Starting phenix.real_space_refine
on Fri Aug 22 17:15:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9v0u_64672/08_2025/9v0u_64672.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9v0u_64672/08_2025/9v0u_64672.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.51
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9v0u_64672/08_2025/9v0u_64672.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9v0u_64672/08_2025/9v0u_64672.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9v0u_64672/08_2025/9v0u_64672.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9v0u_64672/08_2025/9v0u_64672.cif"
  }
  resolution = 3.51
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.026
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      40      5.16       5
     C    3978      2.51       5
     N    1028      2.21       5
     O    1159      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6205
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "R"
      Number of atoms: 1920
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 1920
          Classifications: {'peptide': 270}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'PTRANS': 6, 'TRANS': 263}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 184
          Unresolved non-hydrogen angles: 231
          Unresolved non-hydrogen dihedrals: 153
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'ASN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 4, 'HIS:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'PHE:plan': 2, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 99
    Chain: "A"
      Number of atoms: 1538
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 205, 1538
          Classifications: {'peptide': 205}
          Incomplete info: {'truncation_to_alanine': 38}
          Link IDs: {'PTRANS': 3, 'TRANS': 201}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 169
          Unresolved non-hydrogen angles: 198
          Unresolved non-hydrogen dihedrals: 145
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 12, 'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 109
    Chain: "G"
      Number of atoms: 360
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 360
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 64
          Unresolved non-hydrogen angles: 74
          Unresolved non-hydrogen dihedrals: 54
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 33
    Chain: "C"
      Number of atoms: 2387
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2387
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PTRANS': 5, 'TRANS': 328}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 181
          Unresolved non-hydrogen angles: 218
          Unresolved non-hydrogen dihedrals: 144
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 6, 'ARG:plan': 12, 'GLU:plan': 5, 'ASN:plan1': 4}
          Unresolved non-hydrogen planarities: 134
  Time building chain proxies: 1.46, per 1000 atoms: 0.24
  Number of scatterers: 6205
  At special positions: 0
  Unit cell: (66.96, 101.37, 120.9, 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      40     16.00
     O    1159      8.00
     N    1028      7.00
     C    3978      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 632 " - pdb=" SG  CYS R 704 " 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: 0.55
  Conformation dependent library (CDL) restraints added in 404.0 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1638

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 8 sheets defined
      45.7% alpha, 15.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'R' and resid 546 through 551
      removed outlier: 3.516A  pdb=" N   MET R 551 " --> pdb=" O   ALA R 548 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 559 through 591
      removed outlier: 3.841A  pdb=" N   VAL R 564 " --> pdb=" O   ARG R 560 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   ALA R 565 " --> pdb=" O   GLY R 561 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU R 581 " --> pdb=" O   SER R 577 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ALA R 583 " --> pdb=" O   LEU R 579 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   THR R 584 " --> pdb=" O   CYS R 580 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 601 through 625
      removed outlier: 3.779A  pdb=" N   ILE R 621 " --> pdb=" O   VAL R 617 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ARG R 624 " --> pdb=" O   LEU R 620 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 629 through 662
      removed outlier: 4.228A  pdb=" N   VAL R 637 " --> pdb=" O   GLN R 633 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   LEU R 638 " --> pdb=" O   VAL R 634 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU R 639 " --> pdb=" O   MET R 635 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   HIS R 640 " --> pdb=" O   ALA R 636 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   SER R 659 " --> pdb=" O   LEU R 655 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 671 through 695
      removed outlier: 3.976A  pdb=" N   GLY R 677 " --> pdb=" O   ARG R 673 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   PHE R 682 " --> pdb=" O   MET R 678 " (cutoff:3.500A)
      Proline residue:  R 683  - end of helix
    Processing helix  chain 'R' and resid 696 through 698
      No H-bonds generated for 'chain 'R' and resid 696 through 698'
    Processing helix  chain 'R' and resid 713 through 740
      Proline residue:  R 719  - end of helix
    Processing helix  chain 'R' and resid 741 through 743
      No H-bonds generated for 'chain 'R' and resid 741 through 743'
    Processing helix  chain 'R' and resid 756 through 770
      removed outlier: 3.533A  pdb=" N   VAL R 762 " --> pdb=" O   THR R 758 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LEU R 765 " --> pdb=" O   ALA R 761 " (cutoff:3.500A)
      Proline residue:  R 767  - end of helix
    Processing helix  chain 'R' and resid 773 through 778
      removed outlier: 4.154A  pdb=" N   VAL R 777 " --> pdb=" O   TRP R 773 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LEU R 778 " --> pdb=" O   VAL R 774 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 773 through 778'
    Processing helix  chain 'R' and resid 785 through 795
      removed outlier: 3.510A  pdb=" N   TYR R 789 " --> pdb=" O   VAL R 785 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   THR R 793 " --> pdb=" O   TYR R 789 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ASN R 795 " --> pdb=" O   PHE R 791 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 797 through 807
    Processing helix  chain 'R' and resid 810 through 826
    Processing helix  chain 'A' and resid 10 through 33
      removed outlier: 3.643A  pdb=" N   CYS A  22 " --> pdb=" O   GLU A  18 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   THR A  28 " --> pdb=" O   SER A  24 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   TYR A  29 " --> pdb=" O   ARG A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 44
    Processing helix  chain 'A' and resid 45 through 55
      removed outlier: 3.793A  pdb=" N   GLN A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 98
      removed outlier: 4.020A  pdb=" N   PHE A  97 " --> pdb=" O   ARG A  93 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   GLU A  98 " --> pdb=" O   LYS A  94 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 93 through 98'
    Processing helix  chain 'A' and resid 99 through 101
      No H-bonds generated for 'chain 'A' and resid 99 through 101'
    Processing helix  chain 'A' and resid 114 through 116
      No H-bonds generated for 'chain 'A' and resid 114 through 116'
    Processing helix  chain 'A' and resid 117 through 130
      removed outlier: 3.590A  pdb=" N   GLU A 126 " --> pdb=" O   LEU A 122 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   THR A 127 " --> pdb=" O   ASN A 123 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ILE A 128 " --> pdb=" O   ASP A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 153
      removed outlier: 4.101A  pdb=" N   GLU A 151 " --> pdb=" O   ASP A 147 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   LYS A 152 " --> pdb=" O   LEU A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 162
      removed outlier: 4.013A  pdb=" N   TYR A 161 " --> pdb=" O   SER A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 187
      removed outlier: 3.520A  pdb=" N   LEU A 179 " --> pdb=" O   VAL A 175 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   VAL A 180 " --> pdb=" O   GLN A 176 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ARG A 187 " --> pdb=" O   PHE A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 228
    Processing helix  chain 'G' and resid 9 through 24
      removed outlier: 3.804A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'C' and resid 5 through 26
      removed outlier: 3.701A  pdb=" N   GLU C  12 " --> pdb=" O   ARG C   8 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   GLN C  13 " --> pdb=" O   GLN C   9 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LEU C  14 " --> pdb=" O   GLU C  10 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   LYS C  15 " --> pdb=" O   ALA C  11 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ASN C  16 " --> pdb=" O   GLU C  12 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLN C  17 " --> pdb=" O   GLN C  13 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LYS C  23 " --> pdb=" O   ARG C  19 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 34
    Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 70
      removed outlier: 3.644A  pdb=" N   VAL A  86 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   LEU A  37 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
      removed outlier: 7.646A  pdb=" N   LEU A 109 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   LEU A  39 " --> pdb=" O   LEU A 109 " (cutoff:3.500A)
      removed outlier: 8.879A  pdb=" N   ASP A 111 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   ILE A 106 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   PHE A 142 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 5.954A  pdb=" N   PHE A 108 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ASN A 144 " --> pdb=" O   PHE A 108 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   VAL A 110 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   ILE A 139 " --> pdb=" O   TYR A 196 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   HIS A 198 " --> pdb=" O   ILE A 139 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   LEU A 141 " --> pdb=" O   HIS A 198 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 58 through 63
      removed outlier: 3.555A  pdb=" N   ALA C  60 " --> pdb=" O   ALA C  73 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   SER C  74 " --> pdb=" O   LYS C  78 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   HIS C  91 " --> pdb=" O   ILE C  81 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   ASP C  83 " --> pdb=" O   LYS C  89 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   LYS C  89 " --> pdb=" O   ASP C  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 105
      removed outlier: 6.886A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 5.155A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 7.358A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   ILE C 123 " --> pdb=" O   SER C 136 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ARG C 134 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 148 through 151
      removed outlier: 3.613A  pdb=" N   THR C 178 " --> pdb=" O   LEU C 168 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 189 through 192
      removed outlier: 3.530A  pdb=" N   SER C 191 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLN C 220 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   CYS C 218 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 229 through 234
      removed outlier: 7.009A  pdb=" N   GLY C 244 " --> pdb=" O   ASN C 230 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   ILE C 232 " --> pdb=" O   ALA C 242 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   ALA C 242 " --> pdb=" O   ILE C 232 " (cutoff:3.500A)
      removed outlier: 4.979A  pdb=" N   PHE C 234 " --> pdb=" O   ALA C 240 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   ALA C 240 " --> pdb=" O   PHE C 234 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   PHE C 253 " --> pdb=" O   PHE C 241 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   MET C 262 " --> pdb=" O   LEU C 252 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   ASP C 254 " --> pdb=" O   GLU C 260 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   GLU C 260 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 276 through 278
    Processing sheet with id=AA8, first strand: chain 'C' and resid 315 through 320

    298 hydrogen bonds defined for protein.
    870 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.09

  Time building geometry restraints manager: 0.74 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: 1929
        1.34 -     1.45: 938
        1.45 -     1.57: 3405
        1.57 -     1.69: 0
        1.69 -     1.81: 55
  Bond restraints: 6327
  Sorted by residual:
  bond pdb=" CA  GLN A 226 "
       pdb=" C   GLN A 226 "
    ideal  model  delta    sigma   weight residual
    1.524  1.496  0.028 1.32e-02 5.74e+03 4.46e+00
  bond pdb=" CA  LYS C 301 "
       pdb=" C   LYS C 301 "
    ideal  model  delta    sigma   weight residual
    1.532  1.512  0.020 1.15e-02 7.56e+03 2.91e+00
  bond pdb=" CA  ARG C 304 "
       pdb=" C   ARG C 304 "
    ideal  model  delta    sigma   weight residual
    1.530  1.511  0.018 1.11e-02 8.12e+03 2.74e+00
  bond pdb=" CA  VAL A  86 "
       pdb=" C   VAL A  86 "
    ideal  model  delta    sigma   weight residual
    1.527  1.511  0.016 9.70e-03 1.06e+04 2.73e+00
  bond pdb=" N   GLN R 616 "
       pdb=" CA  GLN R 616 "
    ideal  model  delta    sigma   weight residual
    1.459  1.439  0.020 1.20e-02 6.94e+03 2.71e+00
  ... (remaining 6322 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.22: 8102
        1.22 -     2.44: 435
        2.44 -     3.66: 80
        3.66 -     4.88: 27
        4.88 -     6.09: 8
  Bond angle restraints: 8652
  Sorted by residual:
  angle pdb=" N   CYS C 271 "
        pdb=" CA  CYS C 271 "
        pdb=" C   CYS C 271 "
      ideal   model   delta    sigma   weight residual
     111.07  115.11   -4.04 1.07e+00 8.73e-01 1.42e+01
  angle pdb=" N   THR C 165 "
        pdb=" CA  THR C 165 "
        pdb=" C   THR C 165 "
      ideal   model   delta    sigma   weight residual
     108.90  114.99   -6.09 1.63e+00 3.76e-01 1.40e+01
  angle pdb=" C   GLN A 226 "
        pdb=" CA  GLN A 226 "
        pdb=" CB  GLN A 226 "
      ideal   model   delta    sigma   weight residual
     110.81  105.14    5.67 1.60e+00 3.91e-01 1.26e+01
  angle pdb=" N   ASP C 291 "
        pdb=" CA  ASP C 291 "
        pdb=" C   ASP C 291 "
      ideal   model   delta    sigma   weight residual
     112.93  109.04    3.89 1.12e+00 7.97e-01 1.20e+01
  angle pdb=" C   LYS C 301 "
        pdb=" CA  LYS C 301 "
        pdb=" CB  LYS C 301 "
      ideal   model   delta    sigma   weight residual
     114.40  110.23    4.17 1.25e+00 6.40e-01 1.11e+01
  ... (remaining 8647 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.51: 3356
       17.51 -    35.02: 256
       35.02 -    52.53: 37
       52.53 -    70.04: 6
       70.04 -    87.55: 3
  Dihedral angle restraints: 3658
    sinusoidal: 1146
      harmonic: 2512
  Sorted by residual:
  dihedral pdb=" CB  CYS R 632 "
           pdb=" SG  CYS R 632 "
           pdb=" SG  CYS R 704 "
           pdb=" CB  CYS R 704 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -139.84   53.84     1      1.00e+01 1.00e-02 3.94e+01
  dihedral pdb=" CA  LYS R 663 "
           pdb=" C   LYS R 663 "
           pdb=" N   VAL R 664 "
           pdb=" CA  VAL R 664 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.64  -19.36     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" CA  THR C 249 "
           pdb=" C   THR C 249 "
           pdb=" N   CYS C 250 "
           pdb=" CA  CYS C 250 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.87   16.13     0      5.00e+00 4.00e-02 1.04e+01
  ... (remaining 3655 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 716
       0.036 -    0.073: 256
       0.073 -    0.109: 75
       0.109 -    0.145: 15
       0.145 -    0.182: 1
  Chirality restraints: 1063
  Sorted by residual:
  chirality pdb=" CA  ASP C 333 "
            pdb=" N   ASP C 333 "
            pdb=" C   ASP C 333 "
            pdb=" CB  ASP C 333 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.24e-01
  chirality pdb=" CA  VAL A  86 "
            pdb=" N   VAL A  86 "
            pdb=" C   VAL A  86 "
            pdb=" CB  VAL A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.11e-01
  chirality pdb=" CA  VAL A 156 "
            pdb=" N   VAL A 156 "
            pdb=" C   VAL A 156 "
            pdb=" CB  VAL A 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.58e-01
  ... (remaining 1060 not shown)

  Planarity restraints: 1092
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R 793 "   -0.010 2.00e-02 2.50e+03   2.14e-02 4.57e+00
        pdb=" C   THR R 793 "    0.037 2.00e-02 2.50e+03
        pdb=" O   THR R 793 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   LEU R 794 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C 235 "   -0.035 5.00e-02 4.00e+02   5.23e-02 4.38e+00
        pdb=" N   PRO C 236 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO C 236 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO C 236 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR R 630 "   -0.021 5.00e-02 4.00e+02   3.19e-02 1.63e+00
        pdb=" N   PRO R 631 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO R 631 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO R 631 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1089 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 406
        2.73 -     3.27: 6783
        3.27 -     3.81: 10439
        3.81 -     4.36: 12582
        4.36 -     4.90: 20602
  Nonbonded interactions: 50812
  Sorted by model distance:
  nonbonded pdb=" O   LEU R 708 "
            pdb=" CD1 LEU R 708 "
     model   vdw
     2.186 3.460
  nonbonded pdb=" OG1 THR A 200 "
            pdb=" OD1 ASN A 207 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" OD1 ASN A 144 "
            pdb=" N   LYS A 145 "
     model   vdw
     2.230 3.120
  nonbonded pdb=" ND2 ASN R 727 "
            pdb=" O   LEU R 769 "
     model   vdw
     2.244 3.120
  nonbonded pdb=" O   PHE R 588 "
            pdb=" OG  SER R 592 "
     model   vdw
     2.246 3.040
  ... (remaining 50807 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.530
  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:             0.020
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.630
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7097
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      :  0.003   0.034   6328  Z= 0.212
  Angle     :  0.658   6.094   8654  Z= 0.410
  Chirality :  0.041   0.182   1063
  Planarity :  0.003   0.052   1092
  Dihedral  : 12.777  87.547   2017
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 15.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  4.33 %
    Favored  : 94.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.35 (0.29), residues: 844
  helix:  0.64 (0.29), residues: 310
  sheet: -0.95 (0.42), residues: 161
  loop : -0.51 (0.34), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  54 
 TYR   0.019   0.001   TYR C  59 
 PHE   0.016   0.001   PHE C 234 
 TRP   0.011   0.001   TRP C 339 
 HIS   0.005   0.001   HIS C 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 6327)
  covalent geometry    : angle       0.65758 ( 8652)
  SS BOND              : bond        0.00256 (    1)
  SS BOND              : angle       2.36400 (    2)
  hydrogen bonds       : bond        0.26726 (  298)
  hydrogen bonds       : angle       8.73124 (  870)

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 199
  time to evaluate  : 0.144 
Fit side-chains
REVERT: R  618 LEU cc_start: 0.6636 (tp) cc_final: 0.6394 (tp)
REVERT: R  655 LEU cc_start: 0.7960 (mt) cc_final: 0.7641 (mt)
REVERT: R  701 SER cc_start: 0.8478 (t) cc_final: 0.7913 (p)
REVERT: A   98 GLU cc_start: 0.6623 (mp0) cc_final: 0.6274 (mp0)
REVERT: A  106 ILE cc_start: 0.8409 (mt) cc_final: 0.8171 (mt)
REVERT: A  124 ASP cc_start: 0.7638 (t0) cc_final: 0.6677 (t0)
REVERT: A  211 ILE cc_start: 0.7362 (mm) cc_final: 0.6996 (mt)
REVERT: A  228 MET cc_start: 0.6488 (OUTLIER) cc_final: 0.6142 (mtp)
REVERT: C  217 MET cc_start: 0.5928 (ptt) cc_final: 0.4708 (ptt)
REVERT: C  230 ASN cc_start: 0.8077 (m110) cc_final: 0.7706 (m110)
REVERT: C  233 CYS cc_start: 0.7221 (t) cc_final: 0.6750 (t)
REVERT: C  278 PHE cc_start: 0.7136 (m-80) cc_final: 0.6320 (m-80)
REVERT: C  339 TRP cc_start: 0.7251 (m-10) cc_final: 0.6718 (m-10)
  outliers start: 5
  outliers final: 1
  residues processed: 201
  average time/residue: 0.0629
  time to fit residues: 16.8624
Evaluate side-chains
  188 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 186
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain C residue  225 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0570
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
A 136 ASN
A 226 GLN
** C  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  75 GLN
C 183 HIS
C 239 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.131986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.113609 restraints weight = 10380.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.117409 restraints weight = 4890.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.119755 restraints weight = 2860.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.121177 restraints weight = 1983.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.122121 restraints weight = 1556.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7073
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6328  Z= 0.145
  Angle     :  0.569   8.203   8654  Z= 0.302
  Chirality :  0.044   0.220   1063
  Planarity :  0.004   0.052   1092
  Dihedral  :  5.006  48.757    896
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 17.80 %
    Favored  : 80.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.30), residues: 844
  helix:  1.28 (0.29), residues: 331
  sheet: -0.56 (0.41), residues: 156
  loop : -0.23 (0.35), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 214 
 TYR   0.015   0.001   TYR C  59 
 PHE   0.020   0.001   PHE A  74 
 TRP   0.010   0.002   TRP C 339 
 HIS   0.004   0.001   HIS C 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 6327)
  covalent geometry    : angle       0.56879 ( 8652)
  SS BOND              : bond        0.00022 (    1)
  SS BOND              : angle       1.18433 (    2)
  hydrogen bonds       : bond        0.04557 (  298)
  hydrogen bonds       : angle       5.24502 (  870)

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 206
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  655 LEU cc_start: 0.7659 (mt) cc_final: 0.7320 (mt)
REVERT: R  701 SER cc_start: 0.8556 (t) cc_final: 0.8053 (p)
REVERT: A   78 ASN cc_start: 0.7303 (t0) cc_final: 0.6954 (t0)
REVERT: A   98 GLU cc_start: 0.6658 (mp0) cc_final: 0.6452 (mp0)
REVERT: A  228 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.6586 (mpp)
REVERT: G   38 MET cc_start: 0.7272 (tpt) cc_final: 0.7050 (tpt)
REVERT: C  152 LEU cc_start: 0.8181 (tt) cc_final: 0.7945 (tp)
REVERT: C  204 CYS cc_start: 0.6888 (m) cc_final: 0.6561 (m)
REVERT: C  223 THR cc_start: 0.8531 (p) cc_final: 0.8315 (m)
REVERT: C  230 ASN cc_start: 0.7848 (m110) cc_final: 0.7547 (m110)
REVERT: C  233 CYS cc_start: 0.7135 (t) cc_final: 0.6910 (t)
REVERT: C  277 SER cc_start: 0.7852 (t) cc_final: 0.7530 (p)
REVERT: C  278 PHE cc_start: 0.7093 (m-80) cc_final: 0.6782 (m-80)
REVERT: C  283 ARG cc_start: 0.7862 (tpt-90) cc_final: 0.7636 (tpt-90)
REVERT: C  294 CYS cc_start: 0.7307 (t) cc_final: 0.7098 (t)
  outliers start: 12
  outliers final: 9
  residues processed: 207
  average time/residue: 0.0672
  time to fit residues: 18.4456
Evaluate side-chains
  204 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 194
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  558 LEU
Chi-restraints excluded: chain R residue  620 LEU
Chi-restraints excluded: chain R residue  741 ILE
Chi-restraints excluded: chain R residue  772 SER
Chi-restraints excluded: chain R residue  774 VAL
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  225 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 59 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 54 optimal weight:    9.9990
   chunk 31 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 79 optimal weight:    0.1980
   chunk 12 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 136 ASN
** C  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  75 GLN
C 230 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.130911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.112362 restraints weight = 10254.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.116075 restraints weight = 4921.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.118406 restraints weight = 2933.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.119863 restraints weight = 2053.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.121102 restraints weight = 1613.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7097
moved from start:          0.2343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6328  Z= 0.161
  Angle     :  0.551   7.488   8654  Z= 0.294
  Chirality :  0.043   0.197   1063
  Planarity :  0.004   0.052   1092
  Dihedral  :  5.016  51.614    896
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 19.30 %
    Favored  : 76.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.30), residues: 844
  helix:  1.43 (0.29), residues: 334
  sheet: -0.42 (0.42), residues: 153
  loop : -0.28 (0.35), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  90 
 TYR   0.016   0.001   TYR A  29 
 PHE   0.017   0.001   PHE A  74 
 TRP   0.011   0.002   TRP R 649 
 HIS   0.003   0.001   HIS C 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 6327)
  covalent geometry    : angle       0.55094 ( 8652)
  SS BOND              : bond        0.00581 (    1)
  SS BOND              : angle       1.14019 (    2)
  hydrogen bonds       : bond        0.03968 (  298)
  hydrogen bonds       : angle       4.80548 (  870)

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 205
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
REVERT: R  551 MET cc_start: 0.6121 (mmm) cc_final: 0.5864 (mmm)
REVERT: R  655 LEU cc_start: 0.7681 (mt) cc_final: 0.7462 (mt)
REVERT: R  701 SER cc_start: 0.8595 (t) cc_final: 0.8125 (p)
REVERT: R  708 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7465 (pp)
REVERT: A   78 ASN cc_start: 0.7389 (t0) cc_final: 0.7030 (t0)
REVERT: A   98 GLU cc_start: 0.6736 (mp0) cc_final: 0.6401 (mp0)
REVERT: A  228 MET cc_start: 0.7284 (OUTLIER) cc_final: 0.6377 (mpp)
REVERT: G   38 MET cc_start: 0.7196 (tpt) cc_final: 0.6990 (tpt)
REVERT: C  204 CYS cc_start: 0.6926 (m) cc_final: 0.6524 (m)
REVERT: C  223 THR cc_start: 0.8416 (p) cc_final: 0.8198 (m)
REVERT: C  230 ASN cc_start: 0.7919 (m-40) cc_final: 0.7633 (m110)
REVERT: C  233 CYS cc_start: 0.7052 (t) cc_final: 0.6841 (t)
REVERT: C  278 PHE cc_start: 0.7132 (m-80) cc_final: 0.6782 (m-80)
  outliers start: 24
  outliers final: 16
  residues processed: 215
  average time/residue: 0.0621
  time to fit residues: 17.8020
Evaluate side-chains
  220 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 202
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  558 LEU
Chi-restraints excluded: chain R residue  576 LEU
Chi-restraints excluded: chain R residue  580 CYS
Chi-restraints excluded: chain R residue  590 VAL
Chi-restraints excluded: chain R residue  594 VAL
Chi-restraints excluded: chain R residue  613 LEU
Chi-restraints excluded: chain R residue  620 LEU
Chi-restraints excluded: chain R residue  708 LEU
Chi-restraints excluded: chain R residue  724 ILE
Chi-restraints excluded: chain R residue  785 VAL
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  200 VAL
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  225 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 83 optimal weight:    0.7980
   chunk 9 optimal weight:    0.5980
   chunk 35 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 77 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
R 788 GLN
A  70 HIS
** C  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.130214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.111486 restraints weight = 10414.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.115341 restraints weight = 4957.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.117498 restraints weight = 2916.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.119258 restraints weight = 2068.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.120111 restraints weight = 1589.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7113
moved from start:          0.2626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6328  Z= 0.170
  Angle     :  0.557   5.994   8654  Z= 0.296
  Chirality :  0.044   0.220   1063
  Planarity :  0.004   0.054   1092
  Dihedral  :  5.098  54.117    896
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 20.63 %
    Favored  : 74.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.44 (0.30), residues: 844
  helix:  1.47 (0.29), residues: 333
  sheet: -0.48 (0.42), residues: 156
  loop : -0.38 (0.35), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 214 
 TYR   0.013   0.001   TYR C  59 
 PHE   0.017   0.001   PHE R 642 
 TRP   0.010   0.002   TRP C  63 
 HIS   0.010   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 6327)
  covalent geometry    : angle       0.55667 ( 8652)
  SS BOND              : bond        0.00164 (    1)
  SS BOND              : angle       0.94856 (    2)
  hydrogen bonds       : bond        0.03740 (  298)
  hydrogen bonds       : angle       4.63649 (  870)

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 209
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
REVERT: R  551 MET cc_start: 0.6074 (mmm) cc_final: 0.5777 (mmm)
REVERT: R  655 LEU cc_start: 0.7669 (mt) cc_final: 0.7457 (mt)
REVERT: R  701 SER cc_start: 0.8615 (t) cc_final: 0.8091 (p)
REVERT: A   78 ASN cc_start: 0.7477 (t0) cc_final: 0.7158 (t0)
REVERT: A   98 GLU cc_start: 0.6738 (mp0) cc_final: 0.6363 (mp0)
REVERT: G   38 MET cc_start: 0.7262 (tpt) cc_final: 0.7037 (tpt)
REVERT: C  204 CYS cc_start: 0.6845 (m) cc_final: 0.6490 (m)
REVERT: C  230 ASN cc_start: 0.8022 (m-40) cc_final: 0.7686 (m-40)
REVERT: C  273 ILE cc_start: 0.7873 (mp) cc_final: 0.7625 (mp)
REVERT: C  278 PHE cc_start: 0.7133 (m-80) cc_final: 0.6787 (m-80)
  outliers start: 31
  outliers final: 26
  residues processed: 221
  average time/residue: 0.0575
  time to fit residues: 17.1405
Evaluate side-chains
  228 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 202
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  558 LEU
Chi-restraints excluded: chain R residue  576 LEU
Chi-restraints excluded: chain R residue  580 CYS
Chi-restraints excluded: chain R residue  587 THR
Chi-restraints excluded: chain R residue  590 VAL
Chi-restraints excluded: chain R residue  594 VAL
Chi-restraints excluded: chain R residue  613 LEU
Chi-restraints excluded: chain R residue  620 LEU
Chi-restraints excluded: chain R residue  724 ILE
Chi-restraints excluded: chain R residue  758 THR
Chi-restraints excluded: chain R residue  771 THR
Chi-restraints excluded: chain R residue  785 VAL
Chi-restraints excluded: chain A residue   16 SER
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain C residue   88 ASN
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  188 MET
Chi-restraints excluded: chain C residue  200 VAL
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  225 HIS
Chi-restraints excluded: chain C residue  296 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 52 optimal weight:   20.0000
   chunk 75 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 79 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 41 optimal weight:    0.4980
   chunk 65 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 197 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.129268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.111678 restraints weight = 10318.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.115226 restraints weight = 4769.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.117326 restraints weight = 2790.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.118947 restraints weight = 1952.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.119874 restraints weight = 1497.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7136
moved from start:          0.2831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   6328  Z= 0.229
  Angle     :  0.617   8.170   8654  Z= 0.327
  Chirality :  0.046   0.217   1063
  Planarity :  0.004   0.060   1092
  Dihedral  :  5.436  59.957    896
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  6.66 %
    Allowed  : 23.63 %
    Favored  : 69.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.30), residues: 844
  helix:  1.25 (0.29), residues: 332
  sheet: -0.46 (0.42), residues: 156
  loop : -0.51 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  90 
 TYR   0.012   0.001   TYR C  59 
 PHE   0.019   0.002   PHE R 642 
 TRP   0.012   0.002   TRP C  63 
 HIS   0.011   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 ( 6327)
  covalent geometry    : angle       0.61645 ( 8652)
  SS BOND              : bond        0.00094 (    1)
  SS BOND              : angle       0.97008 (    2)
  hydrogen bonds       : bond        0.03983 (  298)
  hydrogen bonds       : angle       4.69739 (  870)

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 201
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
REVERT: R  551 MET cc_start: 0.6063 (mmm) cc_final: 0.5727 (mmm)
REVERT: R  701 SER cc_start: 0.8596 (t) cc_final: 0.8121 (p)
REVERT: R  708 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7283 (pp)
REVERT: A   78 ASN cc_start: 0.7585 (t0) cc_final: 0.7209 (t0)
REVERT: A   98 GLU cc_start: 0.6689 (mp0) cc_final: 0.6221 (mp0)
REVERT: G   38 MET cc_start: 0.7233 (tpt) cc_final: 0.7013 (tpt)
REVERT: C  204 CYS cc_start: 0.6770 (m) cc_final: 0.6476 (m)
REVERT: C  230 ASN cc_start: 0.8059 (m-40) cc_final: 0.7824 (m-40)
REVERT: C  273 ILE cc_start: 0.7858 (mp) cc_final: 0.7597 (mp)
REVERT: C  278 PHE cc_start: 0.7196 (m-80) cc_final: 0.6927 (m-80)
  outliers start: 40
  outliers final: 31
  residues processed: 216
  average time/residue: 0.0616
  time to fit residues: 17.8661
Evaluate side-chains
  228 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 196
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  558 LEU
Chi-restraints excluded: chain R residue  576 LEU
Chi-restraints excluded: chain R residue  580 CYS
Chi-restraints excluded: chain R residue  585 LEU
Chi-restraints excluded: chain R residue  587 THR
Chi-restraints excluded: chain R residue  590 VAL
Chi-restraints excluded: chain R residue  594 VAL
Chi-restraints excluded: chain R residue  613 LEU
Chi-restraints excluded: chain R residue  620 LEU
Chi-restraints excluded: chain R residue  697 SER
Chi-restraints excluded: chain R residue  708 LEU
Chi-restraints excluded: chain R residue  724 ILE
Chi-restraints excluded: chain R residue  758 THR
Chi-restraints excluded: chain R residue  771 THR
Chi-restraints excluded: chain R residue  785 VAL
Chi-restraints excluded: chain A residue   16 SER
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  126 GLU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain C residue   88 ASN
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  188 MET
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  218 CYS
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  337 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 68 optimal weight:    0.0470
   chunk 65 optimal weight:    0.8980
   chunk 81 optimal weight:    0.0980
   chunk 50 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 72 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0000
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.3882

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.131309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.112876 restraints weight = 10322.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.116680 restraints weight = 4886.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.119040 restraints weight = 2888.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.120482 restraints weight = 2005.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.121659 restraints weight = 1571.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7083
moved from start:          0.3008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6328  Z= 0.118
  Angle     :  0.549   6.707   8654  Z= 0.287
  Chirality :  0.043   0.207   1063
  Planarity :  0.004   0.058   1092
  Dihedral  :  4.820  59.676    894
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 25.46 %
    Favored  : 69.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.30), residues: 844
  helix:  1.60 (0.29), residues: 333
  sheet: -0.31 (0.43), residues: 156
  loop : -0.55 (0.34), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  90 
 TYR   0.009   0.001   TYR A  29 
 PHE   0.015   0.001   PHE A  49 
 TRP   0.010   0.001   TRP R 649 
 HIS   0.003   0.001   HIS C 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 6327)
  covalent geometry    : angle       0.54897 ( 8652)
  SS BOND              : bond        0.00286 (    1)
  SS BOND              : angle       0.81284 (    2)
  hydrogen bonds       : bond        0.03269 (  298)
  hydrogen bonds       : angle       4.40607 (  870)

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 196
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
REVERT: R  551 MET cc_start: 0.5875 (mmm) cc_final: 0.5520 (mmm)
REVERT: R  701 SER cc_start: 0.8587 (t) cc_final: 0.8057 (p)
REVERT: A   78 ASN cc_start: 0.7547 (t0) cc_final: 0.7237 (t0)
REVERT: A   98 GLU cc_start: 0.6763 (mp0) cc_final: 0.6308 (mp0)
REVERT: A  176 GLN cc_start: 0.8682 (tp40) cc_final: 0.8373 (mm-40)
REVERT: G   38 MET cc_start: 0.7264 (tpt) cc_final: 0.7010 (tpt)
REVERT: C  190 LEU cc_start: 0.7535 (tt) cc_final: 0.7264 (tp)
REVERT: C  204 CYS cc_start: 0.6765 (m) cc_final: 0.6427 (m)
REVERT: C  230 ASN cc_start: 0.7944 (m-40) cc_final: 0.7657 (m-40)
REVERT: C  273 ILE cc_start: 0.7819 (mp) cc_final: 0.7605 (mp)
REVERT: C  278 PHE cc_start: 0.7065 (m-80) cc_final: 0.6760 (m-80)
  outliers start: 31
  outliers final: 25
  residues processed: 211
  average time/residue: 0.0566
  time to fit residues: 16.3446
Evaluate side-chains
  217 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 192
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  558 LEU
Chi-restraints excluded: chain R residue  576 LEU
Chi-restraints excluded: chain R residue  580 CYS
Chi-restraints excluded: chain R residue  590 VAL
Chi-restraints excluded: chain R residue  594 VAL
Chi-restraints excluded: chain R residue  613 LEU
Chi-restraints excluded: chain R residue  620 LEU
Chi-restraints excluded: chain R residue  692 SER
Chi-restraints excluded: chain R residue  697 SER
Chi-restraints excluded: chain R residue  724 ILE
Chi-restraints excluded: chain A residue   16 SER
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  126 GLU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain C residue   58 ILE
Chi-restraints excluded: chain C residue   88 ASN
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  200 VAL
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  308 LEU
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  337 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 20 optimal weight:    0.4980
   chunk 75 optimal weight:    0.9980
   chunk 55 optimal weight:    5.9990
   chunk 9 optimal weight:    0.5980
   chunk 76 optimal weight:    0.8980
   chunk 79 optimal weight:    0.6980
   chunk 19 optimal weight:    0.2980
   chunk 50 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
C 239 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.131124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.113572 restraints weight = 10314.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.117183 restraints weight = 4742.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.119333 restraints weight = 2746.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.120776 restraints weight = 1907.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.121842 restraints weight = 1479.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7090
moved from start:          0.3108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6328  Z= 0.139
  Angle     :  0.560   6.455   8654  Z= 0.293
  Chirality :  0.043   0.211   1063
  Planarity :  0.004   0.060   1092
  Dihedral  :  4.782  58.210    894
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 26.96 %
    Favored  : 67.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.30), residues: 844
  helix:  1.68 (0.29), residues: 334
  sheet: -0.31 (0.42), residues: 156
  loop : -0.55 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 251 
 TYR   0.008   0.001   TYR C  59 
 PHE   0.014   0.001   PHE A  74 
 TRP   0.010   0.001   TRP R 649 
 HIS   0.012   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6327)
  covalent geometry    : angle       0.56003 ( 8652)
  SS BOND              : bond        0.00024 (    1)
  SS BOND              : angle       0.91261 (    2)
  hydrogen bonds       : bond        0.03377 (  298)
  hydrogen bonds       : angle       4.39431 (  870)

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 197
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
REVERT: R  551 MET cc_start: 0.5910 (mmm) cc_final: 0.5572 (mmm)
REVERT: R  701 SER cc_start: 0.8592 (t) cc_final: 0.8075 (p)
REVERT: A   78 ASN cc_start: 0.7579 (t0) cc_final: 0.7275 (t0)
REVERT: A   98 GLU cc_start: 0.6766 (mp0) cc_final: 0.6317 (mp0)
REVERT: A  118 LEU cc_start: 0.8422 (mt) cc_final: 0.8200 (mp)
REVERT: A  176 GLN cc_start: 0.8661 (tp40) cc_final: 0.8310 (mm-40)
REVERT: G   38 MET cc_start: 0.7242 (tpt) cc_final: 0.6973 (tpt)
REVERT: C  176 GLN cc_start: 0.8029 (pt0) cc_final: 0.7751 (pt0)
REVERT: C  204 CYS cc_start: 0.6707 (m) cc_final: 0.6388 (m)
REVERT: C  230 ASN cc_start: 0.7959 (m-40) cc_final: 0.7684 (m-40)
REVERT: C  273 ILE cc_start: 0.7864 (mp) cc_final: 0.7638 (mp)
REVERT: C  278 PHE cc_start: 0.7104 (m-80) cc_final: 0.6843 (m-80)
  outliers start: 34
  outliers final: 27
  residues processed: 213
  average time/residue: 0.0585
  time to fit residues: 16.7876
Evaluate side-chains
  223 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 196
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  558 LEU
Chi-restraints excluded: chain R residue  576 LEU
Chi-restraints excluded: chain R residue  580 CYS
Chi-restraints excluded: chain R residue  585 LEU
Chi-restraints excluded: chain R residue  587 THR
Chi-restraints excluded: chain R residue  594 VAL
Chi-restraints excluded: chain R residue  613 LEU
Chi-restraints excluded: chain R residue  620 LEU
Chi-restraints excluded: chain R residue  692 SER
Chi-restraints excluded: chain R residue  697 SER
Chi-restraints excluded: chain R residue  724 ILE
Chi-restraints excluded: chain R residue  771 THR
Chi-restraints excluded: chain A residue   16 SER
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  126 GLU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain C residue   58 ILE
Chi-restraints excluded: chain C residue   88 ASN
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  200 VAL
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  308 LEU
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  337 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 52 optimal weight:   20.0000
   chunk 53 optimal weight:    6.9990
   chunk 44 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 78 optimal weight:    3.9990
   chunk 46 optimal weight:    0.5980
   chunk 24 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
C  88 ASN
C 239 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.130354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.112835 restraints weight = 10266.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.116370 restraints weight = 4725.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.118599 restraints weight = 2755.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.119933 restraints weight = 1900.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.120815 restraints weight = 1494.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7112
moved from start:          0.3200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6328  Z= 0.167
  Angle     :  0.589   7.115   8654  Z= 0.311
  Chirality :  0.044   0.211   1063
  Planarity :  0.004   0.062   1092
  Dihedral  :  4.907  58.736    894
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 28.29 %
    Favored  : 66.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.48 (0.30), residues: 844
  helix:  1.62 (0.29), residues: 334
  sheet: -0.32 (0.42), residues: 156
  loop : -0.58 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 256 
 TYR   0.009   0.001   TYR C  59 
 PHE   0.015   0.001   PHE R 642 
 TRP   0.010   0.002   TRP C  63 
 HIS   0.012   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 6327)
  covalent geometry    : angle       0.58857 ( 8652)
  SS BOND              : bond        0.00066 (    1)
  SS BOND              : angle       1.10563 (    2)
  hydrogen bonds       : bond        0.03518 (  298)
  hydrogen bonds       : angle       4.44193 (  870)

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 198
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
REVERT: R  551 MET cc_start: 0.5881 (mmm) cc_final: 0.5555 (mmm)
REVERT: R  601 ARG cc_start: 0.7750 (ptt90) cc_final: 0.7488 (ptt180)
REVERT: R  701 SER cc_start: 0.8612 (t) cc_final: 0.8092 (p)
REVERT: A   98 GLU cc_start: 0.6690 (mp0) cc_final: 0.6225 (mp0)
REVERT: A  118 LEU cc_start: 0.8407 (mt) cc_final: 0.8061 (mt)
REVERT: G   38 MET cc_start: 0.7357 (tpt) cc_final: 0.7075 (tpt)
REVERT: C  190 LEU cc_start: 0.7504 (tt) cc_final: 0.7268 (tp)
REVERT: C  204 CYS cc_start: 0.6713 (m) cc_final: 0.6410 (m)
REVERT: C  230 ASN cc_start: 0.7964 (m-40) cc_final: 0.7724 (m-40)
REVERT: C  273 ILE cc_start: 0.7865 (mp) cc_final: 0.7657 (mp)
REVERT: C  278 PHE cc_start: 0.7119 (m-80) cc_final: 0.6875 (m-80)
REVERT: C  340 ASN cc_start: 0.7862 (t0) cc_final: 0.7445 (t0)
  outliers start: 32
  outliers final: 28
  residues processed: 214
  average time/residue: 0.0572
  time to fit residues: 16.5325
Evaluate side-chains
  223 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 195
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  558 LEU
Chi-restraints excluded: chain R residue  576 LEU
Chi-restraints excluded: chain R residue  580 CYS
Chi-restraints excluded: chain R residue  585 LEU
Chi-restraints excluded: chain R residue  587 THR
Chi-restraints excluded: chain R residue  594 VAL
Chi-restraints excluded: chain R residue  613 LEU
Chi-restraints excluded: chain R residue  620 LEU
Chi-restraints excluded: chain R residue  692 SER
Chi-restraints excluded: chain R residue  697 SER
Chi-restraints excluded: chain R residue  724 ILE
Chi-restraints excluded: chain R residue  771 THR
Chi-restraints excluded: chain A residue   16 SER
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  126 GLU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain C residue   58 ILE
Chi-restraints excluded: chain C residue   88 ASN
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  200 VAL
Chi-restraints excluded: chain C residue  218 CYS
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  337 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 66 optimal weight:    0.1980
   chunk 2 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
C  88 ASN
C 239 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.131511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.113957 restraints weight = 10302.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.117536 restraints weight = 4728.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.119771 restraints weight = 2747.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.121214 restraints weight = 1893.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.122012 restraints weight = 1469.347|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7095
moved from start:          0.3294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6328  Z= 0.145
  Angle     :  0.591   7.385   8654  Z= 0.310
  Chirality :  0.044   0.274   1063
  Planarity :  0.004   0.062   1092
  Dihedral  :  4.825  58.199    894
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 29.12 %
    Favored  : 66.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.30), residues: 844
  helix:  1.66 (0.29), residues: 334
  sheet: -0.26 (0.42), residues: 156
  loop : -0.56 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 251 
 TYR   0.010   0.001   TYR C  59 
 PHE   0.013   0.001   PHE A  74 
 TRP   0.010   0.001   TRP R 649 
 HIS   0.013   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6327)
  covalent geometry    : angle       0.59122 ( 8652)
  SS BOND              : bond        0.00008 (    1)
  SS BOND              : angle       1.05979 (    2)
  hydrogen bonds       : bond        0.03381 (  298)
  hydrogen bonds       : angle       4.42833 (  870)

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 194
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  551 MET cc_start: 0.5851 (mmm) cc_final: 0.5487 (mmm)
REVERT: R  601 ARG cc_start: 0.7734 (ptt90) cc_final: 0.7467 (ptt180)
REVERT: R  701 SER cc_start: 0.8613 (t) cc_final: 0.8109 (p)
REVERT: A  118 LEU cc_start: 0.8410 (mt) cc_final: 0.8176 (mp)
REVERT: A  176 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8360 (mm-40)
REVERT: A  186 LYS cc_start: 0.8359 (mmmt) cc_final: 0.8157 (tptm)
REVERT: G   38 MET cc_start: 0.7313 (tpt) cc_final: 0.7013 (tpt)
REVERT: C  204 CYS cc_start: 0.6701 (m) cc_final: 0.6377 (m)
REVERT: C  230 ASN cc_start: 0.7952 (m-40) cc_final: 0.7708 (m-40)
REVERT: C  273 ILE cc_start: 0.7859 (mp) cc_final: 0.7627 (mp)
REVERT: C  278 PHE cc_start: 0.7096 (m-80) cc_final: 0.6845 (m-80)
  outliers start: 29
  outliers final: 27
  residues processed: 209
  average time/residue: 0.0627
  time to fit residues: 17.6603
Evaluate side-chains
  218 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 191
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  558 LEU
Chi-restraints excluded: chain R residue  576 LEU
Chi-restraints excluded: chain R residue  580 CYS
Chi-restraints excluded: chain R residue  585 LEU
Chi-restraints excluded: chain R residue  587 THR
Chi-restraints excluded: chain R residue  594 VAL
Chi-restraints excluded: chain R residue  613 LEU
Chi-restraints excluded: chain R residue  620 LEU
Chi-restraints excluded: chain R residue  692 SER
Chi-restraints excluded: chain R residue  697 SER
Chi-restraints excluded: chain R residue  724 ILE
Chi-restraints excluded: chain R residue  771 THR
Chi-restraints excluded: chain A residue   16 SER
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  126 GLU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain C residue   58 ILE
Chi-restraints excluded: chain C residue   88 ASN
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  200 VAL
Chi-restraints excluded: chain C residue  218 CYS
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  337 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 47 optimal weight:    4.9990
   chunk 78 optimal weight:    2.9990
   chunk 36 optimal weight:    0.3980
   chunk 72 optimal weight:    4.9990
   chunk 38 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 66 optimal weight:    0.0050
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.5594

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

Flipped N/Q/H residues before XYZ refinement:
C  88 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.132066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.114614 restraints weight = 10250.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.118126 restraints weight = 4737.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.120342 restraints weight = 2765.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.121872 restraints weight = 1917.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.122761 restraints weight = 1479.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7086
moved from start:          0.3359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6328  Z= 0.139
  Angle     :  0.592   7.667   8654  Z= 0.310
  Chirality :  0.044   0.210   1063
  Planarity :  0.004   0.062   1092
  Dihedral  :  4.850  57.977    894
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 29.62 %
    Favored  : 65.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.30), residues: 844
  helix:  1.68 (0.29), residues: 334
  sheet: -0.21 (0.41), residues: 156
  loop : -0.57 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 251 
 TYR   0.012   0.001   TYR C  59 
 PHE   0.013   0.001   PHE A  74 
 TRP   0.011   0.001   TRP C  63 
 HIS   0.013   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 6327)
  covalent geometry    : angle       0.59176 ( 8652)
  SS BOND              : bond        0.00018 (    1)
  SS BOND              : angle       0.98980 (    2)
  hydrogen bonds       : bond        0.03341 (  298)
  hydrogen bonds       : angle       4.37992 (  870)

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 190
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  551 MET cc_start: 0.5818 (mmm) cc_final: 0.5464 (mmm)
REVERT: R  701 SER cc_start: 0.8614 (t) cc_final: 0.8112 (p)
REVERT: A  118 LEU cc_start: 0.8419 (mt) cc_final: 0.8062 (mt)
REVERT: G   38 MET cc_start: 0.7286 (tpt) cc_final: 0.6978 (tpt)
REVERT: C  204 CYS cc_start: 0.6729 (m) cc_final: 0.6391 (m)
REVERT: C  230 ASN cc_start: 0.7927 (m-40) cc_final: 0.7684 (m-40)
REVERT: C  273 ILE cc_start: 0.7868 (mp) cc_final: 0.7653 (mp)
REVERT: C  278 PHE cc_start: 0.7084 (m-80) cc_final: 0.6843 (m-80)
  outliers start: 30
  outliers final: 28
  residues processed: 205
  average time/residue: 0.0600
  time to fit residues: 16.4640
Evaluate side-chains
  219 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 191
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  558 LEU
Chi-restraints excluded: chain R residue  576 LEU
Chi-restraints excluded: chain R residue  580 CYS
Chi-restraints excluded: chain R residue  585 LEU
Chi-restraints excluded: chain R residue  587 THR
Chi-restraints excluded: chain R residue  594 VAL
Chi-restraints excluded: chain R residue  613 LEU
Chi-restraints excluded: chain R residue  620 LEU
Chi-restraints excluded: chain R residue  692 SER
Chi-restraints excluded: chain R residue  697 SER
Chi-restraints excluded: chain R residue  724 ILE
Chi-restraints excluded: chain R residue  771 THR
Chi-restraints excluded: chain A residue   16 SER
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  126 GLU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  228 MET
Chi-restraints excluded: chain C residue   58 ILE
Chi-restraints excluded: chain C residue   88 ASN
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  176 GLN
Chi-restraints excluded: chain C residue  200 VAL
Chi-restraints excluded: chain C residue  218 CYS
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  337 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 66 optimal weight:    0.5980
   chunk 45 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 30 optimal weight:    0.8980
   chunk 68 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 76 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 50 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
C  88 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.131551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.113883 restraints weight = 10179.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.117446 restraints weight = 4720.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.119766 restraints weight = 2754.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.121058 restraints weight = 1891.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.122145 restraints weight = 1493.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7093
moved from start:          0.3392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6328  Z= 0.149
  Angle     :  0.594   7.555   8654  Z= 0.312
  Chirality :  0.044   0.211   1063
  Planarity :  0.004   0.062   1092
  Dihedral  :  4.880  57.917    894
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 29.28 %
    Favored  : 65.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.55 (0.30), residues: 844
  helix:  1.67 (0.29), residues: 334
  sheet: -0.23 (0.41), residues: 156
  loop : -0.57 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 251 
 TYR   0.012   0.001   TYR C  59 
 PHE   0.013   0.001   PHE R 642 
 TRP   0.012   0.001   TRP C  63 
 HIS   0.013   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 6327)
  covalent geometry    : angle       0.59371 ( 8652)
  SS BOND              : bond        0.00002 (    1)
  SS BOND              : angle       0.91768 (    2)
  hydrogen bonds       : bond        0.03388 (  298)
  hydrogen bonds       : angle       4.37984 (  870)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1093.42 seconds
wall clock time: 19 minutes 30.43 seconds (1170.43 seconds total)