Starting phenix.real_space_refine
on Thu Jun 12 21:26:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y5u_33625/06_2025/7y5u_33625.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y5u_33625/06_2025/7y5u_33625.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y5u_33625/06_2025/7y5u_33625.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y5u_33625/06_2025/7y5u_33625.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y5u_33625/06_2025/7y5u_33625.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y5u_33625/06_2025/7y5u_33625.cif"
  }
  resolution = 3.8
  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=   0.015
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 6842 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      38      5.16       5
     C    5599      2.51       5
     N    1553      2.21       5
     O    1675      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8865
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1256
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 176, 1256
          Classifications: {'peptide': 176}
          Incomplete info: {'truncation_to_alanine': 45}
          Link IDs: {'PTRANS': 7, 'TRANS': 168}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 190
          Unresolved non-hydrogen angles: 238
          Unresolved non-hydrogen dihedrals: 164
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 123
    Chain: "D"
      Number of atoms: 898
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 898
          Classifications: {'peptide': 110}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 4, 'TRANS': 105}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 3
    Chain: "E"
      Number of atoms: 642
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 642
          Classifications: {'peptide': 81}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
          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: "C"
      Number of atoms: 3165
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 401, 3165
          Classifications: {'peptide': 401}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 22, 'TRANS': 378}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 19
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "B"
      Number of atoms: 2904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2904
          Classifications: {'peptide': 371}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 15, 'TRANS': 355}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 16
  Time building chain proxies: 5.74, per 1000 atoms: 0.65
  Number of scatterers: 8865
  At special positions: 0
  Unit cell: (81, 98, 133, 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      38     16.00
     O    1675      8.00
     N    1553      7.00
     C    5599      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.37
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2146

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 16 sheets defined
      20.5% alpha, 25.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 491 through 500
    Processing helix  chain 'A' and resid 550 through 554
    Processing helix  chain 'A' and resid 599 through 604
    Processing helix  chain 'A' and resid 635 through 647
    Processing helix  chain 'A' and resid 652 through 674
    Processing helix  chain 'A' and resid 675 through 677
      No H-bonds generated for 'chain 'A' and resid 675 through 677'
    Processing helix  chain 'A' and resid 697 through 706
    Processing helix  chain 'D' and resid 51 through 55
    Processing helix  chain 'D' and resid 63 through 79
      removed outlier: 3.836A  pdb=" N   PHE D  67 " --> pdb=" O   ARG D  63 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 85 through 114
    Processing helix  chain 'D' and resid 120 through 132
    Processing helix  chain 'E' and resid 25 through 29
      removed outlier: 4.361A  pdb=" N   ILE E  29 " --> pdb=" O   ILE E  26 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 30 through 41
    Processing helix  chain 'E' and resid 49 through 76
      removed outlier: 4.450A  pdb=" N   GLU E  53 " --> pdb=" O   LEU E  49 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 82 through 94
    Processing helix  chain 'C' and resid 12 through 32
      Proline residue:  C  29  - end of helix
    Processing helix  chain 'C' and resid 89 through 93
      removed outlier: 3.534A  pdb=" N   PHE C  93 " --> pdb=" O   ASP C  90 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 155 through 157
      No H-bonds generated for 'chain 'C' and resid 155 through 157'
    Processing helix  chain 'C' and resid 355 through 359
    Processing helix  chain 'C' and resid 405 through 410
      removed outlier: 4.199A  pdb=" N   TYR C 409 " --> pdb=" O   ALA C 405 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ASN C 410 " --> pdb=" O   GLU C 406 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 405 through 410'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 570 through 572
      removed outlier: 6.360A  pdb=" N   LEU A 559 " --> pdb=" O   VAL C  35 " (cutoff:3.500A)
      removed outlier: 8.220A  pdb=" N   THR C  37 " --> pdb=" O   LEU A 559 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   GLN A 561 " --> pdb=" O   THR C  37 " (cutoff:3.500A)
      removed outlier: 8.815A  pdb=" N   ALA C  39 " --> pdb=" O   GLN A 561 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   ILE C 398 " --> pdb=" O   SER C 394 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 684 through 686
      removed outlier: 3.807A  pdb=" N   TYR B 340 " --> pdb=" O   ILE A 686 " (cutoff:3.500A)
      removed outlier: 7.692A  pdb=" N   ARG B 316 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 7.571A  pdb=" N   VAL B 296 " --> pdb=" O   ARG B 316 " (cutoff:3.500A)
      removed outlier: 5.158A  pdb=" N   VAL B 318 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 710 through 711
      removed outlier: 5.742A  pdb=" N   TYR B 267 " --> pdb=" O   PRO B 252 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   PHE B 269 " --> pdb=" O   LEU B 250 " (cutoff:3.500A)
      removed outlier: 5.469A  pdb=" N   LEU B 250 " --> pdb=" O   PHE B 269 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 118 through 119
      removed outlier: 3.560A  pdb=" N   ILE D 119 " --> pdb=" O   ARG E  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 47 through 54
      removed outlier: 7.632A  pdb=" N   LEU C  50 " --> pdb=" O   VAL C  67 " (cutoff:3.500A)
      removed outlier: 8.305A  pdb=" N   VAL C  67 " --> pdb=" O   LEU C  50 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   ASP C  52 " --> pdb=" O   ARG C  65 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   ARG C  65 " --> pdb=" O   ASP C  52 " (cutoff:3.500A)
      removed outlier: 7.365A  pdb=" N   ASN C  77 " --> pdb=" O   ASN C 122 " (cutoff:3.500A)
      removed outlier: 4.671A  pdb=" N   ASN C 122 " --> pdb=" O   ASN C  77 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   LEU C  79 " --> pdb=" O   LYS C 120 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   LYS C 120 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   ILE C  81 " --> pdb=" O   GLU C 118 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 130 through 133
      removed outlier: 10.266A  pdb=" N   ARG C 131 " --> pdb=" O   CYS C 138 " (cutoff:3.500A)
      removed outlier: 8.973A  pdb=" N   CYS C 138 " --> pdb=" O   ARG C 131 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   MET C 133 " --> pdb=" O   ASN C 136 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   ARG C 172 " --> pdb=" O   VAL C 217 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 182 through 185
      removed outlier: 4.105A  pdb=" N   GLY C 182 " --> pdb=" O   ALA C 196 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 230 through 235
    Processing sheet with id=AA9, first strand: chain 'C' and resid 276 through 281
      removed outlier: 6.862A  pdb=" N   GLY C 292 " --> pdb=" O   ASN C 277 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   LEU C 279 " --> pdb=" O   ALA C 290 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   ALA C 290 " --> pdb=" O   LEU C 279 " (cutoff:3.500A)
      removed outlier: 5.350A  pdb=" N   PHE C 281 " --> pdb=" O   ILE C 288 " (cutoff:3.500A)
      removed outlier: 8.198A  pdb=" N   ILE C 288 " --> pdb=" O   PHE C 281 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   HIS C 311 " --> pdb=" O   LEU C 300 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 320 through 325
      removed outlier: 5.722A  pdb=" N   ASP C 346 " --> pdb=" O   LEU C 366 " (cutoff:3.500A)
      removed outlier: 5.763A  pdb=" N   LEU C 366 " --> pdb=" O   ASP C 346 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 2 through 5
      removed outlier: 6.957A  pdb=" N   PHE B 360 " --> pdb=" O   TRP B 354 " (cutoff:3.500A)
      removed outlier: 4.695A  pdb=" N   TRP B 354 " --> pdb=" O   PHE B 360 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   ALA B 362 " --> pdb=" O   ILE B 352 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   ILE B 352 " --> pdb=" O   ALA B 362 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   SER B 364 " --> pdb=" O   SER B 350 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 16 through 20
      removed outlier: 6.721A  pdb=" N   ALA B  35 " --> pdb=" O   TYR B  17 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   LEU B  19 " --> pdb=" O   ALA B  33 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ALA B  33 " --> pdb=" O   LEU B  19 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   VAL B  41 " --> pdb=" O   ASN B  61 " (cutoff:3.500A)
      removed outlier: 4.661A  pdb=" N   ASN B  61 " --> pdb=" O   VAL B  41 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ILE B  43 " --> pdb=" O   LEU B  59 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   GLU B  47 " --> pdb=" O   ILE B  55 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   ILE B  55 " --> pdb=" O   GLU B  47 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 69 through 71
      removed outlier: 6.997A  pdb=" N   GLY B  84 " --> pdb=" O   ASN B  70 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   LYS B  94 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)
      removed outlier: 5.862A  pdb=" N   VAL B 121 " --> pdb=" O   LYS B  94 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 132 through 137
      removed outlier: 6.436A  pdb=" N   ASP B 157 " --> pdb=" O   LYS B 163 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   LYS B 163 " --> pdb=" O   ASP B 157 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 174 through 179
      removed outlier: 4.217A  pdb=" N   GLY B 176 " --> pdb=" O   LEU B 189 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   VAL B 194 " --> pdb=" O   SER B 190 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   SER B 199 " --> pdb=" O   VAL B 205 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   VAL B 205 " --> pdb=" O   SER B 199 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 211 through 213

    315 hydrogen bonds defined for protein.
    855 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.74

  Time building geometry restraints manager: 2.73 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2880
        1.34 -     1.46: 1276
        1.46 -     1.57: 4851
        1.57 -     1.69: 1
        1.69 -     1.81: 56
  Bond restraints: 9064
  Sorted by residual:
  bond pdb=" CA  ASP B 150 "
       pdb=" C   ASP B 150 "
    ideal  model  delta    sigma   weight residual
    1.522  1.576 -0.054 1.72e-02 3.38e+03 9.88e+00
  bond pdb=" N   ASN B  12 "
       pdb=" CA  ASN B  12 "
    ideal  model  delta    sigma   weight residual
    1.457  1.475 -0.018 1.29e-02 6.01e+03 1.89e+00
  bond pdb=" CA  PHE E 100 "
       pdb=" CB  PHE E 100 "
    ideal  model  delta    sigma   weight residual
    1.528  1.510  0.019 1.39e-02 5.18e+03 1.82e+00
  bond pdb=" CA  PHE E 100 "
       pdb=" C   PHE E 100 "
    ideal  model  delta    sigma   weight residual
    1.524  1.507  0.017 1.31e-02 5.83e+03 1.75e+00
  bond pdb=" CB  LYS B 286 "
       pdb=" CG  LYS B 286 "
    ideal  model  delta    sigma   weight residual
    1.520  1.559 -0.039 3.00e-02 1.11e+03 1.68e+00
  ... (remaining 9059 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 12111
        2.07 -     4.15: 157
        4.15 -     6.22: 27
        6.22 -     8.29: 4
        8.29 -    10.36: 3
  Bond angle restraints: 12302
  Sorted by residual:
  angle pdb=" N   GLU D  97 "
        pdb=" CA  GLU D  97 "
        pdb=" CB  GLU D  97 "
      ideal   model   delta    sigma   weight residual
     110.16  116.20   -6.04 1.48e+00 4.57e-01 1.66e+01
  angle pdb=" CB  LYS B 286 "
        pdb=" CG  LYS B 286 "
        pdb=" CD  LYS B 286 "
      ideal   model   delta    sigma   weight residual
     111.30  120.13   -8.83 2.30e+00 1.89e-01 1.47e+01
  angle pdb=" CA  MET C 133 "
        pdb=" CB  MET C 133 "
        pdb=" CG  MET C 133 "
      ideal   model   delta    sigma   weight residual
     114.10  121.36   -7.26 2.00e+00 2.50e-01 1.32e+01
  angle pdb=" C   HIS B 347 "
        pdb=" CA  HIS B 347 "
        pdb=" CB  HIS B 347 "
      ideal   model   delta    sigma   weight residual
     110.45  116.39   -5.94 1.73e+00 3.34e-01 1.18e+01
  angle pdb=" C   SER A 614 "
        pdb=" N   HIS A 615 "
        pdb=" CA  HIS A 615 "
      ideal   model   delta    sigma   weight residual
     122.32  128.01   -5.69 1.76e+00 3.23e-01 1.05e+01
  ... (remaining 12297 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.57: 4968
       16.57 -    33.13: 359
       33.13 -    49.70: 72
       49.70 -    66.26: 8
       66.26 -    82.83: 7
  Dihedral angle restraints: 5414
    sinusoidal: 2107
      harmonic: 3307
  Sorted by residual:
  dihedral pdb=" CA  MET C 133 "
           pdb=" C   MET C 133 "
           pdb=" N   PRO C 134 "
           pdb=" CA  PRO C 134 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.78  -28.22     0      5.00e+00 4.00e-02 3.18e+01
  dihedral pdb=" CA  PHE B 236 "
           pdb=" C   PHE B 236 "
           pdb=" N   PHE B 237 "
           pdb=" CA  PHE B 237 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.83  -19.17     0      5.00e+00 4.00e-02 1.47e+01
  dihedral pdb=" CA  ASP C  52 "
           pdb=" CB  ASP C  52 "
           pdb=" CG  ASP C  52 "
           pdb=" OD1 ASP C  52 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.73   59.73     1      2.00e+01 2.50e-03 1.19e+01
  ... (remaining 5411 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 911
       0.037 -    0.073: 299
       0.073 -    0.110: 109
       0.110 -    0.147: 43
       0.147 -    0.183: 2
  Chirality restraints: 1364
  Sorted by residual:
  chirality pdb=" CA  THR C  28 "
            pdb=" N   THR C  28 "
            pdb=" C   THR C  28 "
            pdb=" CB  THR C  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.18 2.00e-01 2.50e+01 8.39e-01
  chirality pdb=" CA  GLU D  97 "
            pdb=" N   GLU D  97 "
            pdb=" C   GLU D  97 "
            pdb=" CB  GLU D  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.35e-01
  chirality pdb=" CA  LEU D  65 "
            pdb=" N   LEU D  65 "
            pdb=" C   LEU D  65 "
            pdb=" CB  LEU D  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.18e-01
  ... (remaining 1361 not shown)

  Planarity restraints: 1594
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A 615 "    0.020 2.00e-02 2.50e+03   2.55e-02 9.72e+00
        pdb=" CG  HIS A 615 "   -0.054 2.00e-02 2.50e+03
        pdb=" ND1 HIS A 615 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 HIS A 615 "    0.019 2.00e-02 2.50e+03
        pdb=" CE1 HIS A 615 "    0.002 2.00e-02 2.50e+03
        pdb=" NE2 HIS A 615 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B 347 "    0.017 2.00e-02 2.50e+03   2.00e-02 5.97e+00
        pdb=" CG  HIS B 347 "   -0.043 2.00e-02 2.50e+03
        pdb=" ND1 HIS B 347 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 HIS B 347 "    0.014 2.00e-02 2.50e+03
        pdb=" CE1 HIS B 347 "    0.003 2.00e-02 2.50e+03
        pdb=" NE2 HIS B 347 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B 283 "    0.037 5.00e-02 4.00e+02   5.57e-02 4.96e+00
        pdb=" N   PRO B 284 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO B 284 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 284 "    0.031 5.00e-02 4.00e+02
  ... (remaining 1591 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 850
        2.75 -     3.29: 8672
        3.29 -     3.82: 15009
        3.82 -     4.36: 17059
        4.36 -     4.90: 29554
  Nonbonded interactions: 71144
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C  72 "
            pdb=" O   GLU C  75 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" OD2 ASP B 180 "
            pdb=" NH2 ARG B 271 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" OG  SER C  44 "
            pdb=" O   THR C  46 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   LEU D  48 "
            pdb=" OH  TYR B 369 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" NH1 ARG B  73 "
            pdb=" O   ILE B 135 "
     model   vdw
     2.284 3.120
  ... (remaining 71139 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:             1.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.100
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.420
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6948
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      :  0.002   0.056   9064  Z= 0.123
  Angle     :  0.622  10.363  12302  Z= 0.323
  Chirality :  0.044   0.183   1364
  Planarity :  0.004   0.056   1594
  Dihedral  : 12.266  82.829   3268
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.32 %
    Favored  : 99.57 %
  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: -0.20 (0.25), residues: 1121
  helix:  2.60 (0.36), residues: 202
  sheet: -0.03 (0.31), residues: 299
  loop : -1.15 (0.23), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP C 345 
 HIS   0.032   0.002   HIS A 615 
 PHE   0.018   0.001   PHE B 269 
 TYR   0.017   0.001   TYR C  98 
 ARG   0.006   0.000   ARG C 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09348 (  315)
  hydrogen bonds       : angle       5.97794 (  855)
  covalent geometry    : bond        0.00250 ( 9064)
  covalent geometry    : angle       0.62186 (12302)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 209
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  171 LEU cc_start: 0.5853 (mt) cc_final: 0.5422 (mp)
REVERT: C  333 LEU cc_start: 0.7613 (tp) cc_final: 0.7388 (tt)
REVERT: C  391 CYS cc_start: 0.7292 (t) cc_final: 0.7027 (t)
  outliers start: 1
  outliers final: 1
  residues processed: 210
  average time/residue: 0.2172
  time to fit residues: 61.8864
Evaluate side-chains
  129 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  613 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 95 optimal weight:   10.0000
   chunk 85 optimal weight:    1.9990
   chunk 47 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9980
   chunk 57 optimal weight:    8.9990
   chunk 45 optimal weight:    0.0870
   chunk 88 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 53 optimal weight:    8.9990
   chunk 65 optimal weight:    6.9990
   chunk 102 optimal weight:    0.9990
   overall best weight:    0.9962

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

Flipped N/Q/H residues before XYZ refinement:
C  64 HIS
C 277 ASN
** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 403 GLN
B  70 ASN
** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.082816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.064716 restraints weight = 35431.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.067201 restraints weight = 19686.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.068915 restraints weight = 13490.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.1936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9064  Z= 0.134
  Angle     :  0.641  10.169  12302  Z= 0.317
  Chirality :  0.046   0.239   1364
  Planarity :  0.004   0.040   1594
  Dihedral  :  4.103  25.643   1222
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 14.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 11.11 %
    Favored  : 87.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.25), residues: 1121
  helix:  2.36 (0.36), residues: 208
  sheet:  0.00 (0.30), residues: 306
  loop : -1.16 (0.23), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  10 
 HIS   0.011   0.001   HIS B 347 
 PHE   0.016   0.002   PHE B 242 
 TYR   0.012   0.001   TYR D  41 
 ARG   0.005   0.001   ARG E  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03197 (  315)
  hydrogen bonds       : angle       5.29845 (  855)
  covalent geometry    : bond        0.00304 ( 9064)
  covalent geometry    : angle       0.64052 (12302)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 147
  time to evaluate  : 1.013 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  561 GLN cc_start: 0.8040 (tm-30) cc_final: 0.7398 (tm-30)
REVERT: D   67 PHE cc_start: 0.9480 (t80) cc_final: 0.9249 (t80)
REVERT: E   40 ARG cc_start: 0.9488 (mtp-110) cc_final: 0.8860 (ptp-110)
REVERT: E   52 GLU cc_start: 0.8379 (pp20) cc_final: 0.8116 (pp20)
REVERT: E   53 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8724 (mm-30)
REVERT: E   67 ARG cc_start: 0.8774 (ttm110) cc_final: 0.8534 (ttm110)
REVERT: C  253 MET cc_start: 0.7859 (mmm) cc_final: 0.7514 (mmm)
REVERT: C  399 MET cc_start: 0.8591 (tmm) cc_final: 0.8092 (tmm)
REVERT: B   14 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8609 (mm-30)
REVERT: B   20 ASP cc_start: 0.7790 (t0) cc_final: 0.7454 (m-30)
REVERT: B  131 ASP cc_start: 0.8656 (m-30) cc_final: 0.8249 (m-30)
REVERT: B  133 TYR cc_start: 0.8886 (m-80) cc_final: 0.8468 (m-80)
REVERT: B  227 MET cc_start: 0.8409 (ptp) cc_final: 0.8126 (pmm)
REVERT: B  236 PHE cc_start: 0.9302 (OUTLIER) cc_final: 0.7885 (t80)
REVERT: B  237 PHE cc_start: 0.8467 (m-10) cc_final: 0.8088 (m-10)
  outliers start: 10
  outliers final: 5
  residues processed: 149
  average time/residue: 0.2145
  time to fit residues: 45.0478
Evaluate side-chains
  136 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 130
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  578 THR
Chi-restraints excluded: chain D residue   97 GLU
Chi-restraints excluded: chain E residue   96 THR
Chi-restraints excluded: chain B residue   96 ASN
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  236 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 44 optimal weight:    6.9990
   chunk 80 optimal weight:   10.0000
   chunk 48 optimal weight:    0.9980
   chunk 52 optimal weight:    6.9990
   chunk 90 optimal weight:    6.9990
   chunk 89 optimal weight:    0.8980
   chunk 58 optimal weight:    0.0050
   chunk 76 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9980
   chunk 65 optimal weight:    0.1980
   overall best weight:    0.5394

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

Flipped N/Q/H residues before XYZ refinement:
A 706 GLN
** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 347 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.082873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.064880 restraints weight = 35538.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.067390 restraints weight = 19546.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.069100 restraints weight = 13303.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.2234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9064  Z= 0.108
  Angle     :  0.613  11.406  12302  Z= 0.300
  Chirality :  0.045   0.181   1364
  Planarity :  0.004   0.034   1594
  Dihedral  :  4.011  24.539   1220
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 12.29 %
    Favored  : 86.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.25), residues: 1121
  helix:  2.36 (0.37), residues: 208
  sheet: -0.02 (0.30), residues: 306
  loop : -1.13 (0.23), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  10 
 HIS   0.005   0.001   HIS C 226 
 PHE   0.014   0.001   PHE B 375 
 TYR   0.011   0.001   TYR B 330 
 ARG   0.009   0.000   ARG E  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02926 (  315)
  hydrogen bonds       : angle       5.05785 (  855)
  covalent geometry    : bond        0.00243 ( 9064)
  covalent geometry    : angle       0.61327 (12302)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 145
  time to evaluate  : 1.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  589 GLN cc_start: 0.7947 (mm-40) cc_final: 0.6611 (tm-30)
REVERT: A  686 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8996 (tt)
REVERT: E   40 ARG cc_start: 0.9497 (mtp-110) cc_final: 0.9280 (ttm110)
REVERT: E   52 GLU cc_start: 0.8408 (pp20) cc_final: 0.8051 (pp20)
REVERT: E   53 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8681 (mm-30)
REVERT: E   78 ARG cc_start: 0.8556 (mtp-110) cc_final: 0.8042 (mtm180)
REVERT: C  253 MET cc_start: 0.7967 (mmm) cc_final: 0.7642 (mmm)
REVERT: C  399 MET cc_start: 0.8715 (tmm) cc_final: 0.8152 (tmm)
REVERT: B   14 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8677 (mm-30)
REVERT: B  131 ASP cc_start: 0.8034 (m-30) cc_final: 0.7830 (m-30)
REVERT: B  133 TYR cc_start: 0.8834 (m-10) cc_final: 0.8061 (m-80)
REVERT: B  227 MET cc_start: 0.8520 (ptp) cc_final: 0.8196 (pmm)
REVERT: B  236 PHE cc_start: 0.9324 (OUTLIER) cc_final: 0.8061 (t80)
REVERT: B  237 PHE cc_start: 0.8454 (m-10) cc_final: 0.8141 (m-10)
  outliers start: 14
  outliers final: 10
  residues processed: 149
  average time/residue: 0.2099
  time to fit residues: 43.2211
Evaluate side-chains
  142 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 130
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  686 ILE
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   97 GLU
Chi-restraints excluded: chain E residue   62 LEU
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue   96 ASN
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  236 PHE
Chi-restraints excluded: chain B residue  318 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 97 optimal weight:    3.9990
   chunk 102 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0770
   chunk 15 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 8 optimal weight:    3.9990
   chunk 101 optimal weight:    9.9990
   overall best weight:    0.7340

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

Flipped N/Q/H residues before XYZ refinement:
A 706 GLN
D  93 GLN
** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.081890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.063819 restraints weight = 35200.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.066279 restraints weight = 19499.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.067958 restraints weight = 13362.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.2495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9064  Z= 0.112
  Angle     :  0.607  11.631  12302  Z= 0.295
  Chirality :  0.045   0.198   1364
  Planarity :  0.004   0.033   1594
  Dihedral  :  3.932  24.944   1220
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 13.14 %
    Favored  : 84.62 %
  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: -0.20 (0.25), residues: 1121
  helix:  2.34 (0.36), residues: 208
  sheet: -0.08 (0.30), residues: 301
  loop : -1.06 (0.23), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  10 
 HIS   0.004   0.001   HIS C 226 
 PHE   0.023   0.001   PHE D  67 
 TYR   0.011   0.001   TYR B 330 
 ARG   0.005   0.000   ARG E  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02808 (  315)
  hydrogen bonds       : angle       4.95157 (  855)
  covalent geometry    : bond        0.00255 ( 9064)
  covalent geometry    : angle       0.60733 (12302)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 139
  time to evaluate  : 1.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  686 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.9023 (tt)
REVERT: D   94 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8993 (mm-30)
REVERT: D  103 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8687 (mm)
REVERT: E   40 ARG cc_start: 0.9509 (mtp-110) cc_final: 0.9177 (ttm110)
REVERT: E   52 GLU cc_start: 0.8432 (pp20) cc_final: 0.8209 (pp20)
REVERT: E   78 ARG cc_start: 0.8596 (mtp-110) cc_final: 0.8050 (mtm180)
REVERT: E   84 MET cc_start: 0.9046 (tpp) cc_final: 0.8739 (tpp)
REVERT: E   88 TYR cc_start: 0.8986 (m-10) cc_final: 0.8743 (m-10)
REVERT: C   36 MET cc_start: 0.8160 (tpt) cc_final: 0.7733 (ttt)
REVERT: C  253 MET cc_start: 0.8166 (mmm) cc_final: 0.7811 (mmm)
REVERT: C  399 MET cc_start: 0.8770 (tmm) cc_final: 0.8160 (tmm)
REVERT: B   14 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8695 (mm-30)
REVERT: B   20 ASP cc_start: 0.8272 (t0) cc_final: 0.7846 (m-30)
REVERT: B  133 TYR cc_start: 0.8836 (m-10) cc_final: 0.8531 (m-80)
REVERT: B  158 VAL cc_start: 0.7502 (t) cc_final: 0.7236 (m)
REVERT: B  212 MET cc_start: 0.7082 (tmm) cc_final: 0.6644 (tmm)
REVERT: B  227 MET cc_start: 0.8601 (ptp) cc_final: 0.8307 (pmm)
REVERT: B  236 PHE cc_start: 0.9379 (OUTLIER) cc_final: 0.8411 (t80)
REVERT: B  237 PHE cc_start: 0.8524 (m-10) cc_final: 0.8140 (m-10)
  outliers start: 21
  outliers final: 13
  residues processed: 147
  average time/residue: 0.2260
  time to fit residues: 46.3509
Evaluate side-chains
  144 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  686 ILE
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   97 GLU
Chi-restraints excluded: chain D residue  103 LEU
Chi-restraints excluded: chain E residue   62 LEU
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain C residue  237 LEU
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   66 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  236 PHE
Chi-restraints excluded: chain B residue  293 CYS
Chi-restraints excluded: chain B residue  318 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 110 optimal weight:    1.9990
   chunk 30 optimal weight:    9.9990
   chunk 79 optimal weight:    0.8980
   chunk 109 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0470
   chunk 101 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 57 optimal weight:    9.9990
   overall best weight:    1.3884

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

Flipped N/Q/H residues before XYZ refinement:
A 706 GLN
** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 115 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.079663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.061577 restraints weight = 35480.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.063965 restraints weight = 19704.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.065594 restraints weight = 13619.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.2829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9064  Z= 0.147
  Angle     :  0.611  11.906  12302  Z= 0.302
  Chirality :  0.045   0.182   1364
  Planarity :  0.004   0.033   1594
  Dihedral  :  4.069  25.234   1220
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 13.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 13.89 %
    Favored  : 83.97 %
  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: -0.17 (0.25), residues: 1121
  helix:  2.38 (0.37), residues: 208
  sheet: -0.09 (0.29), residues: 304
  loop : -1.03 (0.23), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  10 
 HIS   0.004   0.001   HIS B 280 
 PHE   0.027   0.002   PHE D  67 
 TYR   0.013   0.001   TYR B 330 
 ARG   0.006   0.000   ARG D  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02852 (  315)
  hydrogen bonds       : angle       4.92127 (  855)
  covalent geometry    : bond        0.00327 ( 9064)
  covalent geometry    : angle       0.61077 (12302)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 134
  time to evaluate  : 1.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  556 ARG cc_start: 0.8698 (tmm-80) cc_final: 0.8442 (mmm-85)
REVERT: A  589 GLN cc_start: 0.7897 (mm-40) cc_final: 0.6682 (tm-30)
REVERT: A  686 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.9007 (tt)
REVERT: D   94 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8985 (mm-30)
REVERT: E   40 ARG cc_start: 0.9508 (mtp-110) cc_final: 0.9169 (ttm110)
REVERT: E   52 GLU cc_start: 0.8529 (pp20) cc_final: 0.8248 (pp20)
REVERT: E   67 ARG cc_start: 0.8858 (ttp80) cc_final: 0.8219 (ptp-170)
REVERT: E   78 ARG cc_start: 0.8647 (mtp-110) cc_final: 0.8070 (mtm180)
REVERT: E   84 MET cc_start: 0.9070 (tpp) cc_final: 0.8495 (tpp)
REVERT: E   88 TYR cc_start: 0.9069 (m-10) cc_final: 0.8630 (m-10)
REVERT: C   36 MET cc_start: 0.8230 (tpt) cc_final: 0.7944 (ttt)
REVERT: C  131 ARG cc_start: 0.9077 (mmt90) cc_final: 0.8276 (mmp80)
REVERT: C  253 MET cc_start: 0.8305 (mmm) cc_final: 0.7767 (mmm)
REVERT: C  399 MET cc_start: 0.8814 (tmm) cc_final: 0.8188 (tmm)
REVERT: B   14 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8717 (mm-30)
REVERT: B  131 ASP cc_start: 0.9138 (m-30) cc_final: 0.8672 (m-30)
REVERT: B  133 TYR cc_start: 0.8994 (m-10) cc_final: 0.8460 (m-80)
REVERT: B  227 MET cc_start: 0.8833 (ptp) cc_final: 0.8238 (pmm)
REVERT: B  236 PHE cc_start: 0.9415 (OUTLIER) cc_final: 0.8391 (t80)
REVERT: B  237 PHE cc_start: 0.8780 (m-10) cc_final: 0.8470 (m-10)
  outliers start: 20
  outliers final: 15
  residues processed: 144
  average time/residue: 0.2462
  time to fit residues: 50.0653
Evaluate side-chains
  139 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 122
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  578 THR
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  686 ILE
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   97 GLU
Chi-restraints excluded: chain E residue   62 LEU
Chi-restraints excluded: chain E residue   82 THR
Chi-restraints excluded: chain C residue  237 LEU
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   66 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  236 PHE
Chi-restraints excluded: chain B residue  293 CYS
Chi-restraints excluded: chain B residue  318 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 52 optimal weight:    5.9990
   chunk 104 optimal weight:   10.0000
   chunk 91 optimal weight:    5.9990
   chunk 46 optimal weight:    8.9990
   chunk 97 optimal weight:    5.9990
   chunk 51 optimal weight:    7.9990
   chunk 57 optimal weight:   10.0000
   chunk 56 optimal weight:    1.9990
   chunk 89 optimal weight:    4.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 589 GLN
** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 403 GLN
B  70 ASN
** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.073688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.055655 restraints weight = 36496.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.057799 restraints weight = 21198.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.059262 restraints weight = 15037.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.3985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.067   9064  Z= 0.362
  Angle     :  0.780  11.080  12302  Z= 0.401
  Chirality :  0.049   0.198   1364
  Planarity :  0.005   0.046   1594
  Dihedral  :  4.820  24.549   1220
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 22.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 15.06 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.24), residues: 1121
  helix:  1.94 (0.36), residues: 202
  sheet: -0.39 (0.30), residues: 291
  loop : -1.19 (0.23), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 690 
 HIS   0.008   0.002   HIS C 200 
 PHE   0.021   0.003   PHE B 237 
 TYR   0.015   0.002   TYR C  32 
 ARG   0.008   0.001   ARG B 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03700 (  315)
  hydrogen bonds       : angle       5.67086 (  855)
  covalent geometry    : bond        0.00762 ( 9064)
  covalent geometry    : angle       0.78044 (12302)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 128
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  577 LYS cc_start: 0.8915 (mmtt) cc_final: 0.8691 (mmtt)
REVERT: D   94 GLU cc_start: 0.9338 (mm-30) cc_final: 0.8638 (mm-30)
REVERT: D   97 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8277 (pm20)
REVERT: D  120 MET cc_start: 0.8356 (mmm) cc_final: 0.8147 (mmm)
REVERT: E   40 ARG cc_start: 0.9544 (mtp-110) cc_final: 0.9277 (ttm110)
REVERT: E   52 GLU cc_start: 0.8562 (pp20) cc_final: 0.7920 (pp20)
REVERT: E   53 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8659 (mm-30)
REVERT: E   64 ASN cc_start: 0.9351 (m-40) cc_final: 0.9081 (m-40)
REVERT: E   67 ARG cc_start: 0.8846 (ttp80) cc_final: 0.8198 (ptp-170)
REVERT: E   74 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8155 (tm-30)
REVERT: E   88 TYR cc_start: 0.9308 (m-10) cc_final: 0.9099 (m-10)
REVERT: E   97 LEU cc_start: 0.9481 (tp) cc_final: 0.9245 (tt)
REVERT: C  253 MET cc_start: 0.8503 (mmm) cc_final: 0.7967 (mmm)
REVERT: C  399 MET cc_start: 0.8786 (tmm) cc_final: 0.8028 (tmm)
REVERT: B   14 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8829 (mm-30)
REVERT: B  131 ASP cc_start: 0.9013 (m-30) cc_final: 0.8726 (m-30)
REVERT: B  134 ASP cc_start: 0.8926 (t70) cc_final: 0.7831 (t0)
REVERT: B  227 MET cc_start: 0.9294 (ptp) cc_final: 0.8496 (pmm)
REVERT: B  236 PHE cc_start: 0.9351 (m-80) cc_final: 0.8359 (t80)
REVERT: B  385 LYS cc_start: 0.9280 (mmtt) cc_final: 0.8856 (mmmt)
  outliers start: 27
  outliers final: 21
  residues processed: 144
  average time/residue: 0.2181
  time to fit residues: 43.1707
Evaluate side-chains
  139 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 117
  time to evaluate  : 1.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  578 THR
Chi-restraints excluded: chain A residue  688 CYS
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  699 ASP
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   97 GLU
Chi-restraints excluded: chain E residue   62 LEU
Chi-restraints excluded: chain E residue   82 THR
Chi-restraints excluded: chain C residue  237 LEU
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   66 THR
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  168 ASN
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  293 CYS
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  353 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 112 optimal weight:    5.9990
   chunk 23 optimal weight:    0.8980
   chunk 79 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 12 optimal weight:   10.0000
   chunk 27 optimal weight:    3.9990
   chunk 82 optimal weight:    0.8980
   chunk 20 optimal weight:    7.9990
   chunk 5 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 706 GLN
** C  64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.078326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.060186 restraints weight = 35553.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.062548 restraints weight = 20752.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.064098 restraints weight = 14679.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.3768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9064  Z= 0.136
  Angle     :  0.672  14.453  12302  Z= 0.329
  Chirality :  0.045   0.189   1364
  Planarity :  0.004   0.051   1594
  Dihedral  :  4.405  24.682   1220
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 16.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 16.99 %
    Favored  : 80.98 %
  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: -0.38 (0.25), residues: 1121
  helix:  2.24 (0.37), residues: 202
  sheet: -0.38 (0.30), residues: 293
  loop : -1.04 (0.24), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  10 
 HIS   0.004   0.001   HIS B 128 
 PHE   0.024   0.002   PHE D  67 
 TYR   0.017   0.001   TYR B 330 
 ARG   0.010   0.001   ARG E  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03099 (  315)
  hydrogen bonds       : angle       5.18243 (  855)
  covalent geometry    : bond        0.00312 ( 9064)
  covalent geometry    : angle       0.67156 (12302)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 135
  time to evaluate  : 1.055 
Fit side-chains
   revert: symmetry clash
REVERT: D   94 GLU cc_start: 0.9295 (mm-30) cc_final: 0.8458 (mm-30)
REVERT: D   97 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8160 (pm20)
REVERT: D  120 MET cc_start: 0.8469 (mmm) cc_final: 0.8184 (mmm)
REVERT: E   40 ARG cc_start: 0.9448 (mtp-110) cc_final: 0.9204 (ttm110)
REVERT: E   52 GLU cc_start: 0.8484 (pp20) cc_final: 0.7807 (pp20)
REVERT: E   53 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8517 (mm-30)
REVERT: E   74 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8075 (tm-30)
REVERT: E   78 ARG cc_start: 0.8656 (mtp-110) cc_final: 0.8222 (mtm180)
REVERT: C   36 MET cc_start: 0.8354 (tpt) cc_final: 0.7957 (ttt)
REVERT: C  253 MET cc_start: 0.8504 (mmm) cc_final: 0.8022 (mmm)
REVERT: C  399 MET cc_start: 0.8744 (tmm) cc_final: 0.8252 (tmm)
REVERT: B   14 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8668 (mm-30)
REVERT: B  191 CYS cc_start: 0.8702 (t) cc_final: 0.8152 (t)
REVERT: B  227 MET cc_start: 0.8915 (ptp) cc_final: 0.8370 (pmm)
REVERT: B  236 PHE cc_start: 0.9018 (m-80) cc_final: 0.8550 (t80)
REVERT: B  361 LEU cc_start: 0.8946 (tp) cc_final: 0.8720 (mt)
REVERT: B  385 LYS cc_start: 0.9207 (mmtt) cc_final: 0.8792 (mmmt)
  outliers start: 19
  outliers final: 15
  residues processed: 145
  average time/residue: 0.2217
  time to fit residues: 44.2812
Evaluate side-chains
  146 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 130
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  688 CYS
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   97 GLU
Chi-restraints excluded: chain E residue   62 LEU
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   66 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  152 THR
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  293 CYS
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  353 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 18 optimal weight:    0.0370
   chunk 15 optimal weight:    6.9990
   chunk 7 optimal weight:    4.9990
   chunk 40 optimal weight:    0.0670
   chunk 97 optimal weight:    6.9990
   chunk 86 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9990
   chunk 83 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 46 optimal weight:   10.0000
   overall best weight:    1.6202

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

Flipped N/Q/H residues before XYZ refinement:
A 706 GLN
** C  64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 403 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.077354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.059175 restraints weight = 35958.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.061443 restraints weight = 21154.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.062974 restraints weight = 15076.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.3895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9064  Z= 0.167
  Angle     :  0.697  14.453  12302  Z= 0.339
  Chirality :  0.045   0.194   1364
  Planarity :  0.004   0.051   1594
  Dihedral  :  4.315  24.565   1220
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 16.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 18.38 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.25), residues: 1121
  helix:  2.14 (0.37), residues: 202
  sheet: -0.46 (0.30), residues: 296
  loop : -1.01 (0.24), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 156 
 HIS   0.004   0.001   HIS B 128 
 PHE   0.021   0.002   PHE D  67 
 TYR   0.015   0.001   TYR B 173 
 ARG   0.011   0.001   ARG E  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03032 (  315)
  hydrogen bonds       : angle       5.16754 (  855)
  covalent geometry    : bond        0.00378 ( 9064)
  covalent geometry    : angle       0.69690 (12302)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   94 GLU cc_start: 0.9292 (mm-30) cc_final: 0.8970 (mm-30)
REVERT: D  120 MET cc_start: 0.8484 (mmm) cc_final: 0.8178 (mmm)
REVERT: E   40 ARG cc_start: 0.9468 (mtp-110) cc_final: 0.9219 (ttm110)
REVERT: E   52 GLU cc_start: 0.8496 (pp20) cc_final: 0.8141 (pp20)
REVERT: E   63 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8994 (tm-30)
REVERT: E   67 ARG cc_start: 0.8876 (ttp80) cc_final: 0.8205 (ttp-110)
REVERT: E   74 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8080 (tm-30)
REVERT: E   78 ARG cc_start: 0.8676 (mtp-110) cc_final: 0.8234 (mtm180)
REVERT: C   36 MET cc_start: 0.8403 (tpt) cc_final: 0.7884 (ttt)
REVERT: C  253 MET cc_start: 0.8540 (mmm) cc_final: 0.8063 (mmm)
REVERT: C  399 MET cc_start: 0.8748 (tmm) cc_final: 0.8052 (tmm)
REVERT: C  404 MET cc_start: 0.8998 (mmm) cc_final: 0.8408 (mmm)
REVERT: B   14 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8698 (mm-30)
REVERT: B  134 ASP cc_start: 0.8895 (t70) cc_final: 0.7953 (t0)
REVERT: B  191 CYS cc_start: 0.8633 (t) cc_final: 0.8100 (t)
REVERT: B  227 MET cc_start: 0.8931 (ptp) cc_final: 0.8326 (pmm)
REVERT: B  236 PHE cc_start: 0.9073 (m-80) cc_final: 0.8680 (t80)
REVERT: B  361 LEU cc_start: 0.9009 (tp) cc_final: 0.8731 (mt)
REVERT: B  385 LYS cc_start: 0.9239 (mmtt) cc_final: 0.8816 (mmmt)
  outliers start: 18
  outliers final: 17
  residues processed: 142
  average time/residue: 0.2292
  time to fit residues: 44.6654
Evaluate side-chains
  145 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 128
  time to evaluate  : 1.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  578 THR
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  706 GLN
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   97 GLU
Chi-restraints excluded: chain E residue   82 THR
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   66 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  293 CYS
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  353 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 1 optimal weight:    0.0770
   chunk 92 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 47 optimal weight:    6.9990
   chunk 21 optimal weight:    0.8980
   chunk 16 optimal weight:    9.9990
   chunk 44 optimal weight:    0.0060
   chunk 35 optimal weight:    4.9990
   chunk 98 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 88 optimal weight:    0.7980
   overall best weight:    0.5154

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

Flipped N/Q/H residues before XYZ refinement:
A 706 GLN
** C  64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.079580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.061521 restraints weight = 35276.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.063824 restraints weight = 20675.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.065401 restraints weight = 14677.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.3814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9064  Z= 0.119
  Angle     :  0.705  15.427  12302  Z= 0.335
  Chirality :  0.045   0.199   1364
  Planarity :  0.004   0.055   1594
  Dihedral  :  4.155  25.406   1220
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 14.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 18.80 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.25), residues: 1121
  helix:  2.25 (0.37), residues: 202
  sheet: -0.34 (0.30), residues: 295
  loop : -1.03 (0.24), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  10 
 HIS   0.003   0.001   HIS B 280 
 PHE   0.022   0.001   PHE D  67 
 TYR   0.014   0.001   TYR B 330 
 ARG   0.013   0.001   ARG E  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02967 (  315)
  hydrogen bonds       : angle       5.01454 (  855)
  covalent geometry    : bond        0.00279 ( 9064)
  covalent geometry    : angle       0.70469 (12302)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 132
  time to evaluate  : 1.012 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  589 GLN cc_start: 0.8000 (mm-40) cc_final: 0.6980 (tm-30)
REVERT: D   94 GLU cc_start: 0.9252 (mm-30) cc_final: 0.8901 (mm-30)
REVERT: D  120 MET cc_start: 0.8392 (mmm) cc_final: 0.8062 (mmm)
REVERT: E   40 ARG cc_start: 0.9446 (mtp-110) cc_final: 0.9199 (ttm110)
REVERT: E   52 GLU cc_start: 0.8506 (pp20) cc_final: 0.8116 (pp20)
REVERT: E   67 ARG cc_start: 0.8867 (ttp80) cc_final: 0.8204 (ttp80)
REVERT: E   74 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8128 (tm-30)
REVERT: E   85 ASP cc_start: 0.9188 (m-30) cc_final: 0.8062 (t0)
REVERT: C   36 MET cc_start: 0.8332 (tpt) cc_final: 0.8015 (ttt)
REVERT: C  183 LEU cc_start: 0.8936 (tt) cc_final: 0.8489 (mp)
REVERT: C  253 MET cc_start: 0.8472 (mmm) cc_final: 0.8036 (mmm)
REVERT: C  399 MET cc_start: 0.8723 (tmm) cc_final: 0.8226 (tmm)
REVERT: C  404 MET cc_start: 0.8626 (mmm) cc_final: 0.8186 (mmm)
REVERT: B   14 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8680 (mm-30)
REVERT: B  179 TRP cc_start: 0.8832 (t-100) cc_final: 0.8618 (t-100)
REVERT: B  227 MET cc_start: 0.8773 (ptp) cc_final: 0.8268 (pmm)
REVERT: B  236 PHE cc_start: 0.8961 (m-80) cc_final: 0.8577 (t80)
REVERT: B  385 LYS cc_start: 0.9218 (mmtt) cc_final: 0.8777 (mmmt)
  outliers start: 14
  outliers final: 12
  residues processed: 141
  average time/residue: 0.2189
  time to fit residues: 42.4767
Evaluate side-chains
  137 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  706 GLN
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   97 GLU
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   66 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  318 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 91 optimal weight:    5.9990
   chunk 30 optimal weight:    0.6980
   chunk 102 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 36 optimal weight:    3.9990
   chunk 5 optimal weight:    8.9990
   chunk 100 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.079446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.061313 restraints weight = 35327.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.063618 restraints weight = 20831.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.065166 restraints weight = 14822.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.3871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9064  Z= 0.129
  Angle     :  0.701  14.578  12302  Z= 0.335
  Chirality :  0.045   0.195   1364
  Planarity :  0.004   0.057   1594
  Dihedral  :  4.082  24.653   1220
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 14.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 19.55 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.25), residues: 1121
  helix:  2.15 (0.37), residues: 204
  sheet: -0.34 (0.29), residues: 300
  loop : -0.97 (0.24), residues: 617

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 156 
 HIS   0.003   0.001   HIS B 280 
 PHE   0.016   0.001   PHE A 707 
 TYR   0.014   0.001   TYR C  21 
 ARG   0.013   0.001   ARG E  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02910 (  315)
  hydrogen bonds       : angle       4.98651 (  855)
  covalent geometry    : bond        0.00302 ( 9064)
  covalent geometry    : angle       0.70140 (12302)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 129
  time to evaluate  : 1.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  589 GLN cc_start: 0.7971 (mm-40) cc_final: 0.6959 (tm-30)
REVERT: D   94 GLU cc_start: 0.9239 (mm-30) cc_final: 0.8883 (mm-30)
REVERT: D  120 MET cc_start: 0.8440 (mmm) cc_final: 0.8118 (mmm)
REVERT: E   52 GLU cc_start: 0.8492 (pp20) cc_final: 0.8108 (pp20)
REVERT: E   74 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8068 (tm-30)
REVERT: E   85 ASP cc_start: 0.9095 (m-30) cc_final: 0.7953 (t0)
REVERT: C   36 MET cc_start: 0.8372 (tpt) cc_final: 0.7917 (ttt)
REVERT: C  131 ARG cc_start: 0.8837 (mmt90) cc_final: 0.8245 (mmp80)
REVERT: C  253 MET cc_start: 0.8470 (mmm) cc_final: 0.8038 (mmm)
REVERT: C  399 MET cc_start: 0.8750 (tmm) cc_final: 0.8047 (tmm)
REVERT: C  404 MET cc_start: 0.8565 (mmm) cc_final: 0.8078 (mmm)
REVERT: B   14 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8683 (mm-30)
REVERT: B  134 ASP cc_start: 0.8857 (t70) cc_final: 0.7957 (t0)
REVERT: B  144 MET cc_start: 0.8354 (tpp) cc_final: 0.7627 (mmm)
REVERT: B  227 MET cc_start: 0.8805 (ptp) cc_final: 0.8298 (pmm)
REVERT: B  236 PHE cc_start: 0.8973 (m-80) cc_final: 0.8583 (t80)
REVERT: B  385 LYS cc_start: 0.9213 (mmtt) cc_final: 0.8770 (mmmt)
  outliers start: 12
  outliers final: 11
  residues processed: 136
  average time/residue: 0.2316
  time to fit residues: 43.2825
Evaluate side-chains
  138 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 127
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   97 GLU
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   66 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  318 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 112 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 105 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 79 optimal weight:   10.0000
   chunk 58 optimal weight:    6.9990
   chunk 64 optimal weight:    6.9990
   chunk 57 optimal weight:   10.0000
   chunk 4 optimal weight:    0.0980
   chunk 1 optimal weight:    6.9990
   chunk 39 optimal weight:    0.0670
   overall best weight:    1.6324

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

Flipped N/Q/H residues before XYZ refinement:
A 706 GLN
** C  64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 200 HIS
** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 345 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.078156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.060751 restraints weight = 35550.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.062955 restraints weight = 20920.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.064498 restraints weight = 14846.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.4061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9064  Z= 0.168
  Angle     :  0.721  14.132  12302  Z= 0.346
  Chirality :  0.045   0.197   1364
  Planarity :  0.004   0.054   1594
  Dihedral  :  4.149  24.537   1220
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 16.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 19.34 %
    Favored  : 78.85 %
  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: -0.35 (0.25), residues: 1121
  helix:  2.34 (0.37), residues: 202
  sheet: -0.53 (0.30), residues: 291
  loop : -0.96 (0.24), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B 179 
 HIS   0.004   0.001   HIS B 280 
 PHE   0.014   0.002   PHE C 243 
 TYR   0.015   0.001   TYR B 173 
 ARG   0.013   0.001   ARG E  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02999 (  315)
  hydrogen bonds       : angle       5.04856 (  855)
  covalent geometry    : bond        0.00379 ( 9064)
  covalent geometry    : angle       0.72094 (12302)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2957.33 seconds
wall clock time: 52 minutes 39.01 seconds (3159.01 seconds total)