Starting phenix.real_space_refine
on Tue Jul 29 19:41:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gp3_34188/07_2025/8gp3_34188.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gp3_34188/07_2025/8gp3_34188.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gp3_34188/07_2025/8gp3_34188.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gp3_34188/07_2025/8gp3_34188.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gp3_34188/07_2025/8gp3_34188.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gp3_34188/07_2025/8gp3_34188.cif"
  }
  resolution = 4.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.008
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: 5
    Type Number    sf(0)   Gaussians
     P      10      5.49       5
     S      38      5.16       5
     C    7275      2.51       5
     N    1938      2.21       5
     O    2233      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11494
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2797
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 363, 2797
          Classifications: {'peptide': 363}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 334}
          Unresolved non-hydrogen bonds: 78
          Unresolved non-hydrogen angles: 96
          Unresolved non-hydrogen dihedrals: 63
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 62
    Chain: "V"
      Number of atoms: 89
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 89
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
    Chain: "B"
      Number of atoms: 2805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 363, 2805
          Classifications: {'peptide': 363}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 334}
          Unresolved non-hydrogen bonds: 70
          Unresolved non-hydrogen angles: 86
          Unresolved non-hydrogen dihedrals: 57
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 52
    Chain: "U"
      Number of atoms: 89
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 89
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
    Chain: "H"
      Number of atoms: 1496
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 1496
          Classifications: {'peptide': 204}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 191}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 49
          Unresolved non-hydrogen angles: 58
          Unresolved non-hydrogen dihedrals: 40
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "I"
      Number of atoms: 1496
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 1496
          Classifications: {'peptide': 204}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 191}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 49
          Unresolved non-hydrogen angles: 58
          Unresolved non-hydrogen dihedrals: 40
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "L"
      Number of atoms: 1363
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 185, 1363
          Classifications: {'peptide': 185}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 67
          Unresolved non-hydrogen dihedrals: 47
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 22
    Chain: "M"
      Number of atoms: 1359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 185, 1359
          Classifications: {'peptide': 185}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 72
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 26
  Time building chain proxies: 9.59, per 1000 atoms: 0.83
  Number of scatterers: 11494
  At special positions: 0
  Unit cell: (107.116, 197.55, 99.214, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      38     16.00
     P      10     15.00
     O    2233      8.00
     N    1938      7.00
     C    7275      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 150 " - pdb=" SG  CYS H 206 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  25 " - pdb=" SG  CYS I  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I 150 " - pdb=" SG  CYS I 206 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS M  24 " - pdb=" SG  CYS M  89 " 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: 2.44
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2864

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 30 sheets defined
      6.0% alpha, 45.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.94
  Creating SS restraints...
    Processing helix  chain 'A' and resid 98 through 109
      removed outlier: 3.614A  pdb=" N   ARG A 103 " --> pdb=" O   ARG A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 161
      No H-bonds generated for 'chain 'A' and resid 159 through 161'
    Processing helix  chain 'A' and resid 277 through 282
      removed outlier: 4.024A  pdb=" N   ASN A 280 " --> pdb=" O   PHE A 277 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   ARG A 282 " --> pdb=" O   ALA A 279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 109
      removed outlier: 3.644A  pdb=" N   ARG B 103 " --> pdb=" O   ARG B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 161
      No H-bonds generated for 'chain 'B' and resid 159 through 161'
    Processing helix  chain 'B' and resid 278 through 282
      removed outlier: 4.013A  pdb=" N   ARG B 282 " --> pdb=" O   ALA B 279 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 94
    Processing helix  chain 'I' and resid 90 through 94
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 4.185A  pdb=" N   PHE L  84 " --> pdb=" O   PRO L  81 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 123 through 129
      removed outlier: 3.855A  pdb=" N   LYS L 127 " --> pdb=" O   ASP L 123 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 183 through 190
      removed outlier: 4.261A  pdb=" N   HIS L 190 " --> pdb=" O   ASP L 186 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 80 through 84
      removed outlier: 4.163A  pdb=" N   PHE M  84 " --> pdb=" O   PRO M  81 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 123 through 129
      removed outlier: 3.875A  pdb=" N   LYS M 127 " --> pdb=" O   ASP M 123 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 183 through 190
      removed outlier: 4.258A  pdb=" N   HIS M 190 " --> pdb=" O   ASP M 186 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 117
      removed outlier: 3.520A  pdb=" N   THR A  19 " --> pdb=" O   LEU A  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28
      removed outlier: 3.831A  pdb=" N   VAL A 171 " --> pdb=" O   PHE A  27 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ILE A 168 " --> pdb=" O   TYR A 144 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   TYR A 144 " --> pdb=" O   ILE A 168 " (cutoff:3.500A)
      removed outlier: 7.239A  pdb=" N   LYS A 170 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 9.531A  pdb=" N   VAL A 142 " --> pdb=" O   LYS A 170 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   GLY A 141 " --> pdb=" O   ARG A  62 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   ARG A  62 " --> pdb=" O   GLY A 141 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   ASP A 143 " --> pdb=" O   ALA A  60 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   ALA A  60 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLU A 145 " --> pdb=" O   THR A  58 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   VAL A  53 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   GLN A  85 " --> pdb=" O   VAL A  53 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   VAL A  55 " --> pdb=" O   ASN A  83 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   ASN A  83 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
      removed outlier: 7.197A  pdb=" N   LEU A  57 " --> pdb=" O   VAL A  81 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   VAL A  81 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   CYS A  59 " --> pdb=" O   LEU A  79 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 28
      removed outlier: 3.831A  pdb=" N   VAL A 171 " --> pdb=" O   PHE A  27 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ILE A 168 " --> pdb=" O   TYR A 144 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   TYR A 144 " --> pdb=" O   ILE A 168 " (cutoff:3.500A)
      removed outlier: 7.239A  pdb=" N   LYS A 170 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 9.531A  pdb=" N   VAL A 142 " --> pdb=" O   LYS A 170 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   CYS A 140 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 183 through 188
      removed outlier: 3.562A  pdb=" N   TYR A 272 " --> pdb=" O   VAL A 216 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 207 through 208
      removed outlier: 3.526A  pdb=" N   VAL A 343 " --> pdb=" O   LEU A 327 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   PHE A 349 " --> pdb=" O   TYR A 321 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   TYR A 321 " --> pdb=" O   PHE A 349 " (cutoff:3.500A)
      removed outlier: 8.332A  pdb=" N   LEU A 351 " --> pdb=" O   VAL A 319 " (cutoff:3.500A)
      removed outlier: 9.782A  pdb=" N   VAL A 319 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LYS A 322 " --> pdb=" O   ARG A 236 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LYS A 230 " --> pdb=" O   VAL A 328 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   ILE A 231 " --> pdb=" O   GLU A 257 " (cutoff:3.500A)
      removed outlier: 4.967A  pdb=" N   GLU A 257 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
      removed outlier: 7.192A  pdb=" N   ILE A 233 " --> pdb=" O   MET A 255 " (cutoff:3.500A)
      removed outlier: 4.885A  pdb=" N   MET A 255 " --> pdb=" O   ILE A 233 " (cutoff:3.500A)
      removed outlier: 7.424A  pdb=" N   VAL A 235 " --> pdb=" O   VAL A 253 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   TYR A 249 " --> pdb=" O   ALA A 239 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 112 through 117
      removed outlier: 3.703A  pdb=" N   GLU U 345 " --> pdb=" O   LYS B  10 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 26 through 28
      removed outlier: 3.843A  pdb=" N   VAL B 171 " --> pdb=" O   PHE B  27 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 74 through 85
      removed outlier: 6.544A  pdb=" N   CYS B  59 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   VAL B  81 " --> pdb=" O   LEU B  57 " (cutoff:3.500A)
      removed outlier: 7.194A  pdb=" N   LEU B  57 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   ASN B  83 " --> pdb=" O   VAL B  55 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   VAL B  55 " --> pdb=" O   ASN B  83 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   GLN B  85 " --> pdb=" O   VAL B  53 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   VAL B  53 " --> pdb=" O   GLN B  85 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ALA B  60 " --> pdb=" O   ASP B 143 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ASP B 143 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   ARG B  62 " --> pdb=" O   GLY B 141 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   GLY B 141 " --> pdb=" O   ARG B  62 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 74 through 85
      removed outlier: 6.544A  pdb=" N   CYS B  59 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   VAL B  81 " --> pdb=" O   LEU B  57 " (cutoff:3.500A)
      removed outlier: 7.194A  pdb=" N   LEU B  57 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   ASN B  83 " --> pdb=" O   VAL B  55 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   VAL B  55 " --> pdb=" O   ASN B  83 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   GLN B  85 " --> pdb=" O   VAL B  53 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   VAL B  53 " --> pdb=" O   GLN B  85 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ALA B  60 " --> pdb=" O   ASP B 143 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ASP B 143 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   ARG B  62 " --> pdb=" O   GLY B 141 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   GLY B 141 " --> pdb=" O   ARG B  62 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   CYS B 140 " --> pdb=" O   LEU B 129 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 183 through 188
      removed outlier: 3.555A  pdb=" N   TYR B 272 " --> pdb=" O   VAL B 216 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 207 through 208
      removed outlier: 3.533A  pdb=" N   VAL B 343 " --> pdb=" O   LEU B 327 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   PHE B 349 " --> pdb=" O   TYR B 321 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   TYR B 321 " --> pdb=" O   PHE B 349 " (cutoff:3.500A)
      removed outlier: 8.237A  pdb=" N   LEU B 351 " --> pdb=" O   VAL B 319 " (cutoff:3.500A)
      removed outlier: 9.727A  pdb=" N   VAL B 319 " --> pdb=" O   LEU B 351 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LYS B 322 " --> pdb=" O   ARG B 236 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   LYS B 230 " --> pdb=" O   VAL B 328 " (cutoff:3.500A)
      removed outlier: 7.027A  pdb=" N   ILE B 231 " --> pdb=" O   GLU B 257 " (cutoff:3.500A)
      removed outlier: 4.975A  pdb=" N   GLU B 257 " --> pdb=" O   ILE B 231 " (cutoff:3.500A)
      removed outlier: 7.199A  pdb=" N   ILE B 233 " --> pdb=" O   MET B 255 " (cutoff:3.500A)
      removed outlier: 4.895A  pdb=" N   MET B 255 " --> pdb=" O   ILE B 233 " (cutoff:3.500A)
      removed outlier: 7.414A  pdb=" N   VAL B 235 " --> pdb=" O   VAL B 253 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   TYR B 249 " --> pdb=" O   ALA B 239 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ILE B 241 " --> pdb=" O   ALA B 247 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 6 through 10
      removed outlier: 3.920A  pdb=" N   LEU H  21 " --> pdb=" O   MET H  86 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   MET H  86 " --> pdb=" O   LEU H  21 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   LEU H  23 " --> pdb=" O   LEU H  84 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 14 through 15
      removed outlier: 8.875A  pdb=" N   SER H  35 " --> pdb=" O   SER H  55 " (cutoff:3.500A)
      removed outlier: 6.109A  pdb=" N   SER H  55 " --> pdb=" O   SER H  35 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   TYR H  62 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 14 through 15
      removed outlier: 3.629A  pdb=" N   TYR H 112 " --> pdb=" O   ARG H 101 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 130 through 134
      removed outlier: 3.586A  pdb=" N   LEU H 134 " --> pdb=" O   GLY H 149 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   GLY H 149 " --> pdb=" O   LEU H 134 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   TYR H 186 " --> pdb=" O   ASP H 154 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'H' and resid 130 through 134
      removed outlier: 3.586A  pdb=" N   LEU H 134 " --> pdb=" O   GLY H 149 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   GLY H 149 " --> pdb=" O   LEU H 134 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   TYR H 186 " --> pdb=" O   ASP H 154 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'H' and resid 161 through 164
      removed outlier: 3.581A  pdb=" N   VAL H 208 " --> pdb=" O   VAL H 217 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'I' and resid 6 through 10
      removed outlier: 3.914A  pdb=" N   LEU I  21 " --> pdb=" O   MET I  86 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   MET I  86 " --> pdb=" O   LEU I  21 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   LEU I  23 " --> pdb=" O   LEU I  84 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'I' and resid 14 through 15
      removed outlier: 8.840A  pdb=" N   SER I  35 " --> pdb=" O   SER I  55 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   SER I  55 " --> pdb=" O   SER I  35 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   ILE I  37 " --> pdb=" O   SER I  53 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   SER I  53 " --> pdb=" O   ILE I  37 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   TRP I  39 " --> pdb=" O   VAL I  51 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   TYR I  62 " --> pdb=" O   SER I  53 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'I' and resid 14 through 15
      removed outlier: 3.739A  pdb=" N   TYR I 112 " --> pdb=" O   ARG I 101 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'I' and resid 130 through 134
      removed outlier: 3.584A  pdb=" N   LEU I 134 " --> pdb=" O   GLY I 149 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   GLY I 149 " --> pdb=" O   LEU I 134 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   TYR I 186 " --> pdb=" O   ASP I 154 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'I' and resid 130 through 134
      removed outlier: 3.584A  pdb=" N   LEU I 134 " --> pdb=" O   GLY I 149 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   GLY I 149 " --> pdb=" O   LEU I 134 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   TYR I 186 " --> pdb=" O   ASP I 154 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'I' and resid 161 through 164
      removed outlier: 3.576A  pdb=" N   VAL I 208 " --> pdb=" O   VAL I 217 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'L' and resid 7 through 8
    Processing sheet with id=AC7, first strand: chain 'L' and resid 11 through 14
      removed outlier: 3.614A  pdb=" N   LEU L  12 " --> pdb=" O   LYS L 104 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   GLU L 106 " --> pdb=" O   LEU L  12 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   VAL L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 4.910A  pdb=" N   TYR L  50 " --> pdb=" O   VAL L  34 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'L' and resid 115 through 119
      removed outlier: 3.767A  pdb=" N   VAL L 134 " --> pdb=" O   PHE L 119 " (cutoff:3.500A)
      removed outlier: 5.920A  pdb=" N   TYR L 174 " --> pdb=" O   ASN L 139 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'M' and resid 7 through 8
    Processing sheet with id=AD1, first strand: chain 'M' and resid 11 through 14
      removed outlier: 3.685A  pdb=" N   LEU M  12 " --> pdb=" O   LYS M 104 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   GLU M 106 " --> pdb=" O   LEU M  12 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'M' and resid 49 through 50
    Processing sheet with id=AD3, first strand: chain 'M' and resid 115 through 119
      removed outlier: 3.770A  pdb=" N   VAL M 134 " --> pdb=" O   PHE M 119 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   TYR M 174 " --> pdb=" O   ASN M 139 " (cutoff:3.500A)

    445 hydrogen bonds defined for protein.
    1155 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.99

  Time building geometry restraints manager: 3.01 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3469
        1.33 -     1.45: 1783
        1.45 -     1.57: 6426
        1.57 -     1.69: 34
        1.69 -     1.81: 48
  Bond restraints: 11760
  Sorted by residual:
  bond pdb=" O3P SEP U 346 "
       pdb=" P   SEP U 346 "
    ideal  model  delta    sigma   weight residual
    1.610  1.505  0.105 2.00e-02 2.50e+03 2.75e+01
  bond pdb=" O2P SEP V 344 "
       pdb=" P   SEP V 344 "
    ideal  model  delta    sigma   weight residual
    1.610  1.513  0.097 2.00e-02 2.50e+03 2.33e+01
  bond pdb=" O1P SEP U 346 "
       pdb=" P   SEP U 346 "
    ideal  model  delta    sigma   weight residual
    1.610  1.514  0.096 2.00e-02 2.50e+03 2.31e+01
  bond pdb=" O3P SEP V 344 "
       pdb=" P   SEP V 344 "
    ideal  model  delta    sigma   weight residual
    1.610  1.514  0.096 2.00e-02 2.50e+03 2.29e+01
  bond pdb=" O1P SEP V 344 "
       pdb=" P   SEP V 344 "
    ideal  model  delta    sigma   weight residual
    1.610  1.515  0.095 2.00e-02 2.50e+03 2.25e+01
  ... (remaining 11755 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.37: 15783
        2.37 -     4.73: 241
        4.73 -     7.10: 15
        7.10 -     9.47: 2
        9.47 -    11.83: 2
  Bond angle restraints: 16043
  Sorted by residual:
  angle pdb=" CA  PHE B  75 "
        pdb=" C   PHE B  75 "
        pdb=" N   ARG B  76 "
      ideal   model   delta    sigma   weight residual
     115.51  110.14    5.37 1.24e+00 6.50e-01 1.88e+01
  angle pdb=" N   VAL M  30 "
        pdb=" CA  VAL M  30 "
        pdb=" C   VAL M  30 "
      ideal   model   delta    sigma   weight residual
     113.20  109.05    4.15 9.60e-01 1.09e+00 1.87e+01
  angle pdb=" N   VAL L  30 "
        pdb=" CA  VAL L  30 "
        pdb=" C   VAL L  30 "
      ideal   model   delta    sigma   weight residual
     113.20  109.39    3.81 9.60e-01 1.09e+00 1.57e+01
  angle pdb=" N   GLY A 291 "
        pdb=" CA  GLY A 291 "
        pdb=" C   GLY A 291 "
      ideal   model   delta    sigma   weight residual
     111.36  115.74   -4.38 1.17e+00 7.31e-01 1.40e+01
  angle pdb=" C   CYS A  59 "
        pdb=" N   ALA A  60 "
        pdb=" CA  ALA A  60 "
      ideal   model   delta    sigma   weight residual
     122.59  116.75    5.84 1.57e+00 4.06e-01 1.39e+01
  ... (remaining 16038 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.30: 6446
       17.30 -    34.61: 520
       34.61 -    51.91: 71
       51.91 -    69.21: 21
       69.21 -    86.52: 15
  Dihedral angle restraints: 7073
    sinusoidal: 2629
      harmonic: 4444
  Sorted by residual:
  dihedral pdb=" CA  HIS B 362 "
           pdb=" C   HIS B 362 "
           pdb=" N   ARG B 363 "
           pdb=" CA  ARG B 363 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.36  -15.64     0      5.00e+00 4.00e-02 9.78e+00
  dihedral pdb=" CA  HIS A 362 "
           pdb=" C   HIS A 362 "
           pdb=" N   ARG A 363 "
           pdb=" CA  ARG A 363 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.65  -15.35     0      5.00e+00 4.00e-02 9.42e+00
  dihedral pdb=" N   SEP V 344 "
           pdb=" CA  SEP V 344 "
           pdb=" CB  SEP V 344 "
           pdb=" OG  SEP V 344 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00    3.37   56.63     3      1.50e+01 4.44e-03 9.41e+00
  ... (remaining 7070 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1339
       0.040 -    0.079: 298
       0.079 -    0.119: 182
       0.119 -    0.158: 9
       0.158 -    0.198: 4
  Chirality restraints: 1832
  Sorted by residual:
  chirality pdb=" CA  ARG A  62 "
            pdb=" N   ARG A  62 "
            pdb=" C   ARG A  62 "
            pdb=" CB  ARG A  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.79e-01
  chirality pdb=" CA  LEU B  68 "
            pdb=" N   LEU B  68 "
            pdb=" C   LEU B  68 "
            pdb=" CB  LEU B  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.23e-01
  chirality pdb=" CB  THR A   6 "
            pdb=" CA  THR A   6 "
            pdb=" OG1 THR A   6 "
            pdb=" CG2 THR A   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.72   -0.17 2.00e-01 2.50e+01 7.11e-01
  ... (remaining 1829 not shown)

  Planarity restraints: 2055
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A  61 "    0.020 2.00e-02 2.50e+03   4.13e-02 1.71e+01
        pdb=" C   PHE A  61 "   -0.071 2.00e-02 2.50e+03
        pdb=" O   PHE A  61 "    0.027 2.00e-02 2.50e+03
        pdb=" N   ARG A  62 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B  75 "    0.019 2.00e-02 2.50e+03   4.05e-02 1.64e+01
        pdb=" C   PHE B  75 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   PHE B  75 "    0.027 2.00e-02 2.50e+03
        pdb=" N   ARG B  76 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B  67 "    0.019 2.00e-02 2.50e+03   3.86e-02 1.49e+01
        pdb=" C   ASP B  67 "   -0.067 2.00e-02 2.50e+03
        pdb=" O   ASP B  67 "    0.025 2.00e-02 2.50e+03
        pdb=" N   LEU B  68 "    0.023 2.00e-02 2.50e+03
  ... (remaining 2052 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 201
        2.66 -     3.22: 10561
        3.22 -     3.78: 17522
        3.78 -     4.34: 22386
        4.34 -     4.90: 36829
  Nonbonded interactions: 87499
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN L  90 "
            pdb=" O   GLN L  91 "
     model   vdw
     2.102 3.120
  nonbonded pdb=" NE2 GLN M  90 "
            pdb=" O   GLN M  91 "
     model   vdw
     2.201 3.120
  nonbonded pdb=" O   ILE B  31 "
            pdb=" NH2 ARG B 307 "
     model   vdw
     2.207 3.120
  nonbonded pdb=" O3P SEP V 346 "
            pdb=" OG  SER L  31 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" O   ASP M  83 "
            pdb=" OH  TYR M  87 "
     model   vdw
     2.237 3.040
  ... (remaining 87494 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 6 through 16 or (resid 17 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 18 through 133 or (resid 134 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 135 through 368))
  selection = (chain 'B' and (resid 6 through 176 or (resid 177 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 178 through 311 or (resid 312 and (name N or \ 
 name CA or name C or name O or name CB )) or resid 313 through 358 or (resid 35 \ 
9 and (name N or name CA or name C or name O or name CB )) or resid 360 through  \ 
368))
}
ncs_group {
  reference = chain 'H'
  selection = chain 'I'
}
ncs_group {
  reference = (chain 'L' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 5 through 190))
  selection = chain 'M'
}
ncs_group {
  reference = chain 'U'
  selection = chain 'V'
}

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=0.65 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:             6.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.500
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     31.710
  Find NCS groups from input model:        0.410
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.105  11766  Z= 0.228
  Angle     :  0.654  11.832  16055  Z= 0.361
  Chirality :  0.044   0.198   1832
  Planarity :  0.004   0.041   2055
  Dihedral  : 13.226  86.515   4191
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.24 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.22), residues: 1480
  helix:  0.93 (0.75), residues: 46
  sheet:  0.69 (0.21), residues: 582
  loop : -0.35 (0.21), residues: 852

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP M  36 
 HIS   0.002   0.001   HIS A 210 
 PHE   0.020   0.001   PHE I 105 
 TYR   0.021   0.001   TYR L  50 
 ARG   0.003   0.000   ARG B 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.29577 (  397)
  hydrogen bonds       : angle       9.64581 ( 1155)
  SS BOND              : bond        0.00278 (    6)
  SS BOND              : angle       0.42060 (   12)
  covalent geometry    : bond        0.00383 (11760)
  covalent geometry    : angle       0.65414 (16043)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 1.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   30 PHE cc_start: 0.9010 (p90) cc_final: 0.8702 (p90)
REVERT: H   80 ASN cc_start: 0.9041 (m-40) cc_final: 0.8733 (m-40)
REVERT: H   93 ASP cc_start: 0.7814 (m-30) cc_final: 0.7279 (m-30)
REVERT: I   30 PHE cc_start: 0.9095 (p90) cc_final: 0.8794 (p90)
REVERT: I   93 ASP cc_start: 0.7775 (m-30) cc_final: 0.7237 (m-30)
REVERT: M   50 TYR cc_start: 0.9744 (p90) cc_final: 0.9422 (p90)
REVERT: M  166 GLU cc_start: 0.9744 (tp30) cc_final: 0.9433 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.1831
  time to fit residues: 20.7681
Evaluate side-chains
  51 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 1.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 124 optimal weight:   20.0000
   chunk 112 optimal weight:    0.1980
   chunk 62 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 75 optimal weight:    0.8980
   chunk 59 optimal weight:    7.9990
   chunk 116 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9980
   chunk 86 optimal weight:   10.0000
   chunk 134 optimal weight:    3.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
** H  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 174 HIS
M 125 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.044622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2630 r_free = 0.2630 target = 0.031125 restraints weight = 97637.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.032313 restraints weight = 60860.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.033180 restraints weight = 44498.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.2671
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2672
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2672 r_free = 0.2672    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2672 r_free = 0.2672    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2672
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.1221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11766  Z= 0.147
  Angle     :  0.571   9.556  16055  Z= 0.289
  Chirality :  0.042   0.135   1832
  Planarity :  0.004   0.035   2055
  Dihedral  :  7.390  81.453   1670
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.24 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.21), residues: 1480
  helix:  0.66 (0.71), residues: 46
  sheet:  0.45 (0.19), residues: 664
  loop : -0.17 (0.22), residues: 770

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H 113 
 HIS   0.004   0.001   HIS I  38 
 PHE   0.015   0.001   PHE M  99 
 TYR   0.016   0.001   TYR L  50 
 ARG   0.003   0.000   ARG H  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04052 (  397)
  hydrogen bonds       : angle       6.83116 ( 1155)
  SS BOND              : bond        0.00359 (    6)
  SS BOND              : angle       0.48353 (   12)
  covalent geometry    : bond        0.00306 (11760)
  covalent geometry    : angle       0.57115 (16043)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 1.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 LYS cc_start: 0.9512 (mmmt) cc_final: 0.9283 (mmmt)
REVERT: B  192 MET cc_start: 0.8995 (mpp) cc_final: 0.8741 (mpp)
REVERT: B  249 TYR cc_start: 0.8906 (p90) cc_final: 0.8537 (p90)
REVERT: H   80 ASN cc_start: 0.8782 (m-40) cc_final: 0.8447 (m-40)
REVERT: H   93 ASP cc_start: 0.8054 (m-30) cc_final: 0.7498 (m-30)
REVERT: I   93 ASP cc_start: 0.7967 (m-30) cc_final: 0.7418 (m-30)
REVERT: M    3 ILE cc_start: 0.8411 (mm) cc_final: 0.7633 (mm)
REVERT: M    5 MET cc_start: 0.8870 (mpp) cc_final: 0.8236 (tmm)
REVERT: M  166 GLU cc_start: 0.9758 (tp30) cc_final: 0.9474 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.1858
  time to fit residues: 20.8796
Evaluate side-chains
  45 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 1.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 50 optimal weight:    0.4980
   chunk 65 optimal weight:    8.9990
   chunk 22 optimal weight:    0.0670
   chunk 15 optimal weight:    8.9990
   chunk 26 optimal weight:    8.9990
   chunk 134 optimal weight:    0.8980
   chunk 92 optimal weight:    7.9990
   chunk 20 optimal weight:    0.5980
   chunk 7 optimal weight:    0.3980
   chunk 132 optimal weight:    0.9980
   chunk 36 optimal weight:   10.0000
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
B 210 HIS
H  85 GLN
L  38 GLN
M  38 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.045451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.031937 restraints weight = 98433.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2706 r_free = 0.2706 target = 0.033189 restraints weight = 60765.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.034094 restraints weight = 44085.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.2703
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2705
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2705 r_free = 0.2705    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2705 r_free = 0.2705    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2705
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  11766  Z= 0.094
  Angle     :  0.540  10.914  16055  Z= 0.263
  Chirality :  0.042   0.149   1832
  Planarity :  0.004   0.061   2055
  Dihedral  :  7.084  79.563   1670
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.79 %
    Favored  : 96.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.24 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.21), residues: 1480
  helix:  0.63 (0.69), residues: 46
  sheet:  0.60 (0.20), residues: 660
  loop : -0.11 (0.22), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP L  36 
 HIS   0.002   0.000   HIS B 210 
 PHE   0.011   0.001   PHE I 105 
 TYR   0.019   0.001   TYR M  50 
 ARG   0.012   0.000   ARG H 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03388 (  397)
  hydrogen bonds       : angle       5.98710 ( 1155)
  SS BOND              : bond        0.00381 (    6)
  SS BOND              : angle       0.37915 (   12)
  covalent geometry    : bond        0.00199 (11760)
  covalent geometry    : angle       0.54022 (16043)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 74
  time to evaluate  : 1.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 LYS cc_start: 0.9515 (mmmt) cc_final: 0.9267 (mmmt)
REVERT: B   18 LEU cc_start: 0.9686 (mp) cc_final: 0.9449 (tp)
REVERT: B  192 MET cc_start: 0.8933 (mpp) cc_final: 0.8695 (mpp)
REVERT: B  249 TYR cc_start: 0.8822 (p90) cc_final: 0.8458 (p90)
REVERT: H   86 MET cc_start: 0.8915 (pmm) cc_final: 0.7805 (pmm)
REVERT: H   93 ASP cc_start: 0.8098 (m-30) cc_final: 0.7578 (m-30)
REVERT: I   86 MET cc_start: 0.8878 (pmm) cc_final: 0.7786 (pmm)
REVERT: I   93 ASP cc_start: 0.8054 (m-30) cc_final: 0.7538 (m-30)
REVERT: L   49 ILE cc_start: 0.9378 (mm) cc_final: 0.9076 (tp)
REVERT: M    3 ILE cc_start: 0.8323 (mm) cc_final: 0.7612 (mm)
REVERT: M    5 MET cc_start: 0.8777 (mpp) cc_final: 0.7851 (tmm)
REVERT: M  166 GLU cc_start: 0.9745 (tp30) cc_final: 0.9434 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 75
  average time/residue: 0.2174
  time to fit residues: 26.0155
Evaluate side-chains
  47 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 1.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 28 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 65 optimal weight:    9.9990
   chunk 1 optimal weight:    6.9990
   chunk 14 optimal weight:    9.9990
   chunk 118 optimal weight:    1.9990
   chunk 98 optimal weight:    0.0770
   chunk 18 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 55 optimal weight:    8.9990
   overall best weight:    3.0146

-------------------------------------------------------------------------------
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 = 0.3030 r_free = 0.3030 target = 0.042423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2575 r_free = 0.2575 target = 0.029739 restraints weight = 104627.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2616 r_free = 0.2616 target = 0.030847 restraints weight = 65963.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2646 r_free = 0.2646 target = 0.031646 restraints weight = 48535.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.2614
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2614
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2614 r_free = 0.2614    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2614 r_free = 0.2614    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2614
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.2279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  11766  Z= 0.253
  Angle     :  0.688  11.810  16055  Z= 0.340
  Chirality :  0.044   0.160   1832
  Planarity :  0.005   0.038   2055
  Dihedral  :  7.629  79.927   1670
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 15.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.24 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.21), residues: 1480
  helix:  0.50 (0.68), residues: 46
  sheet:  0.20 (0.21), residues: 610
  loop : -0.46 (0.21), residues: 824

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP H 113 
 HIS   0.009   0.002   HIS A 210 
 PHE   0.018   0.002   PHE M  99 
 TYR   0.020   0.002   TYR A 321 
 ARG   0.004   0.001   ARG I  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03832 (  397)
  hydrogen bonds       : angle       6.27337 ( 1155)
  SS BOND              : bond        0.00713 (    6)
  SS BOND              : angle       1.08625 (   12)
  covalent geometry    : bond        0.00526 (11760)
  covalent geometry    : angle       0.68781 (16043)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 1.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  192 MET cc_start: 0.8958 (mpp) cc_final: 0.8756 (mpp)
REVERT: H   86 MET cc_start: 0.8624 (pmm) cc_final: 0.8318 (pmm)
REVERT: I   86 MET cc_start: 0.8465 (pmm) cc_final: 0.8139 (pmm)
REVERT: L   24 CYS cc_start: 0.3709 (t) cc_final: 0.3370 (t)
REVERT: M    5 MET cc_start: 0.8958 (mpp) cc_final: 0.8550 (mpp)
REVERT: M  166 GLU cc_start: 0.9776 (tp30) cc_final: 0.9511 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.1893
  time to fit residues: 17.6101
Evaluate side-chains
  40 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 1.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 70 optimal weight:    0.1980
   chunk 15 optimal weight:    4.9990
   chunk 112 optimal weight:    5.9990
   chunk 48 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   chunk 107 optimal weight:    0.4980
   chunk 72 optimal weight:    6.9990
   chunk 12 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 105 optimal weight:    0.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.044198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2632 r_free = 0.2632 target = 0.031081 restraints weight = 98170.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2673 r_free = 0.2673 target = 0.032259 restraints weight = 62046.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.033112 restraints weight = 45445.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2678
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2678 r_free = 0.2678    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2678 r_free = 0.2678    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2678
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.2330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  11766  Z= 0.103
  Angle     :  0.563  14.131  16055  Z= 0.270
  Chirality :  0.043   0.137   1832
  Planarity :  0.004   0.038   2055
  Dihedral  :  7.155  77.284   1670
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.24 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.22), residues: 1480
  helix:  0.67 (0.68), residues: 46
  sheet:  0.47 (0.21), residues: 620
  loop : -0.43 (0.21), residues: 814

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP I  39 
 HIS   0.004   0.001   HIS A 210 
 PHE   0.009   0.001   PHE M  99 
 TYR   0.011   0.001   TYR I  98 
 ARG   0.006   0.000   ARG H  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02880 (  397)
  hydrogen bonds       : angle       5.68451 ( 1155)
  SS BOND              : bond        0.00290 (    6)
  SS BOND              : angle       0.78424 (   12)
  covalent geometry    : bond        0.00227 (11760)
  covalent geometry    : angle       0.56315 (16043)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 1.270 
Fit side-chains
   revert: symmetry clash
REVERT: A  229 LYS cc_start: 0.9572 (mmmt) cc_final: 0.9299 (mmmt)
REVERT: B  192 MET cc_start: 0.8933 (mpp) cc_final: 0.8709 (mpp)
REVERT: B  229 LYS cc_start: 0.9569 (mmmt) cc_final: 0.9308 (mmmt)
REVERT: H   80 ASN cc_start: 0.8675 (m-40) cc_final: 0.8435 (m-40)
REVERT: H   86 MET cc_start: 0.8530 (pmm) cc_final: 0.8188 (pmm)
REVERT: H   93 ASP cc_start: 0.8033 (m-30) cc_final: 0.7298 (m-30)
REVERT: I   49 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8623 (pm20)
REVERT: I   86 MET cc_start: 0.8468 (pmm) cc_final: 0.8168 (pmm)
REVERT: I   93 ASP cc_start: 0.8256 (m-30) cc_final: 0.7598 (m-30)
REVERT: L   49 ILE cc_start: 0.9394 (mm) cc_final: 0.9121 (tp)
REVERT: M  166 GLU cc_start: 0.9774 (tp30) cc_final: 0.9508 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.1884
  time to fit residues: 18.9520
Evaluate side-chains
  44 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 1.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 127 optimal weight:    1.9990
   chunk 113 optimal weight:    9.9990
   chunk 109 optimal weight:    6.9990
   chunk 131 optimal weight:   20.0000
   chunk 88 optimal weight:    1.9990
   chunk 140 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0040
   chunk 29 optimal weight:    1.9990
   chunk 136 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    1.1998

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

Flipped N/Q/H residues before XYZ refinement:
** I  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.043738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2621 r_free = 0.2621 target = 0.030787 restraints weight = 100901.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.031964 restraints weight = 63268.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.032817 restraints weight = 46231.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.2663
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2664
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2664 r_free = 0.2664    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2664 r_free = 0.2664    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2664
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.2549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11766  Z= 0.121
  Angle     :  0.563  16.291  16055  Z= 0.269
  Chirality :  0.042   0.149   1832
  Planarity :  0.004   0.038   2055
  Dihedral  :  7.090  77.732   1670
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.24 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.22), residues: 1480
  helix:  0.58 (0.64), residues: 50
  sheet:  0.35 (0.20), residues: 634
  loop : -0.29 (0.22), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP I  39 
 HIS   0.005   0.001   HIS H  38 
 PHE   0.014   0.001   PHE H 105 
 TYR   0.021   0.001   TYR M  50 
 ARG   0.004   0.000   ARG H  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02924 (  397)
  hydrogen bonds       : angle       5.57186 ( 1155)
  SS BOND              : bond        0.00553 (    6)
  SS BOND              : angle       0.64293 (   12)
  covalent geometry    : bond        0.00260 (11760)
  covalent geometry    : angle       0.56300 (16043)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 1.337 
Fit side-chains
   revert: symmetry clash
REVERT: A  229 LYS cc_start: 0.9596 (mmmt) cc_final: 0.9328 (mmmt)
REVERT: B  229 LYS cc_start: 0.9600 (mmmt) cc_final: 0.9332 (mmmt)
REVERT: H   80 ASN cc_start: 0.8652 (m-40) cc_final: 0.8422 (m-40)
REVERT: H   86 MET cc_start: 0.8674 (pmm) cc_final: 0.8347 (pmm)
REVERT: H   93 ASP cc_start: 0.8089 (m-30) cc_final: 0.7354 (m-30)
REVERT: I   93 ASP cc_start: 0.8049 (m-30) cc_final: 0.7444 (m-30)
REVERT: M  166 GLU cc_start: 0.9776 (tp30) cc_final: 0.9513 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.1971
  time to fit residues: 19.2014
Evaluate side-chains
  43 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 1.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 137 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 133 optimal weight:    4.9990
   chunk 93 optimal weight:    7.9990
   chunk 74 optimal weight:    6.9990
   chunk 119 optimal weight:    5.9990
   chunk 76 optimal weight:    0.0060
   chunk 37 optimal weight:    8.9990
   chunk 50 optimal weight:   10.0000
   chunk 30 optimal weight:    5.9990
   overall best weight:    3.0004

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

Flipped N/Q/H residues before XYZ refinement:
** I  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.041940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2567 r_free = 0.2567 target = 0.029429 restraints weight = 107558.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2607 r_free = 0.2607 target = 0.030505 restraints weight = 67921.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2636 r_free = 0.2636 target = 0.031287 restraints weight = 50017.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.2607
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2606
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2606 r_free = 0.2606    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2606 r_free = 0.2606    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2606
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.2992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  11766  Z= 0.244
  Angle     :  0.684  18.096  16055  Z= 0.332
  Chirality :  0.043   0.147   1832
  Planarity :  0.004   0.041   2055
  Dihedral  :  7.571  78.495   1670
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 14.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.24 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.21), residues: 1480
  helix:  0.29 (0.59), residues: 50
  sheet: -0.05 (0.21), residues: 606
  loop : -0.63 (0.21), residues: 824

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP H 106 
 HIS   0.011   0.002   HIS H  38 
 PHE   0.019   0.002   PHE M  99 
 TYR   0.016   0.002   TYR A 321 
 ARG   0.005   0.001   ARG H 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03508 (  397)
  hydrogen bonds       : angle       6.03967 ( 1155)
  SS BOND              : bond        0.00929 (    6)
  SS BOND              : angle       1.28542 (   12)
  covalent geometry    : bond        0.00507 (11760)
  covalent geometry    : angle       0.68377 (16043)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 1.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  215 SER cc_start: 0.8711 (m) cc_final: 0.8445 (p)
REVERT: H   93 ASP cc_start: 0.8169 (m-30) cc_final: 0.7446 (m-30)
REVERT: I   93 ASP cc_start: 0.8173 (m-30) cc_final: 0.7536 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.1974
  time to fit residues: 16.3267
Evaluate side-chains
  41 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 1.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 106 optimal weight:    1.9990
   chunk 83 optimal weight:    6.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 109 optimal weight:    5.9990
   chunk 48 optimal weight:    8.9990
   chunk 78 optimal weight:    6.9990
   chunk 36 optimal weight:   10.0000
   chunk 65 optimal weight:    0.5980
   chunk 28 optimal weight:    0.0970
   overall best weight:    2.1384

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

Flipped N/Q/H residues before XYZ refinement:
** I  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.042196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2575 r_free = 0.2575 target = 0.029576 restraints weight = 106350.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2615 r_free = 0.2615 target = 0.030676 restraints weight = 66968.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2644 r_free = 0.2644 target = 0.031471 restraints weight = 49056.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.2613
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2613
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2613 r_free = 0.2613    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2613 r_free = 0.2613    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.95   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2613
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.3224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  11766  Z= 0.178
  Angle     :  0.620  19.586  16055  Z= 0.296
  Chirality :  0.042   0.149   1832
  Planarity :  0.004   0.040   2055
  Dihedral  :  7.433  78.680   1670
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.05 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.24 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.21), residues: 1480
  helix:  0.28 (0.59), residues: 50
  sheet:  0.07 (0.21), residues: 576
  loop : -0.58 (0.21), residues: 854

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP H  39 
 HIS   0.007   0.001   HIS I  38 
 PHE   0.015   0.001   PHE M  99 
 TYR   0.012   0.001   TYR H  98 
 ARG   0.005   0.000   ARG A 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03051 (  397)
  hydrogen bonds       : angle       5.87390 ( 1155)
  SS BOND              : bond        0.00583 (    6)
  SS BOND              : angle       0.76193 (   12)
  covalent geometry    : bond        0.00376 (11760)
  covalent geometry    : angle       0.61951 (16043)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 1.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  215 SER cc_start: 0.8759 (m) cc_final: 0.8549 (p)
REVERT: B  249 TYR cc_start: 0.8554 (p90) cc_final: 0.8241 (p90)
REVERT: H   93 ASP cc_start: 0.8093 (m-30) cc_final: 0.7417 (m-30)
REVERT: I   93 ASP cc_start: 0.8079 (m-30) cc_final: 0.7465 (m-30)
REVERT: L    3 ILE cc_start: 0.9386 (mt) cc_final: 0.8879 (mt)
REVERT: L    5 MET cc_start: 0.9091 (mpp) cc_final: 0.8303 (tmm)
REVERT: L   55 LEU cc_start: 0.9457 (pp) cc_final: 0.9249 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.1931
  time to fit residues: 17.0018
Evaluate side-chains
  45 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 1.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 3 optimal weight:    7.9990
   chunk 86 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 137 optimal weight:    5.9990
   chunk 90 optimal weight:    7.9990
   chunk 7 optimal weight:    0.9980
   chunk 123 optimal weight:   10.0000
   chunk 93 optimal weight:    5.9990
   chunk 122 optimal weight:    4.9990
   chunk 15 optimal weight:    9.9990
   chunk 11 optimal weight:    0.0980
   overall best weight:    2.6186

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

Flipped N/Q/H residues before XYZ refinement:
** I  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.041519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2557 r_free = 0.2557 target = 0.029169 restraints weight = 107907.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2596 r_free = 0.2596 target = 0.030220 restraints weight = 68097.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2624 r_free = 0.2624 target = 0.030974 restraints weight = 50167.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.2593
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2593
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2593 r_free = 0.2593    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 0.95   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2593 r_free = 0.2593    target_work(ls_wunit_k1) = 0.030         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2593
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.3536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  11766  Z= 0.219
  Angle     :  0.675  19.411  16055  Z= 0.326
  Chirality :  0.044   0.175   1832
  Planarity :  0.004   0.040   2055
  Dihedral  :  7.657  79.640   1670
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 14.37
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.39 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.24 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.21), residues: 1480
  helix:  0.11 (0.58), residues: 50
  sheet: -0.14 (0.21), residues: 592
  loop : -0.66 (0.21), residues: 838

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP I 113 
 HIS   0.010   0.002   HIS I  38 
 PHE   0.019   0.002   PHE M  99 
 TYR   0.012   0.002   TYR A 321 
 ARG   0.003   0.000   ARG I  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03344 (  397)
  hydrogen bonds       : angle       6.12569 ( 1155)
  SS BOND              : bond        0.00872 (    6)
  SS BOND              : angle       0.80772 (   12)
  covalent geometry    : bond        0.00459 (11760)
  covalent geometry    : angle       0.67493 (16043)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 1.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  215 SER cc_start: 0.8758 (m) cc_final: 0.8517 (p)
REVERT: A  249 TYR cc_start: 0.9124 (p90) cc_final: 0.8891 (p90)
REVERT: B  192 MET cc_start: 0.9030 (mpp) cc_final: 0.8821 (mpp)
REVERT: B  249 TYR cc_start: 0.8433 (p90) cc_final: 0.8013 (p90)
REVERT: H   93 ASP cc_start: 0.8161 (m-30) cc_final: 0.7450 (m-30)
REVERT: I   93 ASP cc_start: 0.8151 (m-30) cc_final: 0.7519 (m-30)
REVERT: I  105 PHE cc_start: 0.9386 (m-10) cc_final: 0.9111 (m-10)
REVERT: L    3 ILE cc_start: 0.9328 (mt) cc_final: 0.8904 (mt)
REVERT: L    5 MET cc_start: 0.9016 (mpp) cc_final: 0.8533 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.2024
  time to fit residues: 16.1698
Evaluate side-chains
  38 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 1.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 132 optimal weight:    0.6980
   chunk 62 optimal weight:    5.9990
   chunk 88 optimal weight:    3.9990
   chunk 69 optimal weight:    0.0670
   chunk 139 optimal weight:    5.9990
   chunk 89 optimal weight:    8.9990
   chunk 102 optimal weight:    0.1980
   chunk 40 optimal weight:    0.9990
   chunk 95 optimal weight:    1.9990
   chunk 112 optimal weight:    0.6980
   chunk 32 optimal weight:    7.9990
   overall best weight:    0.5320

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.043241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2609 r_free = 0.2609 target = 0.030311 restraints weight = 101062.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2650 r_free = 0.2650 target = 0.031469 restraints weight = 62393.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.032298 restraints weight = 45438.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.2647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.3504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  11766  Z= 0.100
  Angle     :  0.601  19.121  16055  Z= 0.280
  Chirality :  0.044   0.156   1832
  Planarity :  0.004   0.043   2055
  Dihedral  :  7.094  79.217   1670
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.45 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.24 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.22), residues: 1480
  helix:  0.18 (0.60), residues: 50
  sheet:  0.27 (0.21), residues: 596
  loop : -0.58 (0.21), residues: 834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP H  39 
 HIS   0.006   0.001   HIS A 210 
 PHE   0.011   0.001   PHE L  99 
 TYR   0.013   0.001   TYR A 208 
 ARG   0.002   0.000   ARG H 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02705 (  397)
  hydrogen bonds       : angle       5.51829 ( 1155)
  SS BOND              : bond        0.00458 (    6)
  SS BOND              : angle       1.04465 (   12)
  covalent geometry    : bond        0.00227 (11760)
  covalent geometry    : angle       0.60088 (16043)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 1.251 
Fit side-chains
   revert: symmetry clash
REVERT: A  229 LYS cc_start: 0.9599 (mmmt) cc_final: 0.9356 (mmmt)
REVERT: B  249 TYR cc_start: 0.8419 (p90) cc_final: 0.8088 (p90)
REVERT: H   49 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8377 (tm-30)
REVERT: H   93 ASP cc_start: 0.8103 (m-30) cc_final: 0.7400 (m-30)
REVERT: I   93 ASP cc_start: 0.8096 (m-30) cc_final: 0.7399 (m-30)
REVERT: L    3 ILE cc_start: 0.9312 (mt) cc_final: 0.8856 (mt)
REVERT: L    5 MET cc_start: 0.8904 (mpp) cc_final: 0.8363 (tmm)
REVERT: L   55 LEU cc_start: 0.9440 (pp) cc_final: 0.9235 (pp)
REVERT: M    5 MET cc_start: 0.8404 (mpp) cc_final: 0.8120 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.2068
  time to fit residues: 19.3174
Evaluate side-chains
  41 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 1.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 128 optimal weight:    6.9990
   chunk 135 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 86 optimal weight:    0.5980
   chunk 53 optimal weight:    0.0070
   chunk 36 optimal weight:   10.0000
   chunk 121 optimal weight:    0.9990
   chunk 74 optimal weight:    4.9990
   chunk 42 optimal weight:    9.9990
   chunk 120 optimal weight:    3.9990
   overall best weight:    1.1202

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.042762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2595 r_free = 0.2595 target = 0.029950 restraints weight = 102711.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2637 r_free = 0.2637 target = 0.031092 restraints weight = 63463.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2666 r_free = 0.2666 target = 0.031917 restraints weight = 46196.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.2636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.3605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11766  Z= 0.115
  Angle     :  0.581  17.464  16055  Z= 0.273
  Chirality :  0.043   0.151   1832
  Planarity :  0.004   0.043   2055
  Dihedral  :  7.048  79.198   1670
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.45 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.24 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.22), residues: 1480
  helix:  0.29 (0.60), residues: 50
  sheet:  0.34 (0.21), residues: 588
  loop : -0.54 (0.21), residues: 842

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  39 
 HIS   0.006   0.001   HIS A 210 
 PHE   0.020   0.001   PHE I 105 
 TYR   0.025   0.001   TYR M  50 
 ARG   0.002   0.000   ARG B 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02701 (  397)
  hydrogen bonds       : angle       5.41726 ( 1155)
  SS BOND              : bond        0.00536 (    6)
  SS BOND              : angle       0.73937 (   12)
  covalent geometry    : bond        0.00253 (11760)
  covalent geometry    : angle       0.58135 (16043)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3613.35 seconds
wall clock time: 63 minutes 48.87 seconds (3828.87 seconds total)