: A  133 HIS cc_start: 0.6918 (OUTLIER) cc_final: 0.6469 (p90)
REVERT: A  155 ILE cc_start: 0.7227 (OUTLIER) cc_final: 0.6816 (mt)
REVERT: A  193 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7534 (ppp)
REVERT: A  196 ARG cc_start: 0.7234 (mtt180) cc_final: 0.7002 (mtt180)
REVERT: A  570 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7231 (mtp)
REVERT: A  594 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7449 (mt-10)
REVERT: A  633 TRP cc_start: 0.7010 (p-90) cc_final: 0.6658 (p-90)
REVERT: A  817 LYS cc_start: 0.8128 (mttm) cc_final: 0.7809 (mtmm)
REVERT: A  825 HIS cc_start: 0.8140 (t70) cc_final: 0.7792 (t70)
  outliers start: 29
  outliers final: 21
  residues processed: 181
  average time/residue: 0.2576
  time to fit residues: 62.7791
Evaluate side-chains
  190 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 165
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue  133 HIS
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  193 MET
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  529 PHE
Chi-restraints excluded: chain A residue  570 MET
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  665 MET
Chi-restraints excluded: chain A residue  691 GLU
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  813 LEU
Chi-restraints excluded: chain A residue  833 SER
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain C residue   84 TRP
Chi-restraints excluded: chain C residue  118 MET
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  118 MET
Chi-restraints excluded: chain D residue  119 ILE
Chi-restraints excluded: chain D residue  147 LEU
Chi-restraints excluded: chain E residue   56 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 120 optimal weight:    0.6980
   chunk 58 optimal weight:    0.4980
   chunk 15 optimal weight:    0.3980
   chunk 54 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9980
   chunk 103 optimal weight:    1.9990
   chunk 98 optimal weight:    0.0770
   chunk 9 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 34 optimal weight:    0.3980
   chunk 80 optimal weight:    0.0270
   overall best weight:    0.2796

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

Flipped N/Q/H residues before XYZ refinement:
** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 142 HIS
** A 678 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 = 0.4175 r_free = 0.4175 target = 0.173814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.147388 restraints weight = 15323.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.3811 rms_B_bonded: 1.94
r_work: 0.3682 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3528 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7193
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  10603  Z= 0.137
  Angle     :  0.601  15.807  14463  Z= 0.298
  Chirality :  0.041   0.240   1608
  Planarity :  0.005   0.062   1756
  Dihedral  :  4.286  45.307   1366
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 20.83 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.90 (0.24), residues: 1232
  helix:  2.01 (0.17), residues: 871
  sheet: -0.43 (0.60), residues: 68
  loop : -0.60 (0.37), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D  80 
 HIS   0.006   0.001   HIS A 133 
 PHE   0.011   0.001   PHE A 369 
 TYR   0.019   0.001   TYR C  27 
 ARG   0.016   0.000   ARG E  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04026 (  683)
  hydrogen bonds       : angle       4.06752 ( 2022)
  covalent geometry    : bond        0.00320 (10603)
  covalent geometry    : angle       0.60099 (14463)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 166
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6474 (pm20)
REVERT: A   61 GLU cc_start: 0.7652 (mp0) cc_final: 0.7287 (mp0)
REVERT: A   75 ARG cc_start: 0.7484 (tmt170) cc_final: 0.6613 (tmt170)
REVERT: A  133 HIS cc_start: 0.6899 (OUTLIER) cc_final: 0.6460 (p90)
REVERT: A  193 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7679 (ppp)
REVERT: A  196 ARG cc_start: 0.7204 (mtt180) cc_final: 0.6983 (mtt180)
REVERT: A  570 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7250 (mtp)
REVERT: A  594 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7425 (mt-10)
REVERT: A  633 TRP cc_start: 0.6986 (p-90) cc_final: 0.6581 (p-90)
REVERT: A  817 LYS cc_start: 0.8071 (mttm) cc_final: 0.7745 (mtmm)
REVERT: C   84 TRP cc_start: 0.8504 (OUTLIER) cc_final: 0.7515 (m-10)
  outliers start: 27
  outliers final: 20
  residues processed: 180
  average time/residue: 0.2710
  time to fit residues: 65.6252
Evaluate side-chains
  190 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 165
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   51 GLU
Chi-restraints excluded: chain A residue  133 HIS
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  193 MET
Chi-restraints excluded: chain A residue  201 MET
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  529 PHE
Chi-restraints excluded: chain A residue  570 MET
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  665 MET
Chi-restraints excluded: chain A residue  691 GLU
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  813 LEU
Chi-restraints excluded: chain A residue  833 SER
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain C residue   84 TRP
Chi-restraints excluded: chain C residue  118 MET
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  118 MET
Chi-restraints excluded: chain D residue  119 ILE
Chi-restraints excluded: chain D residue  147 LEU
Chi-restraints excluded: chain E residue   56 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 120 optimal weight:    0.4980
   chunk 31 optimal weight:    0.9980
   chunk 117 optimal weight:    0.5980
   chunk 17 optimal weight:    0.8980
   chunk 76 optimal weight:    0.0870
   chunk 68 optimal weight:    0.9980
   chunk 84 optimal weight:    0.7980
   chunk 83 optimal weight:    0.2980
   chunk 37 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 142 HIS
** A 678 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 = 0.4162 r_free = 0.4162 target = 0.172675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.146340 restraints weight = 15071.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3796 rms_B_bonded: 1.92
r_work: 0.3668 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3515 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7213
moved from start:          0.2116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  10603  Z= 0.175
  Angle     :  0.630  16.667  14463  Z= 0.314
  Chirality :  0.042   0.239   1608
  Planarity :  0.005   0.062   1756
  Dihedral  :  4.345  42.374   1366
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 20.92 %
    Favored  : 76.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.24), residues: 1232
  helix:  1.89 (0.17), residues: 871
  sheet: -0.50 (0.61), residues: 68
  loop : -0.65 (0.37), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D  80 
 HIS   0.024   0.002   HIS A 825 
 PHE   0.030   0.001   PHE A 171 
 TYR   0.026   0.001   TYR D  27 
 ARG   0.016   0.001   ARG E  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04363 (  683)
  hydrogen bonds       : angle       4.18305 ( 2022)
  covalent geometry    : bond        0.00417 (10603)
  covalent geometry    : angle       0.63017 (14463)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7397.84 seconds
wall clock time: 130 minutes 19.03 seconds (7819.03 seconds total)