Starting phenix.real_space_refine
on Wed Mar 12 23:36:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6jxr_9895/03_2025/6jxr_9895.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6jxr_9895/03_2025/6jxr_9895.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6jxr_9895/03_2025/6jxr_9895.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6jxr_9895/03_2025/6jxr_9895.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6jxr_9895/03_2025/6jxr_9895.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6jxr_9895/03_2025/6jxr_9895.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    5379      2.51       5
     N    1386      2.21       5
     O    1618      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8437
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "a"
      Number of atoms: 286
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 286
          Classifications: {'peptide': 36}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 34}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "b"
      Number of atoms: 260
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 260
          Classifications: {'peptide': 32}
          Link IDs: {'PTRANS': 1, 'TRANS': 30}
    Chain: "d"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 840
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 3, 'TRANS': 104}
    Chain: "f"
      Number of atoms: 983
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 983
          Classifications: {'peptide': 124}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 118}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "g"
      Number of atoms: 904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 904
          Classifications: {'peptide': 115}
          Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 111}
    Chain: "m"
      Number of atoms: 1940
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 248, 1940
          Classifications: {'peptide': 248}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 235}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "n"
      Number of atoms: 2246
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2246
          Classifications: {'peptide': 287}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 271}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "e"
      Number of atoms: 978
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 978
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 5, 'TRANS': 117}
  Time building chain proxies: 5.42, per 1000 atoms: 0.64
  Number of scatterers: 8437
  At special positions: 0
  Unit cell: (116.27, 90.902, 133.182, 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      54     16.00
     O    1618      8.00
     N    1386      7.00
     C    5379      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS a  32 " - pdb=" SG  CYS b  32 " distance=2.03
    Simple disulfide: pdb=" SG  CYS d  37 " - pdb=" SG  CYS d  73 " distance=2.04
    Simple disulfide: pdb=" SG  CYS d  93 " - pdb=" SG  CYS d  96 " distance=2.02
    Simple disulfide: pdb=" SG  CYS f  49 " - pdb=" SG  CYS f  98 " distance=2.03
    Simple disulfide: pdb=" SG  CYS f 119 " - pdb=" SG  CYS f 122 " distance=2.02
    Simple disulfide: pdb=" SG  CYS g  46 " - pdb=" SG  CYS g  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS g 104 " - pdb=" SG  CYS g 107 " distance=2.04
    Simple disulfide: pdb=" SG  CYS m  45 " - pdb=" SG  CYS m 111 " distance=2.03
    Simple disulfide: pdb=" SG  CYS m 155 " - pdb=" SG  CYS m 205 " distance=2.03
    Simple disulfide: pdb=" SG  CYS m 227 " - pdb=" SG  CYS n 264 " distance=2.03
    Simple disulfide: pdb=" SG  CYS n  42 " - pdb=" SG  CYS n 110 " distance=2.03
    Simple disulfide: pdb=" SG  CYS n 164 " - pdb=" SG  CYS n 229 " distance=2.02
    Simple disulfide: pdb=" SG  CYS e  49 " - pdb=" SG  CYS e  98 " distance=2.03
    Simple disulfide: pdb=" SG  CYS e 119 " - pdb=" SG  CYS e 122 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.93
  Conformation dependent library (CDL) restraints added in 937.8 milliseconds
  

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2002

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 16 sheets defined
      26.6% alpha, 27.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'a' and resid 28 through 57
      removed outlier: 4.572A  pdb=" N   CYS a  32 " --> pdb=" O   ASP a  28 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 27 through 54
      removed outlier: 4.132A  pdb=" N   LEU b  31 " --> pdb=" O   LEU b  27 " (cutoff:3.500A)
      removed outlier: 5.853A  pdb=" N   TYR b  42 " --> pdb=" O   ILE b  38 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 100 through 128
      removed outlier: 3.763A  pdb=" N   HIS d 128 " --> pdb=" O   CYS d 124 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 104 through 108
    Processing helix  chain 'f' and resid 128 through 155
    Processing helix  chain 'g' and resid 111 through 137
    Processing helix  chain 'm' and resid 102 through 106
      removed outlier: 3.518A  pdb=" N   ASP m 105 " --> pdb=" O   GLN m 102 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   SER m 106 " --> pdb=" O   PRO m 103 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'm' and resid 102 through 106'
    Processing helix  chain 'm' and resid 204 through 208
      removed outlier: 3.570A  pdb=" N   ALA m 208 " --> pdb=" O   CYS m 205 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 228 through 233
      removed outlier: 3.731A  pdb=" N   VAL m 232 " --> pdb=" O   ASP m 228 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 239 through 273
      removed outlier: 3.633A  pdb=" N   ASN m 243 " --> pdb=" O   ASP m 239 " (cutoff:3.500A)
    Processing helix  chain 'n' and resid 101 through 105
      removed outlier: 4.263A  pdb=" N   THR n 105 " --> pdb=" O   PRO n 102 " (cutoff:3.500A)
    Processing helix  chain 'n' and resid 150 through 157
      removed outlier: 3.639A  pdb=" N   ILE n 154 " --> pdb=" O   SER n 150 " (cutoff:3.500A)
    Processing helix  chain 'n' and resid 269 through 308
    Processing helix  chain 'e' and resid 104 through 108
      removed outlier: 3.783A  pdb=" N   ALA e 108 " --> pdb=" O   PRO e 105 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 126 through 154
      removed outlier: 3.529A  pdb=" N   VAL e 130 " --> pdb=" O   ASP e 126 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'd' and resid 26 through 27
      removed outlier: 5.516A  pdb=" N   VAL d  33 " --> pdb=" O   LEU d  60 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'd' and resid 42 through 46
      removed outlier: 6.849A  pdb=" N   ILE d  70 " --> pdb=" O   VAL d  44 " (cutoff:3.500A)
      removed outlier: 9.514A  pdb=" N   TYR e 111 " --> pdb=" O   GLU d  83 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   THR d  85 " --> pdb=" O   TYR e 111 " (cutoff:3.500A)
      removed outlier: 7.953A  pdb=" N   TYR e 113 " --> pdb=" O   THR d  85 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   GLN d  87 " --> pdb=" O   TYR e 113 " (cutoff:3.500A)
      removed outlier: 7.783A  pdb=" N   ARG e 115 " --> pdb=" O   GLN d  87 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   HIS d  89 " --> pdb=" O   ARG e 115 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   PHE e 110 " --> pdb=" O   CYS e  98 " (cutoff:3.500A)
      removed outlier: 5.108A  pdb=" N   CYS e  98 " --> pdb=" O   PHE e 110 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   TRP e  59 " --> pdb=" O   ILE e  66 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'd' and resid 96 through 98
    Processing sheet with id=AA4, first strand: chain 'f' and resid 37 through 41
    Processing sheet with id=AA5, first strand: chain 'f' and resid 65 through 66
      removed outlier: 4.110A  pdb=" N   TRP f  59 " --> pdb=" O   ILE f  66 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   TYR f 111 " --> pdb=" O   GLN g  98 " (cutoff:3.500A)
      removed outlier: 7.552A  pdb=" N   TYR g 100 " --> pdb=" O   TYR f 111 " (cutoff:3.500A)
      removed outlier: 5.809A  pdb=" N   TYR f 113 " --> pdb=" O   TYR g 100 " (cutoff:3.500A)
      removed outlier: 7.339A  pdb=" N   ARG g 102 " --> pdb=" O   TYR f 113 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   ARG f 115 " --> pdb=" O   ARG g 102 " (cutoff:3.500A)
      removed outlier: 5.975A  pdb=" N   LYS g  57 " --> pdb=" O   MET g  61 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   MET g  61 " --> pdb=" O   LYS g  57 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'f' and resid 122 through 123
      removed outlier: 3.756A  pdb=" N   MET f 123 " --> pdb=" O   ILE g 108 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ILE g 108 " --> pdb=" O   MET f 123 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'g' and resid 31 through 34
      removed outlier: 3.575A  pdb=" N   LEU g  43 " --> pdb=" O   TYR g  34 " (cutoff:3.500A)
      removed outlier: 5.812A  pdb=" N   VAL g  42 " --> pdb=" O   LEU g  74 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'm' and resid 27 through 28
    Processing sheet with id=AA9, first strand: chain 'm' and resid 33 through 36
      removed outlier: 6.196A  pdb=" N   LEU m  33 " --> pdb=" O   LEU m 129 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   SER m 131 " --> pdb=" O   LEU m  33 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   VAL m  35 " --> pdb=" O   SER m 131 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   SER m 114 " --> pdb=" O   TYR m  54 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   TYR m  54 " --> pdb=" O   SER m 114 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   PHE m  55 " --> pdb=" O   TYR m  71 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   TYR m  71 " --> pdb=" O   PHE m  55 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   TRP m  57 " --> pdb=" O   LEU m  69 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'm' and resid 33 through 36
      removed outlier: 6.196A  pdb=" N   LEU m  33 " --> pdb=" O   LEU m 129 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   SER m 131 " --> pdb=" O   LEU m  33 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   VAL m  35 " --> pdb=" O   SER m 131 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'm' and resid 140 through 143
      removed outlier: 3.947A  pdb=" N   SER m 153 " --> pdb=" O   SER m 198 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   SER m 198 " --> pdb=" O   SER m 153 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ALA m 196 " --> pdb=" O   CYS m 155 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   MET m 184 " --> pdb=" O   PHE m 189 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'n' and resid 23 through 26
    Processing sheet with id=AB4, first strand: chain 'n' and resid 29 through 33
      removed outlier: 3.509A  pdb=" N   LEU n  32 " --> pdb=" O   THR n 131 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   THR n 133 " --> pdb=" O   LEU n  32 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   MET n  51 " --> pdb=" O   TYR n  67 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   TYR n  67 " --> pdb=" O   MET n  51 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   TRP n  53 " --> pdb=" O   ILE n  65 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   ASP n  57 " --> pdb=" O   GLY n  61 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   GLY n  61 " --> pdb=" O   ASP n  57 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'n' and resid 143 through 147
      removed outlier: 5.244A  pdb=" N   TYR n 207 " --> pdb=" O   GLY n 168 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'n' and resid 183 through 184
      removed outlier: 3.746A  pdb=" N   ALA n 256 " --> pdb=" O   CYS n 229 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'e' and resid 37 through 41

    401 hydrogen bonds defined for protein.
    1083 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: 2.35

  Time building geometry restraints manager: 2.33 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: 2693
        1.34 -     1.46: 2032
        1.46 -     1.59: 3817
        1.59 -     1.71: 1
        1.71 -     1.83: 76
  Bond restraints: 8619
  Sorted by residual:
  bond pdb=" CE  LYS m 190 "
       pdb=" NZ  LYS m 190 "
    ideal  model  delta    sigma   weight residual
    1.489  1.620 -0.131 3.00e-02 1.11e+03 1.90e+01
  bond pdb=" CB  VAL d  33 "
       pdb=" CG2 VAL d  33 "
    ideal  model  delta    sigma   weight residual
    1.521  1.449  0.072 3.30e-02 9.18e+02 4.78e+00
  bond pdb=" C   PHE n 147 "
       pdb=" N   GLU n 148 "
    ideal  model  delta    sigma   weight residual
    1.330  1.300  0.030 1.47e-02 4.63e+03 4.12e+00
  bond pdb=" CB  VAL m 154 "
       pdb=" CG2 VAL m 154 "
    ideal  model  delta    sigma   weight residual
    1.521  1.464  0.057 3.30e-02 9.18e+02 2.96e+00
  bond pdb=" CG  ARG d  57 "
       pdb=" CD  ARG d  57 "
    ideal  model  delta    sigma   weight residual
    1.520  1.473  0.047 3.00e-02 1.11e+03 2.45e+00
  ... (remaining 8614 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.59: 11382
        2.59 -     5.18: 257
        5.18 -     7.76: 35
        7.76 -    10.35: 9
       10.35 -    12.94: 4
  Bond angle restraints: 11687
  Sorted by residual:
  angle pdb=" C   THR m 158 "
        pdb=" N   ASP m 159 "
        pdb=" CA  ASP m 159 "
      ideal   model   delta    sigma   weight residual
     121.54  134.48  -12.94 1.91e+00 2.74e-01 4.59e+01
  angle pdb=" C   LEU b  27 "
        pdb=" N   ASP b  28 "
        pdb=" CA  ASP b  28 "
      ideal   model   delta    sigma   weight residual
     121.62  130.41   -8.79 1.57e+00 4.06e-01 3.13e+01
  angle pdb=" N   PHE n 219 "
        pdb=" CA  PHE n 219 "
        pdb=" C   PHE n 219 "
      ideal   model   delta    sigma   weight residual
     114.04  107.14    6.90 1.24e+00 6.50e-01 3.10e+01
  angle pdb=" C   THR d  76 "
        pdb=" N   ASP d  77 "
        pdb=" CA  ASP d  77 "
      ideal   model   delta    sigma   weight residual
     121.54  131.46   -9.92 1.91e+00 2.74e-01 2.70e+01
  angle pdb=" N   PHE m 160 "
        pdb=" CA  PHE m 160 "
        pdb=" C   PHE m 160 "
      ideal   model   delta    sigma   weight residual
     110.80  121.85  -11.05 2.13e+00 2.20e-01 2.69e+01
  ... (remaining 11682 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.70: 4882
       15.70 -    31.40: 204
       31.40 -    47.10: 65
       47.10 -    62.80: 15
       62.80 -    78.50: 10
  Dihedral angle restraints: 5176
    sinusoidal: 2056
      harmonic: 3120
  Sorted by residual:
  dihedral pdb=" CA  ASP m 217 "
           pdb=" C   ASP m 217 "
           pdb=" N   THR m 218 "
           pdb=" CA  THR m 218 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  129.80   50.20     0      5.00e+00 4.00e-02 1.01e+02
  dihedral pdb=" CA  ILE b  38 "
           pdb=" C   ILE b  38 "
           pdb=" N   LEU b  39 "
           pdb=" CA  LEU b  39 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  132.28   47.72     0      5.00e+00 4.00e-02 9.11e+01
  dihedral pdb=" CA  ASP m 159 "
           pdb=" C   ASP m 159 "
           pdb=" N   PHE m 160 "
           pdb=" CA  PHE m 160 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.29   35.71     0      5.00e+00 4.00e-02 5.10e+01
  ... (remaining 5173 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1040
       0.068 -    0.135: 241
       0.135 -    0.203: 22
       0.203 -    0.270: 5
       0.270 -    0.338: 1
  Chirality restraints: 1309
  Sorted by residual:
  chirality pdb=" CB  ILE d  78 "
            pdb=" CA  ILE d  78 "
            pdb=" CG1 ILE d  78 "
            pdb=" CG2 ILE d  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.31    0.34 2.00e-01 2.50e+01 2.86e+00
  chirality pdb=" CG  LEU f  90 "
            pdb=" CB  LEU f  90 "
            pdb=" CD1 LEU f  90 "
            pdb=" CD2 LEU f  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.36   -0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CA  TYR d  79 "
            pdb=" N   TYR d  79 "
            pdb=" C   TYR d  79 "
            pdb=" CB  TYR d  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.20e+00
  ... (remaining 1306 not shown)

  Planarity restraints: 1492
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE m 157 "   -0.022 2.00e-02 2.50e+03   2.51e-02 1.10e+01
        pdb=" CG  PHE m 157 "    0.058 2.00e-02 2.50e+03
        pdb=" CD1 PHE m 157 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD2 PHE m 157 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 PHE m 157 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE m 157 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE m 157 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN n 222 "   -0.050 5.00e-02 4.00e+02   7.61e-02 9.27e+00
        pdb=" N   PRO n 223 "    0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO n 223 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO n 223 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE n 140 "    0.044 5.00e-02 4.00e+02   6.65e-02 7.07e+00
        pdb=" N   PRO n 141 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO n 141 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO n 141 "    0.036 5.00e-02 4.00e+02
  ... (remaining 1489 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 2100
        2.80 -     3.32: 7266
        3.32 -     3.85: 13211
        3.85 -     4.37: 14744
        4.37 -     4.90: 26395
  Nonbonded interactions: 63716
  Sorted by model distance:
  nonbonded pdb=" O   GLN e  92 "
            pdb=" OH  TYR e  96 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" O   THR d  47 "
            pdb=" OH  TYR d  71 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" NH1 ARG d  57 "
            pdb=" O   ARG m 185 "
     model   vdw
     2.297 3.120
  nonbonded pdb=" OD1 ASP g  35 "
            pdb=" OH  TYR g 101 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" O   PHE m 160 "
            pdb=" OG1 THR m 164 "
     model   vdw
     2.313 3.040
  ... (remaining 63711 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'a' and resid 24 through 55)
  selection = chain 'b'
}
ncs_group {
  reference = chain 'e'
  selection = (chain 'f' and resid 33 through 155)
}

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:             0.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.890
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
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      :  0.008   0.131   8619  Z= 0.490
  Angle     :  1.011  12.938  11687  Z= 0.558
  Chirality :  0.057   0.338   1309
  Planarity :  0.007   0.076   1492
  Dihedral  : 10.827  78.503   3132
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.19 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  3.72 %
    Favored  : 95.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

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: -3.45 (0.21), residues: 1057
  helix: -1.00 (0.26), residues: 249
  sheet: -1.78 (0.27), residues: 270
  loop : -3.29 (0.21), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP n 179 
 HIS   0.008   0.002   HIS n 173 
 PHE   0.058   0.003   PHE m 157 
 TYR   0.039   0.003   TYR e 149 
 ARG   0.007   0.001   ARG n 228 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  357 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 350
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: f  111 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.7800 (m-10)
REVERT: m  138 ASP cc_start: 0.7993 (t0) cc_final: 0.7781 (t0)
REVERT: n   69 VAL cc_start: 0.8985 (m) cc_final: 0.8726 (p)
REVERT: n  208 CYS cc_start: 0.8034 (m) cc_final: 0.7003 (m)
  outliers start: 7
  outliers final: 3
  residues processed: 356
  average time/residue: 0.1938
  time to fit residues: 93.7956
Evaluate side-chains
  211 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 207
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   27 LEU
Chi-restraints excluded: chain f residue  111 TYR
Chi-restraints excluded: chain e residue   92 GLN
Chi-restraints excluded: chain e residue   97 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 41 optimal weight:    7.9990
   chunk 80 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0770
   chunk 49 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   chunk 93 optimal weight:    0.0370
   overall best weight:    0.7620

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

Flipped N/Q/H residues before XYZ refinement:
d  94 GLN
f  92 GLN
g  28 ASN
m  28 GLN
m 199 ASN
m 211 ASN
n 122 GLN
e  60 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.141239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.109367 restraints weight = 13241.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.112806 restraints weight = 8174.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.114257 restraints weight = 5623.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.3167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8619  Z= 0.222
  Angle     :  0.711  12.227  11687  Z= 0.369
  Chirality :  0.045   0.282   1309
  Planarity :  0.005   0.048   1492
  Dihedral  :  6.826  58.776   1167
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.77 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 14.03 %
    Favored  : 82.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

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: -2.07 (0.24), residues: 1057
  helix:  1.11 (0.30), residues: 261
  sheet: -1.19 (0.28), residues: 285
  loop : -2.93 (0.23), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP m 271 
 HIS   0.003   0.001   HIS n 226 
 PHE   0.024   0.002   PHE m 157 
 TYR   0.026   0.002   TYR n  50 
 ARG   0.007   0.001   ARG m 185 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 239
  time to evaluate  : 0.958 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   50 PHE cc_start: 0.7183 (t80) cc_final: 0.6608 (t80)
REVERT: d   55 ILE cc_start: 0.8088 (tt) cc_final: 0.7802 (tt)
REVERT: f   75 ILE cc_start: 0.8809 (mt) cc_final: 0.8567 (mp)
REVERT: f   86 GLU cc_start: 0.8343 (mp0) cc_final: 0.7975 (mp0)
REVERT: f  111 TYR cc_start: 0.7872 (OUTLIER) cc_final: 0.7289 (m-80)
REVERT: f  122 CYS cc_start: 0.3675 (t) cc_final: 0.3148 (t)
REVERT: g  109 GLU cc_start: 0.7210 (mp0) cc_final: 0.6914 (mm-30)
REVERT: m   63 ARG cc_start: 0.7616 (mmm-85) cc_final: 0.7403 (mmm160)
REVERT: m  207 ASN cc_start: 0.8146 (t0) cc_final: 0.7763 (t0)
REVERT: m  233 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7054 (mm-30)
REVERT: n   32 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8164 (pp)
REVERT: n   38 MET cc_start: 0.8478 (tpp) cc_final: 0.7841 (tmm)
REVERT: n  204 ASP cc_start: 0.8067 (p0) cc_final: 0.7805 (p0)
REVERT: e   64 LYS cc_start: 0.8410 (tptm) cc_final: 0.7914 (mtmt)
  outliers start: 30
  outliers final: 23
  residues processed: 255
  average time/residue: 0.1889
  time to fit residues: 66.7293
Evaluate side-chains
  231 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 206
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   27 LEU
Chi-restraints excluded: chain a residue   44 VAL
Chi-restraints excluded: chain d residue   39 THR
Chi-restraints excluded: chain d residue   93 CYS
Chi-restraints excluded: chain f residue  111 TYR
Chi-restraints excluded: chain f residue  119 CYS
Chi-restraints excluded: chain f residue  146 LEU
Chi-restraints excluded: chain g residue   90 SER
Chi-restraints excluded: chain g residue  114 THR
Chi-restraints excluded: chain g residue  127 PHE
Chi-restraints excluded: chain g residue  131 VAL
Chi-restraints excluded: chain m residue   54 TYR
Chi-restraints excluded: chain m residue  106 SER
Chi-restraints excluded: chain m residue  264 LEU
Chi-restraints excluded: chain n residue   32 LEU
Chi-restraints excluded: chain n residue   39 THR
Chi-restraints excluded: chain n residue   40 LEU
Chi-restraints excluded: chain n residue   75 ASP
Chi-restraints excluded: chain n residue  187 SER
Chi-restraints excluded: chain n residue  286 LEU
Chi-restraints excluded: chain n residue  301 LEU
Chi-restraints excluded: chain e residue   39 SER
Chi-restraints excluded: chain e residue   92 GLN
Chi-restraints excluded: chain e residue   97 VAL
Chi-restraints excluded: chain e residue  122 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 87 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 73 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 95 optimal weight:    5.9990
   chunk 82 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 65 optimal weight:    7.9990
   chunk 84 optimal weight:    0.9980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
m 211 ASN
n 104 GLN
n 221 GLN
e  61 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.140639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.109306 restraints weight = 13250.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.112999 restraints weight = 8924.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.114050 restraints weight = 6139.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.3646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   8619  Z= 0.227
  Angle     :  0.656   9.809  11687  Z= 0.342
  Chirality :  0.044   0.263   1309
  Planarity :  0.004   0.045   1492
  Dihedral  :  6.704  58.465   1167
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 14.98 %
    Favored  : 80.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.39 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.25), residues: 1057
  helix:  1.92 (0.31), residues: 261
  sheet: -0.70 (0.29), residues: 280
  loop : -2.75 (0.24), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP m 197 
 HIS   0.003   0.001   HIS f  61 
 PHE   0.020   0.001   PHE m 157 
 TYR   0.026   0.002   TYR n  83 
 ARG   0.006   0.001   ARG m 269 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 218
  time to evaluate  : 1.050 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   50 PHE cc_start: 0.7313 (t80) cc_final: 0.6786 (t80)
REVERT: f   56 GLU cc_start: 0.5741 (tt0) cc_final: 0.5097 (tt0)
REVERT: f  111 TYR cc_start: 0.7754 (OUTLIER) cc_final: 0.7156 (m-80)
REVERT: g  109 GLU cc_start: 0.7471 (mp0) cc_final: 0.6897 (mp0)
REVERT: m   63 ARG cc_start: 0.7675 (mmm-85) cc_final: 0.7447 (mmm160)
REVERT: m  207 ASN cc_start: 0.8115 (t0) cc_final: 0.7792 (t0)
REVERT: n   32 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8137 (pp)
REVERT: n   38 MET cc_start: 0.8400 (tpp) cc_final: 0.7671 (tmm)
REVERT: n   73 ILE cc_start: 0.8571 (mp) cc_final: 0.7861 (tp)
REVERT: n  204 ASP cc_start: 0.8172 (p0) cc_final: 0.7801 (p0)
REVERT: e   64 LYS cc_start: 0.8451 (tptm) cc_final: 0.8031 (mtmt)
REVERT: e  101 ARG cc_start: 0.7613 (mmm160) cc_final: 0.7193 (mmt180)
REVERT: e  124 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7306 (mm-30)
  outliers start: 44
  outliers final: 31
  residues processed: 248
  average time/residue: 0.1876
  time to fit residues: 65.1660
Evaluate side-chains
  234 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 201
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   27 LEU
Chi-restraints excluded: chain a residue   44 VAL
Chi-restraints excluded: chain b residue   39 LEU
Chi-restraints excluded: chain b residue   50 PHE
Chi-restraints excluded: chain d residue   29 LEU
Chi-restraints excluded: chain d residue   39 THR
Chi-restraints excluded: chain d residue   93 CYS
Chi-restraints excluded: chain f residue  107 ASP
Chi-restraints excluded: chain f residue  111 TYR
Chi-restraints excluded: chain f residue  119 CYS
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain f residue  146 LEU
Chi-restraints excluded: chain f residue  148 VAL
Chi-restraints excluded: chain g residue   90 SER
Chi-restraints excluded: chain g residue  114 THR
Chi-restraints excluded: chain g residue  127 PHE
Chi-restraints excluded: chain g residue  131 VAL
Chi-restraints excluded: chain m residue  106 SER
Chi-restraints excluded: chain m residue  154 VAL
Chi-restraints excluded: chain m residue  255 LEU
Chi-restraints excluded: chain m residue  264 LEU
Chi-restraints excluded: chain n residue   32 LEU
Chi-restraints excluded: chain n residue   39 THR
Chi-restraints excluded: chain n residue   40 LEU
Chi-restraints excluded: chain n residue  106 SER
Chi-restraints excluded: chain n residue  286 LEU
Chi-restraints excluded: chain n residue  301 LEU
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain e residue   39 SER
Chi-restraints excluded: chain e residue   92 GLN
Chi-restraints excluded: chain e residue   97 VAL
Chi-restraints excluded: chain e residue  122 CYS
Chi-restraints excluded: chain e residue  146 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 91 optimal weight:    0.9990
   chunk 65 optimal weight:    0.3980
   chunk 90 optimal weight:    0.8980
   chunk 76 optimal weight:    0.8980
   chunk 57 optimal weight:    0.0030
   chunk 42 optimal weight:    2.9990
   chunk 39 optimal weight:    0.1980
   chunk 88 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 52 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.4590

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

Flipped N/Q/H residues before XYZ refinement:
m 211 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.139509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.107705 restraints weight = 13163.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.112334 restraints weight = 7894.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.113679 restraints weight = 5178.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.4059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8619  Z= 0.161
  Angle     :  0.616   9.585  11687  Z= 0.320
  Chirality :  0.043   0.198   1309
  Planarity :  0.004   0.034   1492
  Dihedral  :  6.303  59.371   1167
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 16.37 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.39 %

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: -0.90 (0.25), residues: 1057
  helix:  2.45 (0.31), residues: 263
  sheet: -0.26 (0.30), residues: 269
  loop : -2.54 (0.24), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP m 197 
 HIS   0.005   0.001   HIS f  61 
 PHE   0.016   0.001   PHE m 157 
 TYR   0.018   0.001   TYR n  50 
 ARG   0.008   0.001   ARG m 269 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 224
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   50 PHE cc_start: 0.7245 (t80) cc_final: 0.6730 (t80)
REVERT: b   40 PHE cc_start: 0.7999 (t80) cc_final: 0.7656 (t80)
REVERT: d   23 LYS cc_start: 0.8838 (mmtt) cc_final: 0.8504 (mmtt)
REVERT: f   86 GLU cc_start: 0.8338 (mp0) cc_final: 0.7894 (mp0)
REVERT: f   90 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8112 (mm)
REVERT: f  150 TYR cc_start: 0.7508 (m-80) cc_final: 0.7133 (t80)
REVERT: g   38 GLU cc_start: 0.6774 (pm20) cc_final: 0.6084 (mt-10)
REVERT: g  103 MET cc_start: 0.7296 (mmm) cc_final: 0.7059 (mmm)
REVERT: n   73 ILE cc_start: 0.8679 (mp) cc_final: 0.8063 (tp)
REVERT: n  204 ASP cc_start: 0.8337 (p0) cc_final: 0.7910 (p0)
REVERT: e   64 LYS cc_start: 0.8422 (tptm) cc_final: 0.7908 (mtmt)
  outliers start: 37
  outliers final: 24
  residues processed: 248
  average time/residue: 0.1911
  time to fit residues: 65.4752
Evaluate side-chains
  229 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 204
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   44 VAL
Chi-restraints excluded: chain b residue   39 LEU
Chi-restraints excluded: chain b residue   50 PHE
Chi-restraints excluded: chain d residue   93 CYS
Chi-restraints excluded: chain d residue  120 LEU
Chi-restraints excluded: chain f residue   90 LEU
Chi-restraints excluded: chain f residue  107 ASP
Chi-restraints excluded: chain f residue  111 TYR
Chi-restraints excluded: chain f residue  119 CYS
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain g residue  114 THR
Chi-restraints excluded: chain g residue  127 PHE
Chi-restraints excluded: chain m residue  106 SER
Chi-restraints excluded: chain m residue  255 LEU
Chi-restraints excluded: chain m residue  270 LEU
Chi-restraints excluded: chain n residue   39 THR
Chi-restraints excluded: chain n residue   40 LEU
Chi-restraints excluded: chain n residue  286 LEU
Chi-restraints excluded: chain n residue  301 LEU
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain e residue   39 SER
Chi-restraints excluded: chain e residue   92 GLN
Chi-restraints excluded: chain e residue   97 VAL
Chi-restraints excluded: chain e residue  122 CYS
Chi-restraints excluded: chain e residue  146 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 89 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 68 optimal weight:    8.9990
   chunk 45 optimal weight:    9.9990
   chunk 63 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 99 optimal weight:    0.8980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
m  28 GLN
m 211 ASN
e  60 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.135851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.104545 restraints weight = 13396.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.108076 restraints weight = 8370.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.109690 restraints weight = 5872.541|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.4212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8619  Z= 0.263
  Angle     :  0.648   9.619  11687  Z= 0.338
  Chirality :  0.044   0.208   1309
  Planarity :  0.004   0.055   1492
  Dihedral  :  5.951  57.646   1165
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 18.07 %
    Favored  : 77.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.39 %

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: -0.69 (0.26), residues: 1057
  helix:  2.42 (0.31), residues: 268
  sheet: -0.07 (0.31), residues: 274
  loop : -2.40 (0.25), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP m 197 
 HIS   0.004   0.001   HIS n 226 
 PHE   0.023   0.002   PHE m 157 
 TYR   0.015   0.002   TYR d  71 
 ARG   0.007   0.001   ARG f 117 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 206
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   50 PHE cc_start: 0.7386 (t80) cc_final: 0.7109 (t80)
REVERT: b   40 PHE cc_start: 0.8021 (t80) cc_final: 0.7718 (t80)
REVERT: d   23 LYS cc_start: 0.8940 (mmtt) cc_final: 0.8573 (mmtt)
REVERT: f   86 GLU cc_start: 0.8392 (mp0) cc_final: 0.8062 (mp0)
REVERT: f   90 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8296 (mm)
REVERT: f  111 TYR cc_start: 0.7769 (OUTLIER) cc_final: 0.7003 (m-80)
REVERT: f  149 TYR cc_start: 0.8993 (t80) cc_final: 0.8793 (t80)
REVERT: m  126 THR cc_start: 0.9207 (m) cc_final: 0.8898 (p)
REVERT: n   32 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8080 (pp)
REVERT: n   73 ILE cc_start: 0.8653 (mp) cc_final: 0.8088 (tp)
REVERT: n  204 ASP cc_start: 0.8350 (p0) cc_final: 0.7919 (p0)
REVERT: e   58 LEU cc_start: 0.8772 (mm) cc_final: 0.8520 (mm)
REVERT: e   64 LYS cc_start: 0.8543 (tptm) cc_final: 0.7946 (mtmt)
REVERT: e   92 GLN cc_start: 0.9098 (OUTLIER) cc_final: 0.7728 (mt0)
  outliers start: 41
  outliers final: 30
  residues processed: 231
  average time/residue: 0.1852
  time to fit residues: 60.5242
Evaluate side-chains
  225 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 191
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   26 LEU
Chi-restraints excluded: chain a residue   44 VAL
Chi-restraints excluded: chain b residue   50 PHE
Chi-restraints excluded: chain d residue   29 LEU
Chi-restraints excluded: chain d residue   39 THR
Chi-restraints excluded: chain d residue   93 CYS
Chi-restraints excluded: chain f residue   90 LEU
Chi-restraints excluded: chain f residue  107 ASP
Chi-restraints excluded: chain f residue  111 TYR
Chi-restraints excluded: chain f residue  119 CYS
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain f residue  148 VAL
Chi-restraints excluded: chain g residue   47 ASP
Chi-restraints excluded: chain g residue   90 SER
Chi-restraints excluded: chain g residue  114 THR
Chi-restraints excluded: chain g residue  127 PHE
Chi-restraints excluded: chain g residue  131 VAL
Chi-restraints excluded: chain m residue   54 TYR
Chi-restraints excluded: chain m residue  106 SER
Chi-restraints excluded: chain m residue  255 LEU
Chi-restraints excluded: chain m residue  268 LEU
Chi-restraints excluded: chain m residue  270 LEU
Chi-restraints excluded: chain n residue   32 LEU
Chi-restraints excluded: chain n residue   39 THR
Chi-restraints excluded: chain n residue   40 LEU
Chi-restraints excluded: chain n residue  286 LEU
Chi-restraints excluded: chain n residue  291 LEU
Chi-restraints excluded: chain n residue  301 LEU
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain e residue   39 SER
Chi-restraints excluded: chain e residue   92 GLN
Chi-restraints excluded: chain e residue   97 VAL
Chi-restraints excluded: chain e residue  122 CYS
Chi-restraints excluded: chain e residue  146 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 41 optimal weight:    7.9990
   chunk 88 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0870
   chunk 101 optimal weight:    1.9990
   chunk 91 optimal weight:    0.8980
   chunk 92 optimal weight:    4.9990
   chunk 83 optimal weight:    0.6980
   chunk 16 optimal weight:    0.1980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
** m 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
e  60 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.138220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.106491 restraints weight = 13248.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.110783 restraints weight = 8008.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.111927 restraints weight = 5438.894|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.4456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8619  Z= 0.179
  Angle     :  0.618   9.155  11687  Z= 0.322
  Chirality :  0.043   0.210   1309
  Planarity :  0.004   0.040   1492
  Dihedral  :  5.803  58.008   1165
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 19.02 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.39 %

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: -0.47 (0.26), residues: 1057
  helix:  2.65 (0.31), residues: 269
  sheet:  0.13 (0.32), residues: 269
  loop : -2.32 (0.25), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP m 197 
 HIS   0.005   0.001   HIS f  61 
 PHE   0.014   0.001   PHE m  55 
 TYR   0.016   0.001   TYR d  71 
 ARG   0.006   0.001   ARG m 269 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 209
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   50 PHE cc_start: 0.7341 (t80) cc_final: 0.7115 (t80)
REVERT: b   40 PHE cc_start: 0.7999 (t80) cc_final: 0.7708 (t80)
REVERT: f   86 GLU cc_start: 0.8409 (mp0) cc_final: 0.7951 (mp0)
REVERT: f  150 TYR cc_start: 0.7488 (m-80) cc_final: 0.7111 (t80)
REVERT: g   84 MET cc_start: 0.8086 (mmp) cc_final: 0.7858 (mmp)
REVERT: n   32 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8081 (pp)
REVERT: n   73 ILE cc_start: 0.8649 (mp) cc_final: 0.8141 (tp)
REVERT: e   64 LYS cc_start: 0.8476 (tptm) cc_final: 0.7930 (mtmt)
REVERT: e   92 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.7444 (mp10)
  outliers start: 35
  outliers final: 27
  residues processed: 230
  average time/residue: 0.1980
  time to fit residues: 62.3555
Evaluate side-chains
  219 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 190
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   44 VAL
Chi-restraints excluded: chain b residue   50 PHE
Chi-restraints excluded: chain d residue   39 THR
Chi-restraints excluded: chain d residue   40 SER
Chi-restraints excluded: chain d residue   93 CYS
Chi-restraints excluded: chain f residue   39 SER
Chi-restraints excluded: chain f residue  107 ASP
Chi-restraints excluded: chain f residue  111 TYR
Chi-restraints excluded: chain f residue  119 CYS
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain g residue  114 THR
Chi-restraints excluded: chain g residue  127 PHE
Chi-restraints excluded: chain m residue   54 TYR
Chi-restraints excluded: chain m residue  106 SER
Chi-restraints excluded: chain m residue  154 VAL
Chi-restraints excluded: chain m residue  255 LEU
Chi-restraints excluded: chain m residue  264 LEU
Chi-restraints excluded: chain m residue  270 LEU
Chi-restraints excluded: chain n residue   32 LEU
Chi-restraints excluded: chain n residue   33 LYS
Chi-restraints excluded: chain n residue   39 THR
Chi-restraints excluded: chain n residue  187 SER
Chi-restraints excluded: chain n residue  286 LEU
Chi-restraints excluded: chain n residue  301 LEU
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain e residue   39 SER
Chi-restraints excluded: chain e residue   92 GLN
Chi-restraints excluded: chain e residue   97 VAL
Chi-restraints excluded: chain e residue  146 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 84 optimal weight:    0.0870
   chunk 47 optimal weight:    4.9990
   chunk 64 optimal weight:    0.0770
   chunk 37 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   overall best weight:    1.0322

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

Flipped N/Q/H residues before XYZ refinement:
** d  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** m 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.136616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.105266 restraints weight = 13426.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.108070 restraints weight = 8369.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.109449 restraints weight = 6191.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.4627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8619  Z= 0.232
  Angle     :  0.632   9.280  11687  Z= 0.331
  Chirality :  0.043   0.213   1309
  Planarity :  0.004   0.040   1492
  Dihedral  :  5.741  53.121   1165
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 19.13 %
    Favored  : 76.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.39 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.26), residues: 1057
  helix:  2.90 (0.30), residues: 262
  sheet:  0.16 (0.33), residues: 263
  loop : -2.30 (0.25), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP m 197 
 HIS   0.004   0.001   HIS f  61 
 PHE   0.023   0.001   PHE m 262 
 TYR   0.017   0.001   TYR d  71 
 ARG   0.009   0.001   ARG m 269 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 195
  time to evaluate  : 1.015 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   50 PHE cc_start: 0.7448 (t80) cc_final: 0.7192 (t80)
REVERT: b   40 PHE cc_start: 0.8000 (t80) cc_final: 0.7722 (t80)
REVERT: f   86 GLU cc_start: 0.8433 (mp0) cc_final: 0.7947 (mp0)
REVERT: f  111 TYR cc_start: 0.7716 (OUTLIER) cc_final: 0.6939 (m-80)
REVERT: g   38 GLU cc_start: 0.6875 (pm20) cc_final: 0.6187 (mp0)
REVERT: n   32 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8010 (pp)
REVERT: n   73 ILE cc_start: 0.8675 (mp) cc_final: 0.8133 (tp)
REVERT: e   64 LYS cc_start: 0.8459 (tptm) cc_final: 0.7863 (mtmt)
REVERT: e   92 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.7204 (mp10)
  outliers start: 42
  outliers final: 30
  residues processed: 218
  average time/residue: 0.1867
  time to fit residues: 57.1633
Evaluate side-chains
  218 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 185
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   44 VAL
Chi-restraints excluded: chain b residue   50 PHE
Chi-restraints excluded: chain d residue   39 THR
Chi-restraints excluded: chain d residue   93 CYS
Chi-restraints excluded: chain f residue   39 SER
Chi-restraints excluded: chain f residue   40 ILE
Chi-restraints excluded: chain f residue  111 TYR
Chi-restraints excluded: chain f residue  119 CYS
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain g residue   47 ASP
Chi-restraints excluded: chain g residue   90 SER
Chi-restraints excluded: chain g residue  114 THR
Chi-restraints excluded: chain g residue  127 PHE
Chi-restraints excluded: chain m residue   54 TYR
Chi-restraints excluded: chain m residue  106 SER
Chi-restraints excluded: chain m residue  154 VAL
Chi-restraints excluded: chain m residue  205 CYS
Chi-restraints excluded: chain m residue  255 LEU
Chi-restraints excluded: chain m residue  264 LEU
Chi-restraints excluded: chain m residue  270 LEU
Chi-restraints excluded: chain n residue   32 LEU
Chi-restraints excluded: chain n residue   33 LYS
Chi-restraints excluded: chain n residue   39 THR
Chi-restraints excluded: chain n residue   40 LEU
Chi-restraints excluded: chain n residue  106 SER
Chi-restraints excluded: chain n residue  189 VAL
Chi-restraints excluded: chain n residue  286 LEU
Chi-restraints excluded: chain n residue  301 LEU
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain e residue   39 SER
Chi-restraints excluded: chain e residue   92 GLN
Chi-restraints excluded: chain e residue   97 VAL
Chi-restraints excluded: chain e residue  146 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 89 optimal weight:    0.9980
   chunk 102 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 44 optimal weight:    7.9990
   chunk 11 optimal weight:    0.0870
   chunk 25 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 13 optimal weight:    0.3980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.6560

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

Flipped N/Q/H residues before XYZ refinement:
** d  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
m  28 GLN
m 211 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.137963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.106703 restraints weight = 13556.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.109797 restraints weight = 8323.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.111222 restraints weight = 5999.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.4878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8619  Z= 0.188
  Angle     :  0.634   8.946  11687  Z= 0.329
  Chirality :  0.042   0.222   1309
  Planarity :  0.004   0.041   1492
  Dihedral  :  5.596  48.847   1165
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 19.55 %
    Favored  : 76.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

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: -0.27 (0.26), residues: 1057
  helix:  3.09 (0.31), residues: 263
  sheet:  0.23 (0.32), residues: 269
  loop : -2.29 (0.25), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP m  57 
 HIS   0.005   0.001   HIS f  61 
 PHE   0.030   0.001   PHE m  55 
 TYR   0.017   0.001   TYR d  71 
 ARG   0.008   0.001   ARG m  63 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 191
  time to evaluate  : 0.914 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   50 PHE cc_start: 0.7413 (t80) cc_final: 0.7162 (t80)
REVERT: b   40 PHE cc_start: 0.7964 (t80) cc_final: 0.7680 (t80)
REVERT: f   86 GLU cc_start: 0.8426 (mp0) cc_final: 0.7979 (mp0)
REVERT: g   84 MET cc_start: 0.8128 (mmp) cc_final: 0.7737 (mmp)
REVERT: n   32 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8010 (pp)
REVERT: n   73 ILE cc_start: 0.8677 (mp) cc_final: 0.8137 (tp)
REVERT: e   64 LYS cc_start: 0.8441 (tptm) cc_final: 0.7882 (mtmt)
REVERT: e   92 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.7237 (mp10)
  outliers start: 37
  outliers final: 29
  residues processed: 213
  average time/residue: 0.1783
  time to fit residues: 53.5289
Evaluate side-chains
  214 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 183
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   44 VAL
Chi-restraints excluded: chain b residue   31 LEU
Chi-restraints excluded: chain b residue   50 PHE
Chi-restraints excluded: chain d residue   39 THR
Chi-restraints excluded: chain d residue   93 CYS
Chi-restraints excluded: chain f residue   40 ILE
Chi-restraints excluded: chain f residue  111 TYR
Chi-restraints excluded: chain f residue  119 CYS
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain g residue  114 THR
Chi-restraints excluded: chain g residue  127 PHE
Chi-restraints excluded: chain g residue  136 ILE
Chi-restraints excluded: chain m residue   54 TYR
Chi-restraints excluded: chain m residue  106 SER
Chi-restraints excluded: chain m residue  154 VAL
Chi-restraints excluded: chain m residue  211 ASN
Chi-restraints excluded: chain m residue  255 LEU
Chi-restraints excluded: chain m residue  264 LEU
Chi-restraints excluded: chain m residue  270 LEU
Chi-restraints excluded: chain n residue   32 LEU
Chi-restraints excluded: chain n residue   33 LYS
Chi-restraints excluded: chain n residue   39 THR
Chi-restraints excluded: chain n residue   40 LEU
Chi-restraints excluded: chain n residue  286 LEU
Chi-restraints excluded: chain n residue  291 LEU
Chi-restraints excluded: chain n residue  301 LEU
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain e residue   39 SER
Chi-restraints excluded: chain e residue   92 GLN
Chi-restraints excluded: chain e residue   97 VAL
Chi-restraints excluded: chain e residue  126 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 94 optimal weight:    0.9980
   chunk 69 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 101 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 71 optimal weight:    0.7980
   chunk 88 optimal weight:    0.3980
   chunk 31 optimal weight:    3.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** d  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** m  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
m 211 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.140877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.108887 restraints weight = 13366.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.112139 restraints weight = 8286.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.113156 restraints weight = 5903.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.4964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8619  Z= 0.212
  Angle     :  0.649   8.941  11687  Z= 0.333
  Chirality :  0.043   0.215   1309
  Planarity :  0.004   0.049   1492
  Dihedral  :  5.564  45.140   1165
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 20.51 %
    Favored  : 75.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

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 (0.26), residues: 1057
  helix:  3.13 (0.30), residues: 262
  sheet:  0.21 (0.32), residues: 270
  loop : -2.23 (0.25), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP m  57 
 HIS   0.005   0.001   HIS f  61 
 PHE   0.045   0.002   PHE n 219 
 TYR   0.018   0.001   TYR d  71 
 ARG   0.007   0.001   ARG m  63 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 187
  time to evaluate  : 0.879 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   50 PHE cc_start: 0.7455 (t80) cc_final: 0.7185 (t80)
REVERT: b   40 PHE cc_start: 0.7962 (t80) cc_final: 0.7732 (t80)
REVERT: b   52 ARG cc_start: 0.4844 (mtt180) cc_final: 0.4599 (tmm160)
REVERT: f   59 TRP cc_start: 0.8526 (m100) cc_final: 0.8188 (m100)
REVERT: f   86 GLU cc_start: 0.8381 (mp0) cc_final: 0.7968 (mp0)
REVERT: g   38 GLU cc_start: 0.6886 (pm20) cc_final: 0.6020 (mp0)
REVERT: n   32 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.7992 (pp)
REVERT: n   73 ILE cc_start: 0.8681 (mp) cc_final: 0.8133 (tp)
REVERT: e   64 LYS cc_start: 0.8418 (tptm) cc_final: 0.7873 (mtmt)
  outliers start: 36
  outliers final: 33
  residues processed: 207
  average time/residue: 0.1830
  time to fit residues: 53.2174
Evaluate side-chains
  215 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 181
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   44 VAL
Chi-restraints excluded: chain b residue   32 CYS
Chi-restraints excluded: chain b residue   50 PHE
Chi-restraints excluded: chain d residue   29 LEU
Chi-restraints excluded: chain d residue   39 THR
Chi-restraints excluded: chain d residue   93 CYS
Chi-restraints excluded: chain f residue   39 SER
Chi-restraints excluded: chain f residue   40 ILE
Chi-restraints excluded: chain f residue   97 VAL
Chi-restraints excluded: chain f residue  111 TYR
Chi-restraints excluded: chain f residue  119 CYS
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain f residue  147 LEU
Chi-restraints excluded: chain g residue  114 THR
Chi-restraints excluded: chain g residue  127 PHE
Chi-restraints excluded: chain m residue   54 TYR
Chi-restraints excluded: chain m residue  106 SER
Chi-restraints excluded: chain m residue  154 VAL
Chi-restraints excluded: chain m residue  211 ASN
Chi-restraints excluded: chain m residue  255 LEU
Chi-restraints excluded: chain m residue  264 LEU
Chi-restraints excluded: chain m residue  270 LEU
Chi-restraints excluded: chain n residue   32 LEU
Chi-restraints excluded: chain n residue   33 LYS
Chi-restraints excluded: chain n residue   39 THR
Chi-restraints excluded: chain n residue   40 LEU
Chi-restraints excluded: chain n residue  106 SER
Chi-restraints excluded: chain n residue  286 LEU
Chi-restraints excluded: chain n residue  291 LEU
Chi-restraints excluded: chain n residue  301 LEU
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain e residue   39 SER
Chi-restraints excluded: chain e residue   97 VAL
Chi-restraints excluded: chain e residue  126 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 97 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 24 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 95 optimal weight:    9.9990
   chunk 72 optimal weight:    6.9990
   chunk 92 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** d  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** m  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
m 211 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.135540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.103975 restraints weight = 13584.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.106985 restraints weight = 8501.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.108271 restraints weight = 6185.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.5012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8619  Z= 0.279
  Angle     :  0.676   9.124  11687  Z= 0.349
  Chirality :  0.044   0.228   1309
  Planarity :  0.004   0.078   1492
  Dihedral  :  5.403  43.265   1162
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 20.72 %
    Favored  : 75.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

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: -0.28 (0.26), residues: 1057
  helix:  2.99 (0.30), residues: 263
  sheet:  0.11 (0.32), residues: 274
  loop : -2.19 (0.25), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP m  57 
 HIS   0.003   0.001   HIS f  61 
 PHE   0.037   0.002   PHE n 219 
 TYR   0.019   0.001   TYR d  71 
 ARG   0.011   0.001   ARG f 117 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 181
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: b   40 PHE cc_start: 0.8050 (t80) cc_final: 0.7799 (t80)
REVERT: f   86 GLU cc_start: 0.8452 (mp0) cc_final: 0.8016 (mp0)
REVERT: f  111 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.7114 (m-80)
REVERT: g   38 GLU cc_start: 0.6946 (pm20) cc_final: 0.6240 (mp0)
REVERT: n   32 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8026 (pp)
REVERT: n   73 ILE cc_start: 0.8703 (mp) cc_final: 0.8135 (tp)
REVERT: e   64 LYS cc_start: 0.8417 (tptm) cc_final: 0.7845 (mtmt)
  outliers start: 36
  outliers final: 31
  residues processed: 201
  average time/residue: 0.1833
  time to fit residues: 51.8462
Evaluate side-chains
  211 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 178
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   44 VAL
Chi-restraints excluded: chain b residue   32 CYS
Chi-restraints excluded: chain b residue   50 PHE
Chi-restraints excluded: chain d residue   29 LEU
Chi-restraints excluded: chain d residue   39 THR
Chi-restraints excluded: chain d residue   93 CYS
Chi-restraints excluded: chain f residue   39 SER
Chi-restraints excluded: chain f residue   40 ILE
Chi-restraints excluded: chain f residue   97 VAL
Chi-restraints excluded: chain f residue  111 TYR
Chi-restraints excluded: chain f residue  119 CYS
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain f residue  147 LEU
Chi-restraints excluded: chain g residue  114 THR
Chi-restraints excluded: chain g residue  127 PHE
Chi-restraints excluded: chain m residue   54 TYR
Chi-restraints excluded: chain m residue  106 SER
Chi-restraints excluded: chain m residue  154 VAL
Chi-restraints excluded: chain m residue  211 ASN
Chi-restraints excluded: chain m residue  255 LEU
Chi-restraints excluded: chain m residue  264 LEU
Chi-restraints excluded: chain m residue  270 LEU
Chi-restraints excluded: chain n residue   32 LEU
Chi-restraints excluded: chain n residue   33 LYS
Chi-restraints excluded: chain n residue   39 THR
Chi-restraints excluded: chain n residue   40 LEU
Chi-restraints excluded: chain n residue  106 SER
Chi-restraints excluded: chain n residue  291 LEU
Chi-restraints excluded: chain n residue  301 LEU
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain e residue   39 SER
Chi-restraints excluded: chain e residue   97 VAL
Chi-restraints excluded: chain e residue  126 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 72 optimal weight:    7.9990
   chunk 96 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 83 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 102 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** d  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** m  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
m 211 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.137135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.105837 restraints weight = 13591.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.108859 restraints weight = 8362.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.110339 restraints weight = 6100.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.5126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8619  Z= 0.203
  Angle     :  0.652   8.968  11687  Z= 0.335
  Chirality :  0.043   0.230   1309
  Planarity :  0.004   0.056   1492
  Dihedral  :  5.297  43.350   1162
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 21.47 %
    Favored  : 74.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

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: -0.16 (0.26), residues: 1057
  helix:  3.11 (0.30), residues: 263
  sheet:  0.30 (0.33), residues: 258
  loop : -2.13 (0.25), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP m  57 
 HIS   0.005   0.001   HIS f  61 
 PHE   0.034   0.002   PHE n 219 
 TYR   0.019   0.001   TYR d  71 
 ARG   0.008   0.001   ARG f 117 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2822.21 seconds
wall clock time: 49 minutes 37.60 seconds (2977.60 seconds total)