Starting phenix.real_space_refine
on Mon May 12 14:40:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wvu_37869/05_2025/8wvu_37869.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wvu_37869/05_2025/8wvu_37869.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wvu_37869/05_2025/8wvu_37869.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wvu_37869/05_2025/8wvu_37869.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wvu_37869/05_2025/8wvu_37869.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wvu_37869/05_2025/8wvu_37869.cif"
  }
  resolution = 3.61
  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=   0.001 sd=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2063 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    4783      2.51       5
     N    1238      2.21       5
     O    1356      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7427
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5714
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 733, 5714
          Classifications: {'peptide': 733}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 37, 'TRANS': 695}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 771
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 771
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 7, 'TRANS': 94}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 942
          Classifications: {'peptide': 137}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 10, 'TRANS': 126}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 134
          Unresolved non-hydrogen angles: 165
          Unresolved non-hydrogen dihedrals: 126
          Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 93
  Time building chain proxies: 4.79, per 1000 atoms: 0.64
  Number of scatterers: 7427
  At special positions: 0
  Unit cell: (75.65, 85.85, 160.65, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      50     16.00
     O    1356      8.00
     N    1238      7.00
     C    4783      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  29 " - pdb=" SG  CYS A  35 " distance=2.12
    Simple disulfide: pdb=" SG  CYS A  33 " - pdb=" SG  CYS A  43 " distance=2.07
    Simple disulfide: pdb=" SG  CYS A 339 " - pdb=" SG  CYS A 364 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 470 " - pdb=" SG  CYS A 522 " distance=1.67
    Simple disulfide: pdb=" SG  CYS A 471 " - pdb=" SG  CYS A 532 " distance=2.21
    Simple disulfide: pdb=" SG  CYS A 618 " - pdb=" SG  CYS A 693 " distance=2.14
    Simple disulfide: pdb=" SG  CYS B  40 " - pdb=" SG  CYS B  47 " distance=2.30
    Simple disulfide: pdb=" SG  CYS B  44 " - pdb=" SG  CYS B  53 " distance=1.94
    Simple disulfide: pdb=" SG  CYS B  56 " - pdb=" SG  CYS B  75 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  79 " - pdb=" SG  CYS B  94 " distance=1.91
    Simple disulfide: pdb=" SG  CYS B  97 " - pdb=" SG  CYS B 105 " distance=2.10
    Simple disulfide: pdb=" SG  CYS B 102 " - pdb=" SG  CYS B 111 " distance=1.88
    Simple disulfide: pdb=" SG  CYS B 114 " - pdb=" SG  CYS B 125 " distance=2.12
    Simple disulfide: pdb=" SG  CYS B 129 " - pdb=" SG  CYS B 142 " distance=2.05
    Simple disulfide: pdb=" SG  CYS C  91 " - pdb=" SG  CYS C 119 " distance=2.38

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.75
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1834

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 12 sheets defined
      29.2% alpha, 7.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 123 through 128
      removed outlier: 4.264A  pdb=" N   GLY A 127 " --> pdb=" O   ALA A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 174
    Processing helix  chain 'A' and resid 242 through 247
      removed outlier: 3.836A  pdb=" N   LYS A 245 " --> pdb=" O   GLN A 242 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ALA A 246 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU A 247 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 242 through 247'
    Processing helix  chain 'A' and resid 337 through 342
      removed outlier: 4.272A  pdb=" N   GLN A 342 " --> pdb=" O   LEU A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 472
      removed outlier: 3.559A  pdb=" N   GLN A 469 " --> pdb=" O   TYR A 466 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   CYS A 471 " --> pdb=" O   TYR A 468 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   ALA A 472 " --> pdb=" O   GLN A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 564
      removed outlier: 3.946A  pdb=" N   ARG A 542 " --> pdb=" O   SER A 538 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   LEU A 543 " --> pdb=" O   TRP A 539 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   PHE A 554 " --> pdb=" O   LEU A 550 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   LEU A 557 " --> pdb=" O   LEU A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 601
      removed outlier: 3.589A  pdb=" N   SER A 601 " --> pdb=" O   LEU A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 614
    Processing helix  chain 'A' and resid 617 through 646
    Processing helix  chain 'A' and resid 661 through 683
      removed outlier: 3.608A  pdb=" N   LEU A 671 " --> pdb=" O   LEU A 667 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ALA A 673 " --> pdb=" O   ALA A 669 " (cutoff:3.500A)
      Proline residue:  A 680  - end of helix
    Processing helix  chain 'A' and resid 703 through 731
      removed outlier: 4.175A  pdb=" N   THR A 707 " --> pdb=" O   SER A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 741 through 759
      removed outlier: 4.366A  pdb=" N   MET A 745 " --> pdb=" O   SER A 741 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 760 through 768
      removed outlier: 3.618A  pdb=" N   PHE A 768 " --> pdb=" O   ALA A 764 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 768 through 773
      removed outlier: 3.673A  pdb=" N   ILE A 772 " --> pdb=" O   PHE A 768 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 778 through 790
      removed outlier: 3.581A  pdb=" N   MET A 782 " --> pdb=" O   SER A 778 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 791 through 804
      removed outlier: 3.726A  pdb=" N   CYS A 795 " --> pdb=" O   PRO A 791 " (cutoff:3.500A)
      Proline residue:  A 798  - end of helix
      removed outlier: 3.665A  pdb=" N   TYR A 801 " --> pdb=" O   ASN A 797 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 805 through 818
      removed outlier: 3.719A  pdb=" N   LYS A 809 " --> pdb=" O   ASN A 805 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   TRP A 812 " --> pdb=" O   PHE A 808 " (cutoff:3.500A)
      removed outlier: 5.459A  pdb=" N   LYS A 813 " --> pdb=" O   LYS A 809 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   LEU A 814 " --> pdb=" O   GLU A 810 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LEU A 815 " --> pdb=" O   ASP A 811 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ARG A 817 " --> pdb=" O   LYS A 813 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 90
      removed outlier: 3.519A  pdb=" N   LEU C  90 " --> pdb=" O   PRO C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 121 through 132
      removed outlier: 3.779A  pdb=" N   GLU C 131 " --> pdb=" O   ARG C 127 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ARG C 132 " --> pdb=" O   MET C 128 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 144 through 150
      removed outlier: 3.658A  pdb=" N   ALA C 148 " --> pdb=" O   ASP C 144 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 168 through 178
    Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42
      removed outlier: 6.855A  pdb=" N   VAL A  41 " --> pdb=" O   ASP A  63 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLN A  87 " --> pdb=" O   LEU A  62 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72
    Processing sheet with id=AA3, first strand: chain 'A' and resid 157 through 159
      removed outlier: 7.232A  pdb=" N   LEU A 158 " --> pdb=" O   THR A 183 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   LEU A 182 " --> pdb=" O   HIS A 207 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   GLY A 254 " --> pdb=" O   LEU A 230 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 192
      removed outlier: 4.211A  pdb=" N   ILE A 192 " --> pdb=" O   SER A 215 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 262 through 263
    Processing sheet with id=AA6, first strand: chain 'A' and resid 302 through 303
      removed outlier: 3.841A  pdb=" N   LEU A 324 " --> pdb=" O   THR A 347 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   LEU A 348 " --> pdb=" O   SER A 371 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   LEU A 394 " --> pdb=" O   ASP A 419 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   LEU A 439 " --> pdb=" O   SER A 463 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 44 through 46
      removed outlier: 6.624A  pdb=" N   LYS B  55 " --> pdb=" O   GLU B  45 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 64 through 66
    Processing sheet with id=AA9, first strand: chain 'B' and resid 83 through 84
    Processing sheet with id=AB1, first strand: chain 'B' and resid 102 through 104
      removed outlier: 6.879A  pdb=" N   LYS B 113 " --> pdb=" O   GLU B 103 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 119 through 121
    Processing sheet with id=AB3, first strand: chain 'C' and resid 81 through 84
      removed outlier: 7.169A  pdb=" N   PHE C 103 " --> pdb=" O   SER C 135 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   VAL C 137 " --> pdb=" O   PHE C 103 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   SER C 105 " --> pdb=" O   VAL C 137 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   PHE C 139 " --> pdb=" O   SER C 105 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   VAL C 107 " --> pdb=" O   PHE C 139 " (cutoff:3.500A)
      removed outlier: 9.470A  pdb=" N   VAL C 162 " --> pdb=" O   SER C 135 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   VAL C 137 " --> pdb=" O   VAL C 162 " (cutoff:3.500A)

    198 hydrogen bonds defined for protein.
    573 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.93

  Time building geometry restraints manager: 2.06 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1298
        1.31 -     1.44: 1844
        1.44 -     1.56: 4386
        1.56 -     1.69: 0
        1.69 -     1.82: 63
  Bond restraints: 7591
  Sorted by residual:
  bond pdb=" C   ARG C 117 "
       pdb=" N   PRO C 118 "
    ideal  model  delta    sigma   weight residual
    1.330  1.534 -0.204 1.22e-02 6.72e+03 2.79e+02
  bond pdb=" C   ALA B  86 "
       pdb=" N   ARG B  87 "
    ideal  model  delta    sigma   weight residual
    1.330  1.543 -0.213 1.31e-02 5.83e+03 2.65e+02
  bond pdb=" C   PRO C 112 "
       pdb=" N   ARG C 113 "
    ideal  model  delta    sigma   weight residual
    1.334  1.540 -0.205 1.33e-02 5.65e+03 2.39e+02
  bond pdb=" C   LEU A 694 "
       pdb=" N   PRO A 695 "
    ideal  model  delta    sigma   weight residual
    1.336  1.486 -0.151 1.25e-02 6.40e+03 1.45e+02
  bond pdb=" C   HIS C  86 "
       pdb=" N   PRO C  87 "
    ideal  model  delta    sigma   weight residual
    1.335  1.495 -0.160 1.36e-02 5.41e+03 1.38e+02
  ... (remaining 7586 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.03: 10207
        5.03 -    10.07: 94
       10.07 -    15.10: 15
       15.10 -    20.13: 0
       20.13 -    25.16: 4
  Bond angle restraints: 10320
  Sorted by residual:
  angle pdb=" C   ILE C  51 "
        pdb=" N   PRO C  52 "
        pdb=" CA  PRO C  52 "
      ideal   model   delta    sigma   weight residual
     119.92  145.08  -25.16 1.07e+00 8.73e-01 5.53e+02
  angle pdb=" O   ILE C  51 "
        pdb=" C   ILE C  51 "
        pdb=" N   PRO C  52 "
      ideal   model   delta    sigma   weight residual
     121.10   96.64   24.46 1.14e+00 7.69e-01 4.60e+02
  angle pdb=" CA  ILE C  51 "
        pdb=" C   ILE C  51 "
        pdb=" N   PRO C  52 "
      ideal   model   delta    sigma   weight residual
     118.88  142.68  -23.80 1.54e+00 4.22e-01 2.39e+02
  angle pdb=" O   LYS C  81 "
        pdb=" C   LYS C  81 "
        pdb=" N   LEU C  82 "
      ideal   model   delta    sigma   weight residual
     122.96  110.40   12.56 1.13e+00 7.83e-01 1.23e+02
  angle pdb=" O   GLY C  80 "
        pdb=" C   GLY C  80 "
        pdb=" N   LYS C  81 "
      ideal   model   delta    sigma   weight residual
     123.55  111.31   12.24 1.19e+00 7.06e-01 1.06e+02
  ... (remaining 10315 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.34: 4313
       12.34 -    24.69: 203
       24.69 -    37.03: 52
       37.03 -    49.37: 15
       49.37 -    61.71: 10
  Dihedral angle restraints: 4593
    sinusoidal: 1779
      harmonic: 2814
  Sorted by residual:
  dihedral pdb=" C   ARG A 460 "
           pdb=" N   ARG A 460 "
           pdb=" CA  ARG A 460 "
           pdb=" CB  ARG A 460 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.88   12.28     0      2.50e+00 1.60e-01 2.41e+01
  dihedral pdb=" N   SER A 461 "
           pdb=" C   SER A 461 "
           pdb=" CA  SER A 461 "
           pdb=" CB  SER A 461 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  111.76   11.04     0      2.50e+00 1.60e-01 1.95e+01
  dihedral pdb=" C   THR C  58 "
           pdb=" N   THR C  58 "
           pdb=" CA  THR C  58 "
           pdb=" CB  THR C  58 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -111.39  -10.61     0      2.50e+00 1.60e-01 1.80e+01
  ... (remaining 4590 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1028
       0.073 -    0.146: 146
       0.146 -    0.219: 35
       0.219 -    0.292: 3
       0.292 -    0.365: 4
  Chirality restraints: 1216
  Sorted by residual:
  chirality pdb=" CA  LEU C 163 "
            pdb=" N   LEU C 163 "
            pdb=" C   LEU C 163 "
            pdb=" CB  LEU C 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.88   -0.36 2.00e-01 2.50e+01 3.32e+00
  chirality pdb=" CA  ARG A 460 "
            pdb=" N   ARG A 460 "
            pdb=" C   ARG A 460 "
            pdb=" CB  ARG A 460 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.08e+00
  chirality pdb=" CA  THR C  58 "
            pdb=" N   THR C  58 "
            pdb=" C   THR C  58 "
            pdb=" CB  THR C  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.84   -0.31 2.00e-01 2.50e+01 2.47e+00
  ... (remaining 1213 not shown)

  Planarity restraints: 1315
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 184 "    0.024 2.00e-02 2.50e+03   4.85e-02 2.35e+01
        pdb=" C   VAL C 184 "   -0.084 2.00e-02 2.50e+03
        pdb=" O   VAL C 184 "    0.032 2.00e-02 2.50e+03
        pdb=" N   ARG C 185 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C  50 "   -0.023 2.00e-02 2.50e+03   4.44e-02 1.97e+01
        pdb=" C   VAL C  50 "    0.077 2.00e-02 2.50e+03
        pdb=" O   VAL C  50 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   ILE C  51 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY C  80 "   -0.022 2.00e-02 2.50e+03   3.96e-02 1.57e+01
        pdb=" C   GLY C  80 "    0.069 2.00e-02 2.50e+03
        pdb=" O   GLY C  80 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   LYS C  81 "   -0.023 2.00e-02 2.50e+03
  ... (remaining 1312 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 74
        2.57 -     3.15: 6112
        3.15 -     3.74: 10735
        3.74 -     4.32: 14342
        4.32 -     4.90: 23687
  Nonbonded interactions: 54950
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN B  51 "
            pdb=" CD  PRO C  87 "
     model   vdw
     1.989 3.520
  nonbonded pdb=" NH2 ARG B  66 "
            pdb=" CD1 LEU C  99 "
     model   vdw
     2.019 3.540
  nonbonded pdb=" O   VAL C  50 "
            pdb=" O   GLY C  59 "
     model   vdw
     2.132 3.040
  nonbonded pdb=" ND1 HIS B 108 "
            pdb=" OD1 ASN B 109 "
     model   vdw
     2.153 3.120
  nonbonded pdb=" OH  TYR A 468 "
            pdb=" OE2 GLU A 613 "
     model   vdw
     2.193 3.040
  ... (remaining 54945 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     19.880
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6076
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      :  0.014   0.361   7606  Z= 0.937
  Angle     :  1.348  25.163  10350  Z= 0.966
  Chirality :  0.059   0.365   1216
  Planarity :  0.006   0.063   1315
  Dihedral  :  8.443  61.713   2714
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 17.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  :  5.11 %
    Favored  : 92.21 %
  Cbeta Deviations :  0.33 %
  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: -1.23 (0.28), residues: 956
  helix:  0.71 (0.36), residues: 238
  sheet: -2.09 (0.50), residues: 134
  loop : -1.17 (0.26), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 812 
 HIS   0.002   0.000   HIS C  86 
 PHE   0.007   0.001   PHE C 139 
 TYR   0.008   0.001   TYR A 687 
 ARG   0.001   0.000   ARG A  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.26464 (  198)
  hydrogen bonds       : angle       6.48426 (  573)
  SS BOND              : bond        0.17132 (   15)
  SS BOND              : angle       5.22421 (   30)
  covalent geometry    : bond        0.01150 ( 7591)
  covalent geometry    : angle       1.31974 (10320)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 268
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 ILE cc_start: 0.8460 (mt) cc_final: 0.8217 (mt)
REVERT: A  178 THR cc_start: 0.7354 (p) cc_final: 0.6865 (p)
REVERT: A  228 GLU cc_start: 0.6483 (mt-10) cc_final: 0.6275 (mt-10)
REVERT: A  265 ASP cc_start: 0.6958 (m-30) cc_final: 0.6516 (m-30)
REVERT: A  309 VAL cc_start: 0.7898 (t) cc_final: 0.7639 (p)
REVERT: A  373 GLN cc_start: 0.7545 (mt0) cc_final: 0.7005 (mt0)
REVERT: A  379 GLN cc_start: 0.7974 (pt0) cc_final: 0.7638 (pm20)
REVERT: A  402 HIS cc_start: 0.6791 (t70) cc_final: 0.6458 (t70)
REVERT: A  582 VAL cc_start: 0.7540 (t) cc_final: 0.7327 (p)
REVERT: A  587 MET cc_start: 0.7613 (tpp) cc_final: 0.7342 (tpp)
REVERT: A  589 ILE cc_start: 0.7470 (mm) cc_final: 0.7175 (tt)
REVERT: A  667 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7638 (tp)
REVERT: A  799 VAL cc_start: 0.8431 (m) cc_final: 0.8223 (p)
REVERT: B  113 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7551 (tmtm)
REVERT: C  163 LEU cc_start: 0.7639 (mt) cc_final: 0.7406 (mt)
  outliers start: 22
  outliers final: 5
  residues processed: 281
  average time/residue: 0.1751
  time to fit residues: 66.1163
Evaluate side-chains
  237 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 230
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  816 LYS
Chi-restraints excluded: chain B residue  113 LYS
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain C residue  167 ASN
Chi-restraints excluded: chain C residue  172 LEU
Chi-restraints excluded: chain C residue  176 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    0.7980
   chunk 72 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 75 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 87 optimal weight:    1.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 113 GLN
A 140 HIS
A 154 GLN
A 210 ASN
A 218 GLN
A 282 ASN
A 310 GLN
A 320 HIS
A 354 ASN
A 375 ASN
A 417 ASN
** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 740 ASN
** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  67 ASN
B  71 GLN
C  62 ASN
C 167 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.143482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.118574 restraints weight = 11805.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.122377 restraints weight = 6071.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.124889 restraints weight = 3748.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7163
moved from start:          0.3103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7606  Z= 0.198
  Angle     :  0.696   7.247  10350  Z= 0.349
  Chirality :  0.047   0.157   1216
  Planarity :  0.004   0.043   1315
  Dihedral  :  5.433  43.993   1027
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 13.63 %
    Favored  : 83.33 %
  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: -1.17 (0.27), residues: 956
  helix:  1.05 (0.35), residues: 234
  sheet: -2.17 (0.47), residues: 127
  loop : -1.24 (0.25), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 159 
 HIS   0.012   0.001   HIS C  86 
 PHE   0.021   0.002   PHE A 768 
 TYR   0.015   0.002   TYR B  83 
 ARG   0.006   0.001   ARG A  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07104 (  198)
  hydrogen bonds       : angle       5.14798 (  573)
  SS BOND              : bond        0.00370 (   15)
  SS BOND              : angle       1.25747 (   30)
  covalent geometry    : bond        0.00446 ( 7591)
  covalent geometry    : angle       0.69329 (10320)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 235
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 GLN cc_start: 0.8093 (tm-30) cc_final: 0.7830 (tm-30)
REVERT: A   85 GLU cc_start: 0.6346 (tt0) cc_final: 0.6127 (tt0)
REVERT: A  113 GLN cc_start: 0.7465 (tt0) cc_final: 0.7239 (tt0)
REVERT: A  178 THR cc_start: 0.8079 (p) cc_final: 0.7819 (p)
REVERT: A  308 MET cc_start: 0.7332 (mpp) cc_final: 0.7101 (mpp)
REVERT: A  309 VAL cc_start: 0.8518 (t) cc_final: 0.8267 (p)
REVERT: A  468 TYR cc_start: 0.8356 (m-80) cc_final: 0.8145 (m-80)
REVERT: A  547 PHE cc_start: 0.7268 (t80) cc_final: 0.7067 (t80)
REVERT: A  587 MET cc_start: 0.7835 (tpp) cc_final: 0.7311 (tpp)
REVERT: A  595 THR cc_start: 0.7588 (t) cc_final: 0.6199 (p)
REVERT: A  613 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6677 (mt-10)
REVERT: A  630 GLU cc_start: 0.7061 (mm-30) cc_final: 0.6589 (mm-30)
REVERT: A  667 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7789 (tp)
REVERT: A  682 PHE cc_start: 0.7146 (t80) cc_final: 0.6907 (t80)
REVERT: A  745 MET cc_start: 0.6314 (tpp) cc_final: 0.6050 (tpp)
REVERT: B  113 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7231 (tmtm)
  outliers start: 25
  outliers final: 12
  residues processed: 250
  average time/residue: 0.1787
  time to fit residues: 60.6053
Evaluate side-chains
  244 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 230
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain A residue  725 TYR
Chi-restraints excluded: chain A residue  740 ASN
Chi-restraints excluded: chain A residue  802 VAL
Chi-restraints excluded: chain A residue  816 LYS
Chi-restraints excluded: chain B residue   40 CYS
Chi-restraints excluded: chain B residue   62 ILE
Chi-restraints excluded: chain B residue  113 LYS
Chi-restraints excluded: chain C residue   97 ASP
Chi-restraints excluded: chain C residue  172 LEU
Chi-restraints excluded: chain C residue  176 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 92 optimal weight:    4.9990
   chunk 69 optimal weight:    0.5980
   chunk 90 optimal weight:    4.9990
   chunk 1 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0970
   chunk 54 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0670
   chunk 83 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.7118

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

Flipped N/Q/H residues before XYZ refinement:
** B  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.148013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.122523 restraints weight = 11947.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.126557 restraints weight = 6063.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.129168 restraints weight = 3685.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7157
moved from start:          0.3660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7606  Z= 0.144
  Angle     :  0.603   5.579  10350  Z= 0.302
  Chirality :  0.044   0.147   1216
  Planarity :  0.004   0.050   1315
  Dihedral  :  4.818  43.260   1023
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 17.40 %
    Favored  : 79.68 %
  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: -0.98 (0.27), residues: 956
  helix:  1.34 (0.35), residues: 234
  sheet: -1.97 (0.45), residues: 139
  loop : -1.17 (0.25), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 159 
 HIS   0.005   0.001   HIS C  86 
 PHE   0.018   0.001   PHE A 768 
 TYR   0.011   0.001   TYR B  83 
 ARG   0.007   0.001   ARG A 542 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05990 (  198)
  hydrogen bonds       : angle       4.71918 (  573)
  SS BOND              : bond        0.00229 (   15)
  SS BOND              : angle       1.31252 (   30)
  covalent geometry    : bond        0.00323 ( 7591)
  covalent geometry    : angle       0.59953 (10320)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 227
  time to evaluate  : 0.763 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 GLN cc_start: 0.7476 (tt0) cc_final: 0.7218 (tt0)
REVERT: A  178 THR cc_start: 0.8032 (p) cc_final: 0.7768 (p)
REVERT: A  308 MET cc_start: 0.7291 (tpp) cc_final: 0.7037 (mpp)
REVERT: A  309 VAL cc_start: 0.8491 (t) cc_final: 0.8275 (p)
REVERT: A  468 TYR cc_start: 0.8361 (m-80) cc_final: 0.8104 (m-80)
REVERT: A  587 MET cc_start: 0.7829 (tpp) cc_final: 0.7196 (tpp)
REVERT: A  595 THR cc_start: 0.7564 (t) cc_final: 0.6240 (p)
REVERT: A  613 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6679 (mt-10)
REVERT: A  630 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6716 (mm-30)
REVERT: A  667 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7726 (tp)
REVERT: A  674 THR cc_start: 0.7785 (OUTLIER) cc_final: 0.7534 (t)
REVERT: A  706 PHE cc_start: 0.7636 (t80) cc_final: 0.7085 (t80)
REVERT: A  745 MET cc_start: 0.6146 (tpp) cc_final: 0.5889 (tpp)
REVERT: B  109 ASN cc_start: 0.7562 (m-40) cc_final: 0.7286 (m-40)
REVERT: B  113 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.7207 (tmtm)
  outliers start: 24
  outliers final: 13
  residues processed: 236
  average time/residue: 0.1714
  time to fit residues: 55.0003
Evaluate side-chains
  240 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 224
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 CYS
Chi-restraints excluded: chain A residue   53 GLU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain A residue  725 TYR
Chi-restraints excluded: chain A residue  795 CYS
Chi-restraints excluded: chain A residue  802 VAL
Chi-restraints excluded: chain A residue  816 LYS
Chi-restraints excluded: chain B residue   40 CYS
Chi-restraints excluded: chain B residue   62 ILE
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  113 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 93 optimal weight:    5.9990
   chunk 94 optimal weight:    4.9990
   chunk 92 optimal weight:    8.9990
   chunk 49 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   chunk 72 optimal weight:    0.3980
   chunk 77 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  71 GLN
A 282 ASN
** B  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  71 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.146515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.120887 restraints weight = 11935.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.124766 restraints weight = 6096.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.127430 restraints weight = 3775.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7187
moved from start:          0.4121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7606  Z= 0.157
  Angle     :  0.607   5.786  10350  Z= 0.307
  Chirality :  0.044   0.147   1216
  Planarity :  0.004   0.046   1315
  Dihedral  :  4.810  44.489   1020
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 16.67 %
    Favored  : 78.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.18 (0.27), residues: 956
  helix:  1.06 (0.35), residues: 242
  sheet: -1.96 (0.43), residues: 149
  loop : -1.29 (0.25), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 159 
 HIS   0.008   0.001   HIS A  97 
 PHE   0.024   0.002   PHE A 790 
 TYR   0.011   0.001   TYR B 119 
 ARG   0.009   0.001   ARG A  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06227 (  198)
  hydrogen bonds       : angle       4.65614 (  573)
  SS BOND              : bond        0.00218 (   15)
  SS BOND              : angle       1.33626 (   30)
  covalent geometry    : bond        0.00354 ( 7591)
  covalent geometry    : angle       0.60339 (10320)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 229
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7796 (pp30)
REVERT: A  106 GLU cc_start: 0.8142 (mp0) cc_final: 0.7793 (mp0)
REVERT: A  178 THR cc_start: 0.8003 (p) cc_final: 0.7771 (p)
REVERT: A  308 MET cc_start: 0.7320 (tpp) cc_final: 0.7023 (mpp)
REVERT: A  309 VAL cc_start: 0.8506 (t) cc_final: 0.8272 (p)
REVERT: A  468 TYR cc_start: 0.8425 (m-80) cc_final: 0.8155 (m-80)
REVERT: A  532 CYS cc_start: 0.5553 (m) cc_final: 0.5310 (m)
REVERT: A  587 MET cc_start: 0.7848 (tpp) cc_final: 0.7116 (tpp)
REVERT: A  595 THR cc_start: 0.7661 (t) cc_final: 0.6322 (p)
REVERT: A  613 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6711 (mt-10)
REVERT: A  667 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7612 (tp)
REVERT: A  674 THR cc_start: 0.7741 (OUTLIER) cc_final: 0.7516 (t)
REVERT: A  745 MET cc_start: 0.6116 (tpp) cc_final: 0.5845 (tpp)
REVERT: B  109 ASN cc_start: 0.7571 (m-40) cc_final: 0.7365 (m-40)
REVERT: B  113 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.7108 (tmtm)
REVERT: C  100 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6905 (pp20)
  outliers start: 37
  outliers final: 25
  residues processed: 246
  average time/residue: 0.1734
  time to fit residues: 57.7906
Evaluate side-chains
  247 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 217
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 CYS
Chi-restraints excluded: chain A residue   53 GLU
Chi-restraints excluded: chain A residue   71 GLN
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  393 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  539 TRP
Chi-restraints excluded: chain A residue  547 PHE
Chi-restraints excluded: chain A residue  645 LEU
Chi-restraints excluded: chain A residue  659 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain A residue  725 TYR
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  795 CYS
Chi-restraints excluded: chain A residue  802 VAL
Chi-restraints excluded: chain A residue  816 LYS
Chi-restraints excluded: chain B residue   40 CYS
Chi-restraints excluded: chain B residue   62 ILE
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  113 LYS
Chi-restraints excluded: chain C residue  100 GLU
Chi-restraints excluded: chain C residue  141 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 84 optimal weight:    0.0020
   chunk 47 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0570
   chunk 79 optimal weight:    0.5980
   chunk 83 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 95 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.4706

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

Flipped N/Q/H residues before XYZ refinement:
A  71 GLN
** B  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  71 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.143472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.118269 restraints weight = 11759.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.122149 restraints weight = 6067.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.124696 restraints weight = 3749.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.4331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7606  Z= 0.114
  Angle     :  0.567   6.211  10350  Z= 0.285
  Chirality :  0.043   0.155   1216
  Planarity :  0.004   0.045   1315
  Dihedral  :  4.551  43.948   1020
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 19.34 %
    Favored  : 77.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.27), residues: 956
  helix:  1.42 (0.35), residues: 229
  sheet: -1.92 (0.42), residues: 149
  loop : -1.17 (0.25), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 159 
 HIS   0.005   0.001   HIS A  97 
 PHE   0.024   0.001   PHE A 790 
 TYR   0.008   0.001   TYR B  83 
 ARG   0.006   0.001   ARG A 407 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05099 (  198)
  hydrogen bonds       : angle       4.42399 (  573)
  SS BOND              : bond        0.00214 (   15)
  SS BOND              : angle       1.17114 (   30)
  covalent geometry    : bond        0.00255 ( 7591)
  covalent geometry    : angle       0.56465 (10320)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 218
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7739 (pp30)
REVERT: A  106 GLU cc_start: 0.8082 (mp0) cc_final: 0.7759 (mp0)
REVERT: A  113 GLN cc_start: 0.7500 (tt0) cc_final: 0.7195 (tt0)
REVERT: A  307 SER cc_start: 0.8211 (p) cc_final: 0.7606 (p)
REVERT: A  308 MET cc_start: 0.7295 (tpp) cc_final: 0.6867 (mpp)
REVERT: A  309 VAL cc_start: 0.8464 (t) cc_final: 0.8205 (p)
REVERT: A  468 TYR cc_start: 0.8402 (m-80) cc_final: 0.8117 (m-80)
REVERT: A  532 CYS cc_start: 0.5358 (m) cc_final: 0.5113 (m)
REVERT: A  587 MET cc_start: 0.7820 (tpp) cc_final: 0.7172 (tpp)
REVERT: A  595 THR cc_start: 0.7652 (t) cc_final: 0.6300 (p)
REVERT: A  613 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6702 (mt-10)
REVERT: A  667 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7557 (tp)
REVERT: A  674 THR cc_start: 0.7709 (OUTLIER) cc_final: 0.7497 (t)
REVERT: A  745 MET cc_start: 0.5903 (tpp) cc_final: 0.5640 (tpp)
REVERT: B  113 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.7021 (tmtm)
  outliers start: 29
  outliers final: 19
  residues processed: 231
  average time/residue: 0.1798
  time to fit residues: 56.4879
Evaluate side-chains
  246 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 223
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 CYS
Chi-restraints excluded: chain A residue   53 GLU
Chi-restraints excluded: chain A residue   71 GLN
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain A residue  725 TYR
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  795 CYS
Chi-restraints excluded: chain A residue  802 VAL
Chi-restraints excluded: chain A residue  816 LYS
Chi-restraints excluded: chain B residue   40 CYS
Chi-restraints excluded: chain B residue   62 ILE
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  113 LYS
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain C residue  141 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9980
   chunk 35 optimal weight:    0.5980
   chunk 75 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   chunk 49 optimal weight:    0.0070
   chunk 72 optimal weight:    2.9990
   chunk 16 optimal weight:    0.1980
   overall best weight:    0.4798

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

Flipped N/Q/H residues before XYZ refinement:
A  71 GLN
** B  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  71 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.143257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.118073 restraints weight = 11962.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.121931 restraints weight = 6158.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.124508 restraints weight = 3806.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
moved from start:          0.4503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7606  Z= 0.116
  Angle     :  0.572   5.908  10350  Z= 0.286
  Chirality :  0.043   0.163   1216
  Planarity :  0.004   0.043   1315
  Dihedral  :  4.458  44.652   1020
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 20.19 %
    Favored  : 76.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.27), residues: 956
  helix:  1.64 (0.36), residues: 223
  sheet: -1.79 (0.43), residues: 149
  loop : -1.17 (0.25), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 159 
 HIS   0.004   0.001   HIS A  97 
 PHE   0.025   0.001   PHE A 623 
 TYR   0.011   0.001   TYR B 119 
 ARG   0.006   0.001   ARG A 392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04932 (  198)
  hydrogen bonds       : angle       4.35813 (  573)
  SS BOND              : bond        0.00210 (   15)
  SS BOND              : angle       1.29535 (   30)
  covalent geometry    : bond        0.00260 ( 7591)
  covalent geometry    : angle       0.56866 (10320)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 226
  time to evaluate  : 0.784 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 GLU cc_start: 0.8056 (mp0) cc_final: 0.7743 (mp0)
REVERT: A  113 GLN cc_start: 0.7479 (tt0) cc_final: 0.7195 (tt0)
REVERT: A  180 GLN cc_start: 0.8440 (mt0) cc_final: 0.8189 (mt0)
REVERT: A  307 SER cc_start: 0.8195 (p) cc_final: 0.7536 (p)
REVERT: A  308 MET cc_start: 0.7283 (tpp) cc_final: 0.6847 (mpp)
REVERT: A  309 VAL cc_start: 0.8447 (t) cc_final: 0.8181 (p)
REVERT: A  376 GLN cc_start: 0.7893 (mt0) cc_final: 0.7658 (mt0)
REVERT: A  468 TYR cc_start: 0.8410 (m-80) cc_final: 0.8103 (m-80)
REVERT: A  532 CYS cc_start: 0.5488 (m) cc_final: 0.5235 (m)
REVERT: A  536 LEU cc_start: 0.8687 (mt) cc_final: 0.8389 (mp)
REVERT: A  587 MET cc_start: 0.7823 (tpp) cc_final: 0.7062 (tpp)
REVERT: A  595 THR cc_start: 0.7648 (t) cc_final: 0.6321 (p)
REVERT: A  613 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6717 (mt-10)
REVERT: A  667 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7498 (tp)
REVERT: A  745 MET cc_start: 0.5882 (tpp) cc_final: 0.5621 (tpp)
REVERT: B  113 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.6973 (tmtm)
  outliers start: 29
  outliers final: 22
  residues processed: 238
  average time/residue: 0.1786
  time to fit residues: 57.4735
Evaluate side-chains
  246 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 222
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 CYS
Chi-restraints excluded: chain A residue   53 GLU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  379 GLN
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  539 TRP
Chi-restraints excluded: chain A residue  547 PHE
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain A residue  725 TYR
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  795 CYS
Chi-restraints excluded: chain A residue  802 VAL
Chi-restraints excluded: chain A residue  816 LYS
Chi-restraints excluded: chain B residue   40 CYS
Chi-restraints excluded: chain B residue   62 ILE
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  113 LYS
Chi-restraints excluded: chain C residue  141 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 85 optimal weight:    0.7980
   chunk 87 optimal weight:    2.9990
   chunk 46 optimal weight:    0.4980
   chunk 21 optimal weight:    0.0270
   chunk 50 optimal weight:    0.2980
   chunk 1 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0980
   chunk 79 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   chunk 92 optimal weight:    0.8980
   overall best weight:    0.3438

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

Flipped N/Q/H residues before XYZ refinement:
A 154 GLN
A 405 HIS
A 438 GLN
** B  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  71 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.144252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.118543 restraints weight = 11898.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.122456 restraints weight = 6144.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.125060 restraints weight = 3804.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7137
moved from start:          0.4671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7606  Z= 0.105
  Angle     :  0.571   6.091  10350  Z= 0.284
  Chirality :  0.042   0.181   1216
  Planarity :  0.004   0.041   1315
  Dihedral  :  4.369  45.012   1020
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 21.05 %
    Favored  : 75.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.28), residues: 956
  helix:  1.81 (0.36), residues: 223
  sheet: -1.69 (0.43), residues: 149
  loop : -1.10 (0.26), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 159 
 HIS   0.004   0.001   HIS A  97 
 PHE   0.021   0.001   PHE A 790 
 TYR   0.010   0.001   TYR B 119 
 ARG   0.012   0.001   ARG A 460 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04352 (  198)
  hydrogen bonds       : angle       4.20807 (  573)
  SS BOND              : bond        0.00162 (   15)
  SS BOND              : angle       1.44394 (   30)
  covalent geometry    : bond        0.00236 ( 7591)
  covalent geometry    : angle       0.56617 (10320)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 222
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 GLU cc_start: 0.8039 (mp0) cc_final: 0.7749 (mp0)
REVERT: A  113 GLN cc_start: 0.7475 (tt0) cc_final: 0.7183 (tt0)
REVERT: A  180 GLN cc_start: 0.8446 (mt0) cc_final: 0.8190 (mt0)
REVERT: A  307 SER cc_start: 0.8231 (p) cc_final: 0.7493 (p)
REVERT: A  308 MET cc_start: 0.7232 (tpp) cc_final: 0.6740 (mpp)
REVERT: A  309 VAL cc_start: 0.8433 (t) cc_final: 0.8159 (p)
REVERT: A  376 GLN cc_start: 0.7864 (mt0) cc_final: 0.7608 (mt0)
REVERT: A  460 ARG cc_start: 0.7580 (mtm110) cc_final: 0.7313 (mtp-110)
REVERT: A  468 TYR cc_start: 0.8390 (m-80) cc_final: 0.8115 (m-80)
REVERT: A  532 CYS cc_start: 0.5421 (m) cc_final: 0.5163 (m)
REVERT: A  536 LEU cc_start: 0.8675 (mt) cc_final: 0.8377 (mp)
REVERT: A  587 MET cc_start: 0.7844 (tpp) cc_final: 0.7055 (tpp)
REVERT: A  613 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6696 (mt-10)
REVERT: A  667 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7512 (tp)
REVERT: A  745 MET cc_start: 0.5781 (tpp) cc_final: 0.5539 (tpp)
REVERT: B  113 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.6972 (tmtm)
REVERT: C   55 MET cc_start: 0.4116 (ppp) cc_final: 0.3849 (ppp)
  outliers start: 27
  outliers final: 22
  residues processed: 235
  average time/residue: 0.1684
  time to fit residues: 53.9423
Evaluate side-chains
  239 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 215
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 CYS
Chi-restraints excluded: chain A residue   53 GLU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  281 ASP
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  539 TRP
Chi-restraints excluded: chain A residue  547 PHE
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain A residue  725 TYR
Chi-restraints excluded: chain A residue  795 CYS
Chi-restraints excluded: chain A residue  802 VAL
Chi-restraints excluded: chain A residue  816 LYS
Chi-restraints excluded: chain B residue   40 CYS
Chi-restraints excluded: chain B residue   62 ILE
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  113 LYS
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  129 CYS
Chi-restraints excluded: chain C residue  141 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 18 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0000
   chunk 7 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 93 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   overall best weight:    1.1388

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

Flipped N/Q/H residues before XYZ refinement:
A  71 GLN
A 376 GLN
** B  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  71 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.144342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.118990 restraints weight = 11971.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.122839 restraints weight = 6146.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.125476 restraints weight = 3811.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.4864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   7606  Z= 0.202
  Angle     :  0.652   7.282  10350  Z= 0.332
  Chirality :  0.046   0.158   1216
  Planarity :  0.005   0.045   1315
  Dihedral  :  4.920  44.824   1020
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 21.78 %
    Favored  : 74.94 %
  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: -1.30 (0.27), residues: 956
  helix:  1.03 (0.34), residues: 250
  sheet: -2.00 (0.46), residues: 123
  loop : -1.52 (0.25), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 159 
 HIS   0.008   0.001   HIS C  86 
 PHE   0.024   0.002   PHE A 790 
 TYR   0.012   0.002   TYR B 119 
 ARG   0.010   0.001   ARG A 460 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06933 (  198)
  hydrogen bonds       : angle       4.65478 (  573)
  SS BOND              : bond        0.00633 (   15)
  SS BOND              : angle       1.68959 (   30)
  covalent geometry    : bond        0.00461 ( 7591)
  covalent geometry    : angle       0.64616 (10320)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 235
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.8293 (mmpt) cc_final: 0.7936 (mmpt)
REVERT: A  106 GLU cc_start: 0.7996 (mp0) cc_final: 0.7706 (mp0)
REVERT: A  307 SER cc_start: 0.8239 (p) cc_final: 0.7578 (p)
REVERT: A  308 MET cc_start: 0.7319 (tpp) cc_final: 0.6856 (mpp)
REVERT: A  309 VAL cc_start: 0.8499 (t) cc_final: 0.8201 (p)
REVERT: A  376 GLN cc_start: 0.7913 (mt0) cc_final: 0.7637 (mt0)
REVERT: A  468 TYR cc_start: 0.8463 (m-80) cc_final: 0.8192 (m-80)
REVERT: A  532 CYS cc_start: 0.5579 (m) cc_final: 0.5351 (m)
REVERT: A  534 TYR cc_start: 0.7866 (m-10) cc_final: 0.7599 (m-10)
REVERT: A  587 MET cc_start: 0.7832 (tpp) cc_final: 0.7056 (tpp)
REVERT: A  613 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6830 (mt-10)
REVERT: A  667 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7483 (tp)
REVERT: A  745 MET cc_start: 0.6049 (tpp) cc_final: 0.5810 (tpp)
REVERT: B   62 ILE cc_start: 0.8770 (tt) cc_final: 0.8496 (pt)
REVERT: B  109 ASN cc_start: 0.7616 (m-40) cc_final: 0.7352 (m-40)
REVERT: B  113 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7053 (tmtm)
  outliers start: 27
  outliers final: 19
  residues processed: 248
  average time/residue: 0.1846
  time to fit residues: 62.3293
Evaluate side-chains
  251 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 230
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 CYS
Chi-restraints excluded: chain A residue   53 GLU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  539 TRP
Chi-restraints excluded: chain A residue  547 PHE
Chi-restraints excluded: chain A residue  589 ILE
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain A residue  725 TYR
Chi-restraints excluded: chain A residue  795 CYS
Chi-restraints excluded: chain A residue  802 VAL
Chi-restraints excluded: chain A residue  816 LYS
Chi-restraints excluded: chain B residue   40 CYS
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  113 LYS
Chi-restraints excluded: chain C residue  141 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 88 optimal weight:    5.9990
   chunk 52 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0270
   chunk 57 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 92 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9990
   chunk 78 optimal weight:    2.9990
   overall best weight:    0.7640

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

Flipped N/Q/H residues before XYZ refinement:
A  71 GLN
** B  51 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 = 0.3810 r_free = 0.3810 target = 0.141431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.116333 restraints weight = 12056.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.120099 restraints weight = 6275.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.122695 restraints weight = 3914.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7189
moved from start:          0.4965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7606  Z= 0.151
  Angle     :  0.621   7.751  10350  Z= 0.312
  Chirality :  0.045   0.170   1216
  Planarity :  0.005   0.075   1315
  Dihedral  :  4.737  44.744   1020
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 22.87 %
    Favored  : 74.09 %
  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: -1.19 (0.27), residues: 956
  helix:  1.06 (0.35), residues: 245
  sheet: -1.75 (0.43), residues: 147
  loop : -1.39 (0.26), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 159 
 HIS   0.006   0.001   HIS C  86 
 PHE   0.026   0.002   PHE A 790 
 TYR   0.010   0.001   TYR B 119 
 ARG   0.012   0.001   ARG A 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05730 (  198)
  hydrogen bonds       : angle       4.45628 (  573)
  SS BOND              : bond        0.00298 (   15)
  SS BOND              : angle       1.58996 (   30)
  covalent geometry    : bond        0.00345 ( 7591)
  covalent geometry    : angle       0.61626 (10320)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 227
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.8278 (mmpt) cc_final: 0.7941 (mmpt)
REVERT: A  180 GLN cc_start: 0.8472 (mt0) cc_final: 0.8240 (mt0)
REVERT: A  307 SER cc_start: 0.8211 (p) cc_final: 0.7408 (p)
REVERT: A  308 MET cc_start: 0.7256 (tpp) cc_final: 0.6741 (mpp)
REVERT: A  309 VAL cc_start: 0.8465 (t) cc_final: 0.8165 (p)
REVERT: A  376 GLN cc_start: 0.7790 (mt0) cc_final: 0.7512 (mt0)
REVERT: A  468 TYR cc_start: 0.8450 (m-80) cc_final: 0.8189 (m-80)
REVERT: A  532 CYS cc_start: 0.5454 (m) cc_final: 0.5211 (m)
REVERT: A  534 TYR cc_start: 0.7831 (m-10) cc_final: 0.7580 (m-10)
REVERT: A  587 MET cc_start: 0.7823 (tpp) cc_final: 0.7039 (tpp)
REVERT: A  613 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6822 (mt-10)
REVERT: A  667 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7395 (tp)
REVERT: A  745 MET cc_start: 0.5883 (tpp) cc_final: 0.5619 (tpp)
REVERT: B   62 ILE cc_start: 0.8767 (tt) cc_final: 0.8448 (pt)
REVERT: B  109 ASN cc_start: 0.7579 (m-40) cc_final: 0.7324 (m-40)
REVERT: B  113 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.7001 (tmtm)
REVERT: C   55 MET cc_start: 0.4161 (ppp) cc_final: 0.3892 (ppp)
  outliers start: 25
  outliers final: 18
  residues processed: 237
  average time/residue: 0.1625
  time to fit residues: 52.8349
Evaluate side-chains
  250 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 230
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 CYS
Chi-restraints excluded: chain A residue   53 GLU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  539 TRP
Chi-restraints excluded: chain A residue  547 PHE
Chi-restraints excluded: chain A residue  659 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain A residue  725 TYR
Chi-restraints excluded: chain A residue  795 CYS
Chi-restraints excluded: chain A residue  802 VAL
Chi-restraints excluded: chain A residue  816 LYS
Chi-restraints excluded: chain B residue   40 CYS
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  113 LYS
Chi-restraints excluded: chain C residue  141 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 82 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9990
   chunk 88 optimal weight:    0.8980
   chunk 48 optimal weight:    0.6980
   chunk 81 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 94 optimal weight:    0.9990
   chunk 64 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** B  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.145647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.120089 restraints weight = 12040.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.124049 restraints weight = 6202.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.126644 restraints weight = 3814.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7205
moved from start:          0.5101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7606  Z= 0.167
  Angle     :  0.641   8.128  10350  Z= 0.323
  Chirality :  0.045   0.178   1216
  Planarity :  0.005   0.070   1315
  Dihedral  :  4.824  44.792   1020
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 23.24 %
    Favored  : 74.09 %
  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: -1.28 (0.27), residues: 956
  helix:  0.98 (0.35), residues: 245
  sheet: -1.82 (0.43), residues: 148
  loop : -1.44 (0.26), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 159 
 HIS   0.006   0.001   HIS C  86 
 PHE   0.026   0.002   PHE A 790 
 TYR   0.011   0.001   TYR B 119 
 ARG   0.011   0.001   ARG A 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06170 (  198)
  hydrogen bonds       : angle       4.50666 (  573)
  SS BOND              : bond        0.00336 (   15)
  SS BOND              : angle       1.65365 (   30)
  covalent geometry    : bond        0.00383 ( 7591)
  covalent geometry    : angle       0.63603 (10320)

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

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

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1912 Ramachandran restraints generated.
    956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 231
  time to evaluate  : 0.819 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 ASP cc_start: 0.7556 (t0) cc_final: 0.7309 (m-30)
REVERT: A   63 ASP cc_start: 0.6862 (p0) cc_final: 0.6643 (p0)
REVERT: A  106 GLU cc_start: 0.7961 (mp0) cc_final: 0.7654 (mp0)
REVERT: A  180 GLN cc_start: 0.8488 (mt0) cc_final: 0.8256 (mt0)
REVERT: A  307 SER cc_start: 0.8198 (p) cc_final: 0.7375 (p)
REVERT: A  308 MET cc_start: 0.7296 (tpp) cc_final: 0.6777 (mpp)
REVERT: A  309 VAL cc_start: 0.8464 (t) cc_final: 0.8149 (p)
REVERT: A  376 GLN cc_start: 0.7853 (mt0) cc_final: 0.7384 (mt0)
REVERT: A  468 TYR cc_start: 0.8444 (m-80) cc_final: 0.8177 (m-80)
REVERT: A  532 CYS cc_start: 0.5469 (m) cc_final: 0.5222 (m)
REVERT: A  534 TYR cc_start: 0.7854 (m-10) cc_final: 0.7584 (m-10)
REVERT: A  587 MET cc_start: 0.7815 (tpp) cc_final: 0.7045 (tpp)
REVERT: A  613 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6797 (mt-10)
REVERT: A  667 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7400 (tp)
REVERT: A  745 MET cc_start: 0.5973 (tpp) cc_final: 0.5725 (tpp)
REVERT: B   62 ILE cc_start: 0.8763 (tt) cc_final: 0.8430 (pt)
REVERT: B  113 LYS cc_start: 0.7410 (OUTLIER) cc_final: 0.6984 (tmtm)
REVERT: C   55 MET cc_start: 0.4136 (ppp) cc_final: 0.3874 (ppp)
  outliers start: 22
  outliers final: 18
  residues processed: 240
  average time/residue: 0.1659
  time to fit residues: 55.0556
Evaluate side-chains
  257 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 237
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 CYS
Chi-restraints excluded: chain A residue   53 GLU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  150 GLU
Chi-restraints excluded: chain A residue  539 TRP
Chi-restraints excluded: chain A residue  547 PHE
Chi-restraints excluded: chain A residue  659 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain A residue  721 MET
Chi-restraints excluded: chain A residue  725 TYR
Chi-restraints excluded: chain A residue  795 CYS
Chi-restraints excluded: chain A residue  802 VAL
Chi-restraints excluded: chain A residue  816 LYS
Chi-restraints excluded: chain B residue   40 CYS
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  113 LYS
Chi-restraints excluded: chain C residue  141 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 91 optimal weight:    7.9990
   chunk 68 optimal weight:    5.9990
   chunk 67 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 94 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
** B  51 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 = 0.3793 r_free = 0.3793 target = 0.142167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.116879 restraints weight = 11955.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.120679 restraints weight = 6240.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.123238 restraints weight = 3875.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7260
moved from start:          0.5266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058   7606  Z= 0.263
  Angle     :  0.717   8.429  10350  Z= 0.367
  Chirality :  0.049   0.174   1216
  Planarity :  0.006   0.072   1315
  Dihedral  :  5.380  44.935   1020
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.16 %
    Favored  : 91.84 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 23.11 %
    Favored  : 73.84 %
  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: -1.71 (0.26), residues: 956
  helix:  0.57 (0.34), residues: 251
  sheet: -2.11 (0.43), residues: 131
  loop : -1.74 (0.24), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 159 
 HIS   0.010   0.001   HIS C  86 
 PHE   0.033   0.002   PHE A 790 
 TYR   0.014   0.002   TYR A 280 
 ARG   0.010   0.001   ARG A 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07925 (  198)
  hydrogen bonds       : angle       4.89994 (  573)
  SS BOND              : bond        0.00485 (   15)
  SS BOND              : angle       1.88654 (   30)
  covalent geometry    : bond        0.00601 ( 7591)
  covalent geometry    : angle       0.71105 (10320)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2762.20 seconds
wall clock time: 48 minutes 49.47 seconds (2929.47 seconds total)