Starting phenix.real_space_refine
on Sat Jun 14 22:21:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ozd_17305/06_2025/8ozd_17305.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ozd_17305/06_2025/8ozd_17305.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ozd_17305/06_2025/8ozd_17305.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ozd_17305/06_2025/8ozd_17305.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ozd_17305/06_2025/8ozd_17305.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ozd_17305/06_2025/8ozd_17305.cif"
  }
  resolution = 3.89
  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=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 609 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      66      5.49       5
     S      48      5.16       5
     C   10118      2.51       5
     N    2650      2.21       5
     O    3119      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 16001
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3486
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 418, 3486
          Classifications: {'peptide': 418}
          Link IDs: {'PTRANS': 11, 'TRANS': 406}
    Chain: "B"
      Number of atoms: 3821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 473, 3821
          Classifications: {'peptide': 473}
          Link IDs: {'PTRANS': 24, 'TRANS': 448}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 361
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 361
          Classifications: {'RNA': 18}
          Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17}
          Link IDs: {'rna2p': 1, 'rna3p': 16}
    Chain: "F"
      Number of atoms: 360
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 360
          Classifications: {'RNA': 18}
          Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 17}
          Link IDs: {'rna2p': 1, 'rna3p': 16}
    Chain: "J"
      Number of atoms: 333
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 333
          Classifications: {'DNA': 16}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 15}
    Chain: "E"
      Number of atoms: 333
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 333
          Classifications: {'DNA': 16}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 15}
    Chain: "C"
      Number of atoms: 3486
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 418, 3486
          Classifications: {'peptide': 418}
          Link IDs: {'PTRANS': 11, 'TRANS': 406}
    Chain: "D"
      Number of atoms: 3821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 473, 3821
          Classifications: {'peptide': 473}
          Link IDs: {'PTRANS': 24, 'TRANS': 448}
          Chain breaks: 1
  Time building chain proxies: 9.19, per 1000 atoms: 0.57
  Number of scatterers: 16001
  At special positions: 0
  Unit cell: (153.67, 128.26, 117.37, 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      48     16.00
     P      66     15.00
     O    3119      8.00
     N    2650      7.00
     C   10118      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.76
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  3540 Ramachandran restraints generated.
    1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3396

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 20 sheets defined
      40.1% alpha, 17.5% beta
      11 base pairs and 43 stacking pairs defined.
    Time for finding SS restraints: 7.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 29
    Processing helix  chain 'A' and resid 44 through 56
      removed outlier: 3.774A  pdb=" N   GLU A  50 " --> pdb=" O   TRP A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 89
      removed outlier: 3.505A  pdb=" N   LYS A  89 " --> pdb=" O   LYS A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 114
      removed outlier: 4.252A  pdb=" N   ARG A 114 " --> pdb=" O   ILE A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 138
    Processing helix  chain 'A' and resid 147 through 157
    Processing helix  chain 'A' and resid 191 through 194
    Processing helix  chain 'A' and resid 219 through 224
      removed outlier: 4.101A  pdb=" N   PHE A 223 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   THR A 224 " --> pdb=" O   TYR A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 233
      removed outlier: 3.700A  pdb=" N   GLU A 231 " --> pdb=" O   PRO A 228 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   THR A 232 " --> pdb=" O   LYS A 229 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   TYR A 233 " --> pdb=" O   THR A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 238
    Processing helix  chain 'A' and resid 242 through 249
      removed outlier: 3.530A  pdb=" N   ILE A 246 " --> pdb=" O   PRO A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 280
      removed outlier: 3.689A  pdb=" N   ILE A 265 " --> pdb=" O   CYS A 261 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   VAL A 266 " --> pdb=" O   LYS A 262 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   GLN A 267 " --> pdb=" O   ARG A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 302
      No H-bonds generated for 'chain 'A' and resid 300 through 302'
    Processing helix  chain 'A' and resid 353 through 367
      removed outlier: 4.348A  pdb=" N   ASN A 367 " --> pdb=" O   ARG A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 384
    Processing helix  chain 'B' and resid 15 through 17
      No H-bonds generated for 'chain 'B' and resid 15 through 17'
    Processing helix  chain 'B' and resid 22 through 31
    Processing helix  chain 'B' and resid 46 through 61
      removed outlier: 3.953A  pdb=" N   LYS B  51 " --> pdb=" O   LYS B  47 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ILE B  52 " --> pdb=" O   GLN B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 83
    Processing helix  chain 'B' and resid 97 through 106
      removed outlier: 3.669A  pdb=" N   ILE B 101 " --> pdb=" O   THR B  97 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   PHE B 104 " --> pdb=" O   ASP B 100 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   TYR B 106 " --> pdb=" O   GLY B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 132
      removed outlier: 3.949A  pdb=" N   LYS B 124 " --> pdb=" O   LEU B 120 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   GLU B 132 " --> pdb=" O   ALA B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 150
      removed outlier: 3.670A  pdb=" N   TYR B 148 " --> pdb=" O   PRO B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 162
    Processing helix  chain 'B' and resid 205 through 214
      removed outlier: 3.603A  pdb=" N   LEU B 214 " --> pdb=" O   PHE B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 234
      removed outlier: 3.884A  pdb=" N   ASP B 233 " --> pdb=" O   ALA B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 247
      No H-bonds generated for 'chain 'B' and resid 245 through 247'
    Processing helix  chain 'B' and resid 248 through 264
    Processing helix  chain 'B' and resid 331 through 351
      removed outlier: 3.858A  pdb=" N   GLN B 349 " --> pdb=" O   SER B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 377
      removed outlier: 3.795A  pdb=" N   TRP B 370 " --> pdb=" O   ASN B 366 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ALA B 372 " --> pdb=" O   GLN B 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 426 through 430
    Processing helix  chain 'B' and resid 451 through 463
      removed outlier: 4.044A  pdb=" N   LEU B 460 " --> pdb=" O   LEU B 456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 477 through 491
    Processing helix  chain 'B' and resid 502 through 506
    Processing helix  chain 'C' and resid 14 through 29
    Processing helix  chain 'C' and resid 44 through 56
      removed outlier: 3.774A  pdb=" N   GLU C  50 " --> pdb=" O   TRP C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 71 through 89
      removed outlier: 3.505A  pdb=" N   LYS C  89 " --> pdb=" O   LYS C  85 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 109 through 114
      removed outlier: 4.251A  pdb=" N   ARG C 114 " --> pdb=" O   ILE C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 123 through 138
    Processing helix  chain 'C' and resid 147 through 157
    Processing helix  chain 'C' and resid 191 through 194
    Processing helix  chain 'C' and resid 219 through 224
      removed outlier: 4.100A  pdb=" N   PHE C 223 " --> pdb=" O   ALA C 220 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   THR C 224 " --> pdb=" O   TYR C 221 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 227 through 233
      removed outlier: 3.700A  pdb=" N   GLU C 231 " --> pdb=" O   PRO C 228 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   THR C 232 " --> pdb=" O   LYS C 229 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   TYR C 233 " --> pdb=" O   THR C 230 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 234 through 238
    Processing helix  chain 'C' and resid 242 through 249
      removed outlier: 3.531A  pdb=" N   ILE C 246 " --> pdb=" O   PRO C 242 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 257 through 280
      removed outlier: 3.690A  pdb=" N   ILE C 265 " --> pdb=" O   CYS C 261 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   VAL C 266 " --> pdb=" O   LYS C 262 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   GLN C 267 " --> pdb=" O   ARG C 263 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 300 through 302
      No H-bonds generated for 'chain 'C' and resid 300 through 302'
    Processing helix  chain 'C' and resid 353 through 367
      removed outlier: 4.348A  pdb=" N   ASN C 367 " --> pdb=" O   ARG C 363 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 369 through 384
    Processing helix  chain 'D' and resid 15 through 17
      No H-bonds generated for 'chain 'D' and resid 15 through 17'
    Processing helix  chain 'D' and resid 22 through 31
    Processing helix  chain 'D' and resid 46 through 61
      removed outlier: 3.953A  pdb=" N   LYS D  51 " --> pdb=" O   LYS D  47 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ILE D  52 " --> pdb=" O   GLN D  48 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 77 through 83
    Processing helix  chain 'D' and resid 97 through 106
      removed outlier: 3.668A  pdb=" N   ILE D 101 " --> pdb=" O   THR D  97 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   PHE D 104 " --> pdb=" O   ASP D 100 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   TYR D 106 " --> pdb=" O   GLY D 102 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 109 through 132
      removed outlier: 3.950A  pdb=" N   LYS D 124 " --> pdb=" O   LEU D 120 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   GLU D 132 " --> pdb=" O   ALA D 128 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 144 through 150
      removed outlier: 3.671A  pdb=" N   TYR D 148 " --> pdb=" O   PRO D 144 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 158 through 162
    Processing helix  chain 'D' and resid 205 through 214
      removed outlier: 3.604A  pdb=" N   LEU D 214 " --> pdb=" O   PHE D 210 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 230 through 234
      removed outlier: 3.884A  pdb=" N   ASP D 233 " --> pdb=" O   ALA D 230 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 245 through 247
      No H-bonds generated for 'chain 'D' and resid 245 through 247'
    Processing helix  chain 'D' and resid 248 through 264
    Processing helix  chain 'D' and resid 331 through 351
      removed outlier: 3.858A  pdb=" N   GLN D 349 " --> pdb=" O   SER D 345 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 366 through 377
      removed outlier: 3.795A  pdb=" N   TRP D 370 " --> pdb=" O   ASN D 366 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ALA D 372 " --> pdb=" O   GLN D 368 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 426 through 430
    Processing helix  chain 'D' and resid 451 through 463
      removed outlier: 4.045A  pdb=" N   LEU D 460 " --> pdb=" O   LEU D 456 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 477 through 491
    Processing helix  chain 'D' and resid 502 through 506
    Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33
      removed outlier: 5.421A  pdb=" N   ILE A   5 " --> pdb=" O   TRP A  33 " (cutoff:3.500A)
      removed outlier: 7.202A  pdb=" N   LYS A   4 " --> pdb=" O   LYS A  59 " (cutoff:3.500A)
      removed outlier: 8.102A  pdb=" N   LEU A  61 " --> pdb=" O   LYS A   4 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   PHE A   6 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
      removed outlier: 7.419A  pdb=" N   VAL A  63 " --> pdb=" O   PHE A   6 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   SER A   8 " --> pdb=" O   VAL A  63 " (cutoff:3.500A)
      removed outlier: 8.119A  pdb=" N   ILE A 118 " --> pdb=" O   ILE A  94 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 278 through 279
      removed outlier: 7.342A  pdb=" N   CYS B 279 " --> pdb=" O   PHE B 358 " (cutoff:3.500A)
      removed outlier: 7.363A  pdb=" N   HIS B 360 " --> pdb=" O   CYS B 279 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 278 through 279
      removed outlier: 7.342A  pdb=" N   CYS B 279 " --> pdb=" O   PHE B 358 " (cutoff:3.500A)
      removed outlier: 7.363A  pdb=" N   HIS B 360 " --> pdb=" O   CYS B 279 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   GLY B 385 " --> pdb=" O   ASN B 446 " (cutoff:3.500A)
      removed outlier: 5.111A  pdb=" N   VAL B 412 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 7.177A  pdb=" N   GLU B   3 " --> pdb=" O   VAL B 412 " (cutoff:3.500A)
      removed outlier: 7.355A  pdb=" N   LYS A 411 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
      removed outlier: 8.645A  pdb=" N   TYR B   6 " --> pdb=" O   LYS A 411 " (cutoff:3.500A)
      removed outlier: 9.135A  pdb=" N   ASN A 413 " --> pdb=" O   TYR B   6 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   VAL A 414 " --> pdb=" O   LYS A 167 " (cutoff:3.500A)
      removed outlier: 6.002A  pdb=" N   LYS A 167 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 180
      removed outlier: 4.817A  pdb=" N   SER A 177 " --> pdb=" O   SER A 404 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   PHE A 402 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   VAL A 401 " --> pdb=" O   LEU A 393 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 189
    Processing sheet with id=AA6, first strand: chain 'A' and resid 283 through 286
    Processing sheet with id=AA7, first strand: chain 'A' and resid 304 through 305
    Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 314
      removed outlier: 3.610A  pdb=" N   GLY A 312 " --> pdb=" O   TRP A 319 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   TRP A 319 " --> pdb=" O   GLY A 312 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 19 through 20
      removed outlier: 3.836A  pdb=" N   ILE B  12 " --> pdb=" O   CYS B  20 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 92 through 95
      removed outlier: 3.541A  pdb=" N   GLY B  45 " --> pdb=" O   LYS B  94 " (cutoff:3.500A)
      removed outlier: 6.105A  pdb=" N   GLY B  42 " --> pdb=" O   PHE B 140 " (cutoff:3.500A)
      removed outlier: 7.167A  pdb=" N   ILE B 142 " --> pdb=" O   GLY B  42 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   ILE B  44 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   TRP B 139 " --> pdb=" O   GLN B 222 " (cutoff:3.500A)
      removed outlier: 7.312A  pdb=" N   PHE B 224 " --> pdb=" O   TRP B 139 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   VAL B 141 " --> pdb=" O   PHE B 224 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 32 through 33
      removed outlier: 5.421A  pdb=" N   ILE C   5 " --> pdb=" O   TRP C  33 " (cutoff:3.500A)
      removed outlier: 7.202A  pdb=" N   LYS C   4 " --> pdb=" O   LYS C  59 " (cutoff:3.500A)
      removed outlier: 8.103A  pdb=" N   LEU C  61 " --> pdb=" O   LYS C   4 " (cutoff:3.500A)
      removed outlier: 6.109A  pdb=" N   PHE C   6 " --> pdb=" O   LEU C  61 " (cutoff:3.500A)
      removed outlier: 7.418A  pdb=" N   VAL C  63 " --> pdb=" O   PHE C   6 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   SER C   8 " --> pdb=" O   VAL C  63 " (cutoff:3.500A)
      removed outlier: 8.118A  pdb=" N   ILE C 118 " --> pdb=" O   ILE C  94 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 278 through 279
      removed outlier: 7.342A  pdb=" N   CYS D 279 " --> pdb=" O   PHE D 358 " (cutoff:3.500A)
      removed outlier: 7.362A  pdb=" N   HIS D 360 " --> pdb=" O   CYS D 279 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 278 through 279
      removed outlier: 7.342A  pdb=" N   CYS D 279 " --> pdb=" O   PHE D 358 " (cutoff:3.500A)
      removed outlier: 7.362A  pdb=" N   HIS D 360 " --> pdb=" O   CYS D 279 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   GLY D 385 " --> pdb=" O   ASN D 446 " (cutoff:3.500A)
      removed outlier: 5.112A  pdb=" N   VAL D 412 " --> pdb=" O   GLU D   3 " (cutoff:3.500A)
      removed outlier: 7.177A  pdb=" N   GLU D   3 " --> pdb=" O   VAL D 412 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   ASN C 413 " --> pdb=" O   LEU D   4 " (cutoff:3.500A)
      removed outlier: 8.187A  pdb=" N   TYR D   6 " --> pdb=" O   ASN C 413 " (cutoff:3.500A)
      removed outlier: 10.329A  pdb=" N   SER C 415 " --> pdb=" O   TYR D   6 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   VAL C 414 " --> pdb=" O   LYS C 167 " (cutoff:3.500A)
      removed outlier: 6.002A  pdb=" N   LYS C 167 " --> pdb=" O   VAL C 414 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 176 through 180
      removed outlier: 4.817A  pdb=" N   SER C 177 " --> pdb=" O   SER C 404 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   PHE C 402 " --> pdb=" O   LEU C 179 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   VAL C 401 " --> pdb=" O   LEU C 393 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 186 through 189
    Processing sheet with id=AB7, first strand: chain 'C' and resid 283 through 286
    Processing sheet with id=AB8, first strand: chain 'C' and resid 304 through 305
    Processing sheet with id=AB9, first strand: chain 'C' and resid 311 through 314
      removed outlier: 3.609A  pdb=" N   GLY C 312 " --> pdb=" O   TRP C 319 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   TRP C 319 " --> pdb=" O   GLY C 312 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 19 through 20
      removed outlier: 3.836A  pdb=" N   ILE D  12 " --> pdb=" O   CYS D  20 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'D' and resid 92 through 95
      removed outlier: 3.541A  pdb=" N   GLY D  45 " --> pdb=" O   LYS D  94 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   GLY D  42 " --> pdb=" O   PHE D 140 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   ILE D 142 " --> pdb=" O   GLY D  42 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   ILE D  44 " --> pdb=" O   ILE D 142 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   TRP D 139 " --> pdb=" O   GLN D 222 " (cutoff:3.500A)
      removed outlier: 7.312A  pdb=" N   PHE D 224 " --> pdb=" O   TRP D 139 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   VAL D 141 " --> pdb=" O   PHE D 224 " (cutoff:3.500A)

    577 hydrogen bonds defined for protein.
    1581 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      22 hydrogen bonds
      44 hydrogen bond angles
      0 basepair planarities
      11 basepair parallelities
      43 stacking parallelities
  Total time for adding SS restraints: 6.49

  Time building geometry restraints manager: 4.38 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: 3882
        1.33 -     1.45: 3661
        1.45 -     1.57: 8786
        1.57 -     1.69: 130
        1.69 -     1.81: 74
  Bond restraints: 16533
  Sorted by residual:
  bond pdb=" CG  ARG C 374 "
       pdb=" CD  ARG C 374 "
    ideal  model  delta    sigma   weight residual
    1.520  1.487  0.033 3.00e-02 1.11e+03 1.21e+00
  bond pdb=" CG  ARG A 374 "
       pdb=" CD  ARG A 374 "
    ideal  model  delta    sigma   weight residual
    1.520  1.487  0.033 3.00e-02 1.11e+03 1.18e+00
  bond pdb=" CB  ASP C  40 "
       pdb=" CG  ASP C  40 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 2.50e-02 1.60e+03 9.42e-01
  bond pdb=" CB  ASP A  40 "
       pdb=" CG  ASP A  40 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 2.50e-02 1.60e+03 9.22e-01
  bond pdb=" CA  ASP A 146 "
       pdb=" C   ASP A 146 "
    ideal  model  delta    sigma   weight residual
    1.519  1.530 -0.010 1.14e-02 7.69e+03 8.38e-01
  ... (remaining 16528 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 22229
        1.89 -     3.78: 343
        3.78 -     5.68: 49
        5.68 -     7.57: 4
        7.57 -     9.46: 6
  Bond angle restraints: 22631
  Sorted by residual:
  angle pdb=" C   LEU C  39 "
        pdb=" N   ASP C  40 "
        pdb=" CA  ASP C  40 "
      ideal   model   delta    sigma   weight residual
     121.54  130.59   -9.05 1.91e+00 2.74e-01 2.24e+01
  angle pdb=" C   LEU A  39 "
        pdb=" N   ASP A  40 "
        pdb=" CA  ASP A  40 "
      ideal   model   delta    sigma   weight residual
     121.54  130.51   -8.97 1.91e+00 2.74e-01 2.20e+01
  angle pdb=" C   TRP A 369 "
        pdb=" N   ASN A 370 "
        pdb=" CA  ASN A 370 "
      ideal   model   delta    sigma   weight residual
     120.65  124.79   -4.14 1.32e+00 5.74e-01 9.85e+00
  angle pdb=" C   TRP C 369 "
        pdb=" N   ASN C 370 "
        pdb=" CA  ASN C 370 "
      ideal   model   delta    sigma   weight residual
     120.65  124.75   -4.10 1.32e+00 5.74e-01 9.63e+00
  angle pdb=" C   LYS A  86 "
        pdb=" N   GLN A  87 "
        pdb=" CA  GLN A  87 "
      ideal   model   delta    sigma   weight residual
     121.14  116.10    5.04 1.75e+00 3.27e-01 8.29e+00
  ... (remaining 22626 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.21: 9523
       33.21 -    66.42: 428
       66.42 -    99.62: 14
       99.62 -   132.83: 1
      132.83 -   166.04: 6
  Dihedral angle restraints: 9972
    sinusoidal: 4716
      harmonic: 5256
  Sorted by residual:
  dihedral pdb=" O4'   U F  31 "
           pdb=" C1'   U F  31 "
           pdb=" N1    U F  31 "
           pdb=" C2    U F  31 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   33.96  166.04     1      1.50e+01 4.44e-03 8.41e+01
  dihedral pdb=" O4'   U I  13 "
           pdb=" C1'   U I  13 "
           pdb=" N1    U I  13 "
           pdb=" C2    U I  13 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   39.42  160.58     1      1.50e+01 4.44e-03 8.29e+01
  dihedral pdb=" O4'   U F  27 "
           pdb=" C1'   U F  27 "
           pdb=" N1    U F  27 "
           pdb=" C2    U F  27 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -24.95 -135.05     1      1.50e+01 4.44e-03 7.29e+01
  ... (remaining 9969 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1819
       0.039 -    0.078: 449
       0.078 -    0.117: 189
       0.117 -    0.156: 25
       0.156 -    0.195: 2
  Chirality restraints: 2484
  Sorted by residual:
  chirality pdb=" CB  ILE B 223 "
            pdb=" CA  ILE B 223 "
            pdb=" CG1 ILE B 223 "
            pdb=" CG2 ILE B 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.52e-01
  chirality pdb=" CB  ILE D 223 "
            pdb=" CA  ILE D 223 "
            pdb=" CG1 ILE D 223 "
            pdb=" CG2 ILE D 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.42e-01
  chirality pdb=" CA  GLN C 156 "
            pdb=" N   GLN C 156 "
            pdb=" C   GLN C 156 "
            pdb=" CB  GLN C 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.93e-01
  ... (remaining 2481 not shown)

  Planarity restraints: 2620
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 437 "    0.050 5.00e-02 4.00e+02   7.66e-02 9.38e+00
        pdb=" N   PRO B 438 "   -0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO B 438 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO B 438 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL D 437 "   -0.050 5.00e-02 4.00e+02   7.65e-02 9.37e+00
        pdb=" N   PRO D 438 "    0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO D 438 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO D 438 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C 132 "   -0.008 2.00e-02 2.50e+03   1.65e-02 2.74e+00
        pdb=" C   LEU C 132 "    0.029 2.00e-02 2.50e+03
        pdb=" O   LEU C 132 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   GLU C 133 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 2617 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 850
        2.72 -     3.27: 16505
        3.27 -     3.81: 27878
        3.81 -     4.36: 33721
        4.36 -     4.90: 54779
  Nonbonded interactions: 133733
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 162 "
            pdb=" O   PRO B 427 "
     model   vdw
     2.178 3.120
  nonbonded pdb=" OG  SER D 493 "
            pdb=" OD1 ASP D 495 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OG  SER B 493 "
            pdb=" OD1 ASP B 495 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" NZ  LYS C  24 "
            pdb=" O   LEU D  29 "
     model   vdw
     2.224 3.120
  nonbonded pdb=" O   LEU C 227 "
            pdb=" OG1 THR C 230 "
     model   vdw
     2.229 3.040
  ... (remaining 133728 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'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'J'
}
ncs_group {
  reference = chain 'F'
  selection = (chain 'I' and (name P or name OP1 or name OP2 or name O5' or name C5' or name C \ 
4' or name O4' or name C3' or name O3' or name C2' or name O2' or name C1' or na \ 
me N1 or name C2 or name O2 or name N3 or name C4 or name O4 or name C5 or name  \ 
C6 ))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.990
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.090
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.540
  Check model and map are aligned:         0.110
  Set scattering table:                    0.150
  Process input model:                     42.650
  Find NCS groups from input model:        0.510
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7449
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  16533  Z= 0.120
  Angle     :  0.589   9.461  22631  Z= 0.313
  Chirality :  0.041   0.195   2484
  Planarity :  0.004   0.077   2620
  Dihedral  : 16.885 166.041   6576
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 13.09
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  4.75 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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 (0.20), residues: 1770
  helix:  0.76 (0.22), residues: 582
  sheet: -0.35 (0.31), residues: 292
  loop : -0.72 (0.21), residues: 896

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 231 
 HIS   0.004   0.001   HIS B 217 
 PHE   0.018   0.001   PHE C 273 
 TYR   0.007   0.001   TYR A 251 
 ARG   0.010   0.000   ARG C 374 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19776 (  599)
  hydrogen bonds       : angle       8.04104 ( 1625)
  covalent geometry    : bond        0.00254 (16533)
  covalent geometry    : angle       0.58896 (22631)

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

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

  3540 Ramachandran restraints generated.
    1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3540 Ramachandran restraints generated.
    1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 1.772 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ARG cc_start: 0.4934 (ttm110) cc_final: 0.4672 (ttm170)
REVERT: A  277 MET cc_start: 0.6731 (mtp) cc_final: 0.5977 (mmp)
REVERT: A  279 ASP cc_start: 0.7655 (t70) cc_final: 0.7181 (m-30)
REVERT: A  364 GLN cc_start: 0.6917 (tp40) cc_final: 0.6049 (tp40)
REVERT: A  395 MET cc_start: 0.7309 (ppp) cc_final: 0.6913 (ppp)
REVERT: B   58 ASP cc_start: 0.8369 (p0) cc_final: 0.8093 (m-30)
REVERT: B  474 ASP cc_start: 0.8353 (t70) cc_final: 0.7954 (t70)
REVERT: C  193 MET cc_start: 0.6223 (ttt) cc_final: 0.5262 (tmm)
REVERT: D   64 ILE cc_start: 0.8955 (mm) cc_final: 0.8543 (mm)
REVERT: D  247 LYS cc_start: 0.8805 (mppt) cc_final: 0.8515 (mtmt)
REVERT: D  309 ASP cc_start: 0.7700 (p0) cc_final: 0.7370 (p0)
REVERT: D  362 LYS cc_start: 0.8377 (pptt) cc_final: 0.7899 (ptpt)
REVERT: D  466 ASN cc_start: 0.8318 (t0) cc_final: 0.7675 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 251
  average time/residue: 0.2903
  time to fit residues: 107.1729
Evaluate side-chains
  159 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 1.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 151 optimal weight:    0.0670
   chunk 136 optimal weight:    5.9990
   chunk 75 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   chunk 92 optimal weight:    9.9990
   chunk 72 optimal weight:    3.9990
   chunk 141 optimal weight:    0.8980
   chunk 54 optimal weight:    7.9990
   chunk 85 optimal weight:    0.8980
   chunk 105 optimal weight:    0.9990
   chunk 163 optimal weight:    0.8980
   overall best weight:    0.7520

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

Flipped N/Q/H residues before XYZ refinement:
B 360 HIS
B 446 ASN
D 154 ASN
D 360 HIS
D 446 ASN
D 468 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.109341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.087120 restraints weight = 65303.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.089414 restraints weight = 40465.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.090748 restraints weight = 28677.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.1785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  16533  Z= 0.138
  Angle     :  0.635   9.275  22631  Z= 0.329
  Chirality :  0.043   0.149   2484
  Planarity :  0.005   0.058   2620
  Dihedral  : 17.265 179.554   2932
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  4.86 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 10.01 %
    Favored  : 88.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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: -0.25 (0.20), residues: 1770
  helix:  0.85 (0.22), residues: 590
  sheet: -0.28 (0.31), residues: 290
  loop : -0.78 (0.21), residues: 890

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 368 
 HIS   0.016   0.001   HIS A   9 
 PHE   0.017   0.001   PHE C 273 
 TYR   0.019   0.001   TYR D 397 
 ARG   0.009   0.001   ARG A 374 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05095 (  599)
  hydrogen bonds       : angle       5.95220 ( 1625)
  covalent geometry    : bond        0.00309 (16533)
  covalent geometry    : angle       0.63498 (22631)

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

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

  3540 Ramachandran restraints generated.
    1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3540 Ramachandran restraints generated.
    1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 180
  time to evaluate  : 2.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ARG cc_start: 0.4860 (ttm110) cc_final: 0.4537 (ttm110)
REVERT: A  277 MET cc_start: 0.7057 (mtp) cc_final: 0.6456 (ttm)
REVERT: A  279 ASP cc_start: 0.7751 (t70) cc_final: 0.7308 (m-30)
REVERT: A  364 GLN cc_start: 0.7707 (tp40) cc_final: 0.7050 (tp40)
REVERT: A  395 MET cc_start: 0.7747 (ppp) cc_final: 0.7293 (ppp)
REVERT: B    1 MET cc_start: 0.4972 (mmp) cc_final: 0.4533 (mmp)
REVERT: B   92 THR cc_start: 0.8640 (m) cc_final: 0.8303 (p)
REVERT: B  240 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7597 (pp)
REVERT: B  474 ASP cc_start: 0.8473 (t70) cc_final: 0.8113 (t70)
REVERT: C   20 TRP cc_start: 0.7495 (t60) cc_final: 0.7239 (t60)
REVERT: C   87 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8598 (pp30)
REVERT: C  395 MET cc_start: 0.8359 (ppp) cc_final: 0.8129 (ppp)
REVERT: D   12 ILE cc_start: 0.8794 (pt) cc_final: 0.8552 (mm)
REVERT: D   56 TYR cc_start: 0.8844 (t80) cc_final: 0.8524 (t80)
REVERT: D  123 ASP cc_start: 0.8465 (p0) cc_final: 0.8188 (p0)
REVERT: D  161 MET cc_start: 0.2446 (ppp) cc_final: 0.2228 (ppp)
REVERT: D  247 LYS cc_start: 0.8725 (mppt) cc_final: 0.8481 (mtmt)
REVERT: D  303 MET cc_start: 0.8586 (tmm) cc_final: 0.8247 (tmm)
REVERT: D  309 ASP cc_start: 0.7779 (p0) cc_final: 0.7442 (p0)
REVERT: D  466 ASN cc_start: 0.8243 (t0) cc_final: 0.7736 (t0)
  outliers start: 20
  outliers final: 13
  residues processed: 192
  average time/residue: 0.2869
  time to fit residues: 85.1796
Evaluate side-chains
  158 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 143
  time to evaluate  : 1.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  122 MET
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  360 HIS
Chi-restraints excluded: chain B residue  365 PHE
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue   87 GLN
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain D residue  154 ASN
Chi-restraints excluded: chain D residue  299 CYS
Chi-restraints excluded: chain D residue  365 PHE
Chi-restraints excluded: chain D residue  374 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 149 optimal weight:    6.9990
   chunk 118 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 115 optimal weight:    3.9990
   chunk 62 optimal weight:   10.0000
   chunk 122 optimal weight:    5.9990
   chunk 20 optimal weight:   10.0000
   chunk 158 optimal weight:    3.9990
   chunk 131 optimal weight:    9.9990
   chunk 58 optimal weight:    6.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 109 ASN
A 358 HIS
B 129 ASN
B 329 HIS
C 226 HIS
D  59 HIS
D 201 ASN
D 296 ASN
D 329 HIS
D 360 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.100715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.078389 restraints weight = 66126.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.080527 restraints weight = 40445.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.081703 restraints weight = 28952.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.3324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.067  16533  Z= 0.255
  Angle     :  0.719   9.316  22631  Z= 0.379
  Chirality :  0.045   0.201   2484
  Planarity :  0.006   0.064   2620
  Dihedral  : 17.603 176.008   2932
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 16.44
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  5.37 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 13.39 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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: -0.47 (0.20), residues: 1770
  helix:  0.89 (0.21), residues: 586
  sheet: -0.64 (0.30), residues: 292
  loop : -0.98 (0.20), residues: 892

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A  46 
 HIS   0.017   0.002   HIS B 360 
 PHE   0.023   0.002   PHE C  60 
 TYR   0.034   0.002   TYR C 293 
 ARG   0.010   0.001   ARG A 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05097 (  599)
  hydrogen bonds       : angle       5.69863 ( 1625)
  covalent geometry    : bond        0.00567 (16533)
  covalent geometry    : angle       0.71877 (22631)

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

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

  3540 Ramachandran restraints generated.
    1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3540 Ramachandran restraints generated.
    1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 144
  time to evaluate  : 1.845 
Fit side-chains
   revert: symmetry clash
REVERT: A  279 ASP cc_start: 0.7790 (t70) cc_final: 0.7288 (m-30)
REVERT: A  287 MET cc_start: 0.0082 (tpt) cc_final: -0.0399 (tpt)
REVERT: A  364 GLN cc_start: 0.7792 (tp40) cc_final: 0.7170 (tp40)
REVERT: A  395 MET cc_start: 0.7695 (ppp) cc_final: 0.6994 (ppp)
REVERT: B   92 THR cc_start: 0.8754 (m) cc_final: 0.8321 (p)
REVERT: B  303 MET cc_start: 0.8561 (tmm) cc_final: 0.8292 (tmm)
REVERT: B  435 MET cc_start: 0.4157 (mmt) cc_final: 0.3287 (mmp)
REVERT: B  474 ASP cc_start: 0.8453 (t70) cc_final: 0.8138 (t70)
REVERT: C  395 MET cc_start: 0.8816 (ppp) cc_final: 0.8556 (ppp)
REVERT: D   44 ILE cc_start: 0.9642 (OUTLIER) cc_final: 0.9309 (tp)
REVERT: D   56 TYR cc_start: 0.8955 (t80) cc_final: 0.8696 (t80)
REVERT: D   78 PHE cc_start: 0.8430 (t80) cc_final: 0.8006 (t80)
REVERT: D  123 ASP cc_start: 0.8731 (p0) cc_final: 0.8492 (p0)
REVERT: D  303 MET cc_start: 0.8803 (tmm) cc_final: 0.8552 (tmm)
REVERT: D  309 ASP cc_start: 0.8194 (p0) cc_final: 0.7889 (p0)
REVERT: D  456 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9109 (mm)
REVERT: D  466 ASN cc_start: 0.8703 (t0) cc_final: 0.8325 (t0)
REVERT: D  468 ASN cc_start: 0.8467 (t0) cc_final: 0.8116 (t0)
REVERT: D  481 ARG cc_start: 0.8054 (ttm-80) cc_final: 0.7355 (ttm-80)
  outliers start: 35
  outliers final: 19
  residues processed: 169
  average time/residue: 0.2771
  time to fit residues: 74.6097
Evaluate side-chains
  143 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 122
  time to evaluate  : 3.040 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue  215 CYS
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain B residue   25 ASP
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   83 ASP
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  192 TRP
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   59 HIS
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain D residue  215 LEU
Chi-restraints excluded: chain D residue  299 CYS
Chi-restraints excluded: chain D residue  374 LEU
Chi-restraints excluded: chain D residue  456 LEU
Chi-restraints excluded: chain D residue  478 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 22 optimal weight:   10.0000
   chunk 53 optimal weight:    0.6980
   chunk 103 optimal weight:    9.9990
   chunk 104 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   chunk 78 optimal weight:    1.9990
   chunk 133 optimal weight:    0.9990
   chunk 115 optimal weight:    2.9990
   chunk 159 optimal weight:    0.9980
   chunk 93 optimal weight:    4.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 360 HIS
D  59 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.101667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.078973 restraints weight = 66645.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.081059 restraints weight = 41651.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.082274 restraints weight = 30025.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.3598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  16533  Z= 0.158
  Angle     :  0.632   9.443  22631  Z= 0.329
  Chirality :  0.043   0.265   2484
  Planarity :  0.005   0.060   2620
  Dihedral  : 17.484 174.657   2932
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 12.93
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  4.46 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 15.14 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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: -0.33 (0.20), residues: 1770
  helix:  1.03 (0.22), residues: 586
  sheet: -0.51 (0.30), residues: 288
  loop : -0.94 (0.21), residues: 896

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 368 
 HIS   0.017   0.001   HIS D  59 
 PHE   0.026   0.001   PHE A  17 
 TYR   0.023   0.001   TYR C 293 
 ARG   0.005   0.001   ARG A 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04288 (  599)
  hydrogen bonds       : angle       5.39576 ( 1625)
  covalent geometry    : bond        0.00354 (16533)
  covalent geometry    : angle       0.63159 (22631)

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

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

  3540 Ramachandran restraints generated.
    1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3540 Ramachandran restraints generated.
    1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 139
  time to evaluate  : 2.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 TRP cc_start: 0.8116 (m100) cc_final: 0.7820 (m100)
REVERT: A   85 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8181 (tptt)
REVERT: A  155 GLN cc_start: 0.8781 (pm20) cc_final: 0.8542 (pm20)
REVERT: A  217 PHE cc_start: 0.6411 (m-80) cc_final: 0.6091 (m-10)
REVERT: A  279 ASP cc_start: 0.7771 (t70) cc_final: 0.7261 (m-30)
REVERT: A  352 ASP cc_start: 0.6128 (p0) cc_final: 0.4668 (t0)
REVERT: A  364 GLN cc_start: 0.8124 (tp40) cc_final: 0.7780 (tp40)
REVERT: A  395 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7326 (ppp)
REVERT: B   92 THR cc_start: 0.8679 (m) cc_final: 0.8303 (p)
REVERT: B  303 MET cc_start: 0.8523 (tmm) cc_final: 0.8279 (tmm)
REVERT: B  360 HIS cc_start: 0.8568 (m90) cc_final: 0.8293 (m90)
REVERT: B  474 ASP cc_start: 0.8409 (t70) cc_final: 0.8132 (t70)
REVERT: C  155 GLN cc_start: 0.6931 (OUTLIER) cc_final: 0.6702 (pm20)
REVERT: C  156 GLN cc_start: 0.6030 (OUTLIER) cc_final: 0.5694 (pt0)
REVERT: D   12 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8257 (mm)
REVERT: D   44 ILE cc_start: 0.9549 (OUTLIER) cc_final: 0.9162 (tp)
REVERT: D   56 TYR cc_start: 0.8946 (t80) cc_final: 0.8733 (t80)
REVERT: D  123 ASP cc_start: 0.8619 (p0) cc_final: 0.8380 (p0)
REVERT: D  309 ASP cc_start: 0.8273 (p0) cc_final: 0.8050 (p0)
REVERT: D  466 ASN cc_start: 0.8725 (t0) cc_final: 0.8380 (t0)
REVERT: D  476 GLU cc_start: 0.8101 (pm20) cc_final: 0.6132 (pm20)
REVERT: D  481 ARG cc_start: 0.8008 (ttm-80) cc_final: 0.7298 (ttm-80)
  outliers start: 35
  outliers final: 22
  residues processed: 167
  average time/residue: 0.2521
  time to fit residues: 66.6886
Evaluate side-chains
  156 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 128
  time to evaluate  : 2.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue   85 LYS
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  215 CYS
Chi-restraints excluded: chain A residue  395 MET
Chi-restraints excluded: chain B residue   25 ASP
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  348 GLU
Chi-restraints excluded: chain B residue  501 LEU
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue   87 GLN
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  155 GLN
Chi-restraints excluded: chain C residue  156 GLN
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  192 TRP
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   12 ILE
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   59 HIS
Chi-restraints excluded: chain D residue   60 ILE
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain D residue  374 LEU
Chi-restraints excluded: chain D residue  463 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 138 optimal weight:    3.9990
   chunk 35 optimal weight:   20.0000
   chunk 96 optimal weight:    3.9990
   chunk 166 optimal weight:    0.8980
   chunk 112 optimal weight:    2.9990
   chunk 5 optimal weight:    9.9990
   chunk 105 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0070
   chunk 59 optimal weight:    0.7980
   chunk 150 optimal weight:    4.9990
   chunk 86 optimal weight:    4.9990
   overall best weight:    1.1400

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 329 HIS
D  59 HIS
D 129 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.102068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.079552 restraints weight = 66768.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.081688 restraints weight = 40965.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.082842 restraints weight = 29459.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.3807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  16533  Z= 0.136
  Angle     :  0.615  13.112  22631  Z= 0.316
  Chirality :  0.043   0.259   2484
  Planarity :  0.004   0.059   2620
  Dihedral  : 17.420 174.807   2932
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  4.52 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 15.96 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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 (0.20), residues: 1770
  helix:  1.14 (0.22), residues: 586
  sheet: -0.57 (0.29), residues: 310
  loop : -0.93 (0.21), residues: 874

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP C  20 
 HIS   0.024   0.001   HIS D  59 
 PHE   0.020   0.001   PHE A  17 
 TYR   0.022   0.001   TYR C 293 
 ARG   0.005   0.000   ARG A  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04069 (  599)
  hydrogen bonds       : angle       5.25558 ( 1625)
  covalent geometry    : bond        0.00304 (16533)
  covalent geometry    : angle       0.61539 (22631)

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

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

  3540 Ramachandran restraints generated.
    1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3540 Ramachandran restraints generated.
    1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 149
  time to evaluate  : 2.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8207 (tptt)
REVERT: A  217 PHE cc_start: 0.6323 (m-80) cc_final: 0.6000 (m-10)
REVERT: A  279 ASP cc_start: 0.7657 (t70) cc_final: 0.7155 (m-30)
REVERT: A  352 ASP cc_start: 0.6228 (p0) cc_final: 0.4653 (t0)
REVERT: A  364 GLN cc_start: 0.8177 (tp40) cc_final: 0.7813 (tp40)
REVERT: A  395 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7377 (ppp)
REVERT: B   92 THR cc_start: 0.8727 (m) cc_final: 0.8351 (p)
REVERT: B  303 MET cc_start: 0.8440 (tmm) cc_final: 0.8020 (tmm)
REVERT: B  360 HIS cc_start: 0.8461 (m90) cc_final: 0.8172 (m170)
REVERT: B  435 MET cc_start: 0.4153 (mmt) cc_final: 0.3483 (mmp)
REVERT: B  474 ASP cc_start: 0.8336 (t70) cc_final: 0.8050 (t0)
REVERT: C  155 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6771 (pm20)
REVERT: C  156 GLN cc_start: 0.5947 (OUTLIER) cc_final: 0.5558 (pt0)
REVERT: C  309 MET cc_start: 0.8269 (tpp) cc_final: 0.8005 (tpp)
REVERT: D   12 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8186 (mm)
REVERT: D   56 TYR cc_start: 0.8872 (t80) cc_final: 0.8670 (t80)
REVERT: D   78 PHE cc_start: 0.8194 (t80) cc_final: 0.7952 (t80)
REVERT: D  123 ASP cc_start: 0.8588 (p0) cc_final: 0.8374 (p0)
REVERT: D  303 MET cc_start: 0.8767 (tmm) cc_final: 0.8532 (tmm)
REVERT: D  309 ASP cc_start: 0.8228 (p0) cc_final: 0.8016 (p0)
REVERT: D  466 ASN cc_start: 0.8661 (t0) cc_final: 0.8310 (t0)
REVERT: D  476 GLU cc_start: 0.8013 (pm20) cc_final: 0.6982 (pm20)
REVERT: D  481 ARG cc_start: 0.7804 (ttm-80) cc_final: 0.7332 (ttm-80)
  outliers start: 43
  outliers final: 26
  residues processed: 180
  average time/residue: 0.2682
  time to fit residues: 75.3283
Evaluate side-chains
  162 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 131
  time to evaluate  : 1.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue   85 LYS
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  215 CYS
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  395 MET
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   83 ASP
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  348 GLU
Chi-restraints excluded: chain B residue  501 LEU
Chi-restraints excluded: chain B residue  507 ILE
Chi-restraints excluded: chain C residue   40 ASP
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue   87 GLN
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  155 GLN
Chi-restraints excluded: chain C residue  156 GLN
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  192 TRP
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   12 ILE
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   59 HIS
Chi-restraints excluded: chain D residue   60 ILE
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain D residue  365 PHE
Chi-restraints excluded: chain D residue  374 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 52 optimal weight:   10.0000
   chunk 101 optimal weight:    9.9990
   chunk 23 optimal weight:    9.9990
   chunk 69 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 119 optimal weight:    5.9990
   chunk 55 optimal weight:    0.6980
   chunk 67 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 26 optimal weight:    7.9990
   chunk 42 optimal weight:    0.7980
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 357 GLN
D  59 HIS
D 360 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.100244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.077714 restraints weight = 66934.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.079822 restraints weight = 41720.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.081002 restraints weight = 29971.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.4276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  16533  Z= 0.173
  Angle     :  0.647  13.565  22631  Z= 0.331
  Chirality :  0.043   0.273   2484
  Planarity :  0.005   0.060   2620
  Dihedral  : 17.434 173.590   2932
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  4.86 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 17.02 %
    Favored  : 80.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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: -0.33 (0.20), residues: 1770
  helix:  1.19 (0.21), residues: 586
  sheet: -0.67 (0.29), residues: 310
  loop : -1.01 (0.21), residues: 874

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A  46 
 HIS   0.025   0.002   HIS D  59 
 PHE   0.022   0.002   PHE A  17 
 TYR   0.016   0.001   TYR C 293 
 ARG   0.006   0.001   ARG A 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04160 (  599)
  hydrogen bonds       : angle       5.22884 ( 1625)
  covalent geometry    : bond        0.00387 (16533)
  covalent geometry    : angle       0.64672 (22631)

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

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

  3540 Ramachandran restraints generated.
    1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3540 Ramachandran restraints generated.
    1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 141
  time to evaluate  : 1.816 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 TRP cc_start: 0.8104 (m100) cc_final: 0.7874 (m100)
REVERT: A   85 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8291 (tptt)
REVERT: A  203 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8513 (tt)
REVERT: A  279 ASP cc_start: 0.7673 (t70) cc_final: 0.7160 (m-30)
REVERT: A  332 PHE cc_start: 0.8389 (m-80) cc_final: 0.7964 (m-10)
REVERT: A  352 ASP cc_start: 0.6403 (p0) cc_final: 0.4990 (t0)
REVERT: A  395 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7496 (ppp)
REVERT: B   92 THR cc_start: 0.8690 (m) cc_final: 0.8320 (p)
REVERT: B  303 MET cc_start: 0.8475 (tmm) cc_final: 0.8025 (tmm)
REVERT: B  435 MET cc_start: 0.4432 (mmt) cc_final: 0.3647 (mmm)
REVERT: B  470 CYS cc_start: 0.8106 (t) cc_final: 0.7324 (p)
REVERT: C  155 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.6764 (pm20)
REVERT: C  156 GLN cc_start: 0.6052 (OUTLIER) cc_final: 0.5630 (pt0)
REVERT: C  309 MET cc_start: 0.8326 (tpp) cc_final: 0.8015 (tpp)
REVERT: D   12 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8046 (mm)
REVERT: D   56 TYR cc_start: 0.8882 (t80) cc_final: 0.8665 (t80)
REVERT: D  309 ASP cc_start: 0.8370 (p0) cc_final: 0.8147 (p0)
REVERT: D  466 ASN cc_start: 0.8700 (t0) cc_final: 0.8379 (t0)
REVERT: D  476 GLU cc_start: 0.8005 (pm20) cc_final: 0.7182 (pm20)
REVERT: D  481 ARG cc_start: 0.7839 (ttm-80) cc_final: 0.7347 (ttm-80)
  outliers start: 47
  outliers final: 30
  residues processed: 177
  average time/residue: 0.2314
  time to fit residues: 66.4788
Evaluate side-chains
  165 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 129
  time to evaluate  : 1.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue   85 LYS
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  215 CYS
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  395 MET
Chi-restraints excluded: chain B residue   25 ASP
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   83 ASP
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  207 HIS
Chi-restraints excluded: chain B residue  223 ILE
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  501 LEU
Chi-restraints excluded: chain C residue   40 ASP
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue   87 GLN
Chi-restraints excluded: chain C residue  155 GLN
Chi-restraints excluded: chain C residue  156 GLN
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  192 TRP
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   12 ILE
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   59 HIS
Chi-restraints excluded: chain D residue   60 ILE
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain D residue  199 THR
Chi-restraints excluded: chain D residue  223 ILE
Chi-restraints excluded: chain D residue  365 PHE
Chi-restraints excluded: chain D residue  374 LEU
Chi-restraints excluded: chain D residue  463 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 117 optimal weight:    6.9990
   chunk 81 optimal weight:    0.5980
   chunk 119 optimal weight:    2.9990
   chunk 160 optimal weight:    1.9990
   chunk 127 optimal weight:    9.9990
   chunk 132 optimal weight:    7.9990
   chunk 123 optimal weight:    2.9990
   chunk 155 optimal weight:    2.9990
   chunk 47 optimal weight:    0.5980
   chunk 28 optimal weight:    8.9990
   chunk 85 optimal weight:    3.9990
   overall best weight:    1.8386

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 364 GLN
B 360 HIS
C 109 ASN
D  59 HIS
D 302 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.099606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.077459 restraints weight = 68409.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.079495 restraints weight = 42079.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.080634 restraints weight = 30315.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.4610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  16533  Z= 0.170
  Angle     :  0.658   9.294  22631  Z= 0.337
  Chirality :  0.043   0.272   2484
  Planarity :  0.005   0.077   2620
  Dihedral  : 17.373 172.958   2932
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 13.92
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  5.08 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 17.71 %
    Favored  : 79.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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: -0.37 (0.20), residues: 1770
  helix:  1.10 (0.21), residues: 590
  sheet: -0.66 (0.29), residues: 306
  loop : -1.00 (0.21), residues: 874

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP C  20 
 HIS   0.022   0.001   HIS D  59 
 PHE   0.019   0.002   PHE A  17 
 TYR   0.023   0.001   TYR C 293 
 ARG   0.005   0.001   ARG A 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04148 (  599)
  hydrogen bonds       : angle       5.25951 ( 1625)
  covalent geometry    : bond        0.00382 (16533)
  covalent geometry    : angle       0.65819 (22631)

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

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

  3540 Ramachandran restraints generated.
    1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3540 Ramachandran restraints generated.
    1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 137
  time to evaluate  : 1.818 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 TRP cc_start: 0.8063 (m100) cc_final: 0.7812 (m100)
REVERT: A  279 ASP cc_start: 0.7685 (t70) cc_final: 0.7172 (m-30)
REVERT: A  332 PHE cc_start: 0.8519 (m-80) cc_final: 0.8038 (m-10)
REVERT: A  352 ASP cc_start: 0.6305 (p0) cc_final: 0.4832 (t0)
REVERT: A  395 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7553 (ppp)
REVERT: B   92 THR cc_start: 0.8725 (m) cc_final: 0.8334 (p)
REVERT: B  254 TRP cc_start: 0.9439 (m100) cc_final: 0.8850 (m100)
REVERT: B  303 MET cc_start: 0.8544 (tmm) cc_final: 0.8065 (tmm)
REVERT: B  435 MET cc_start: 0.4459 (mmt) cc_final: 0.3823 (mmm)
REVERT: B  470 CYS cc_start: 0.8041 (t) cc_final: 0.7309 (p)
REVERT: C  155 GLN cc_start: 0.7103 (OUTLIER) cc_final: 0.6832 (pm20)
REVERT: C  156 GLN cc_start: 0.6180 (OUTLIER) cc_final: 0.5744 (pt0)
REVERT: C  309 MET cc_start: 0.8350 (tpp) cc_final: 0.8047 (tpp)
REVERT: D   56 TYR cc_start: 0.8882 (t80) cc_final: 0.8654 (t80)
REVERT: D   78 PHE cc_start: 0.8343 (t80) cc_final: 0.8060 (t80)
REVERT: D  309 ASP cc_start: 0.8454 (p0) cc_final: 0.8236 (p0)
REVERT: D  466 ASN cc_start: 0.8720 (t0) cc_final: 0.8391 (t0)
REVERT: D  476 GLU cc_start: 0.7977 (pm20) cc_final: 0.7159 (pm20)
REVERT: D  481 ARG cc_start: 0.7755 (ttm-80) cc_final: 0.7281 (ttm-80)
  outliers start: 45
  outliers final: 32
  residues processed: 168
  average time/residue: 0.2390
  time to fit residues: 64.4428
Evaluate side-chains
  164 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 129
  time to evaluate  : 1.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  215 CYS
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  395 MET
Chi-restraints excluded: chain B residue   25 ASP
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   83 ASP
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  207 HIS
Chi-restraints excluded: chain B residue  223 ILE
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  360 HIS
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  501 LEU
Chi-restraints excluded: chain C residue   40 ASP
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue   87 GLN
Chi-restraints excluded: chain C residue  155 GLN
Chi-restraints excluded: chain C residue  156 GLN
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  192 TRP
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   12 ILE
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   59 HIS
Chi-restraints excluded: chain D residue   60 ILE
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain D residue  223 ILE
Chi-restraints excluded: chain D residue  365 PHE
Chi-restraints excluded: chain D residue  374 LEU
Chi-restraints excluded: chain D residue  463 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 144 optimal weight:    6.9990
   chunk 141 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 90 optimal weight:    6.9990
   chunk 124 optimal weight:    6.9990
   chunk 160 optimal weight:    0.9990
   chunk 71 optimal weight:    5.9990
   chunk 97 optimal weight:    0.9980
   chunk 60 optimal weight:    4.9990
   chunk 152 optimal weight:    1.9990
   chunk 161 optimal weight:    1.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 360 HIS
D  59 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.098821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.076662 restraints weight = 67747.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.078579 restraints weight = 42526.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.079896 restraints weight = 30826.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.4866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  16533  Z= 0.180
  Angle     :  0.677   9.343  22631  Z= 0.347
  Chirality :  0.044   0.270   2484
  Planarity :  0.005   0.062   2620
  Dihedral  : 17.343 172.313   2932
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 14.50
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  5.48 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 17.83 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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: -0.43 (0.20), residues: 1770
  helix:  1.05 (0.21), residues: 590
  sheet: -0.71 (0.30), residues: 296
  loop : -1.04 (0.21), residues: 884

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP C  20 
 HIS   0.021   0.001   HIS D  59 
 PHE   0.017   0.002   PHE A  17 
 TYR   0.023   0.001   TYR C 293 
 ARG   0.006   0.001   ARG A 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04155 (  599)
  hydrogen bonds       : angle       5.31144 ( 1625)
  covalent geometry    : bond        0.00405 (16533)
  covalent geometry    : angle       0.67679 (22631)

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

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

  3540 Ramachandran restraints generated.
    1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3540 Ramachandran restraints generated.
    1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 142
  time to evaluate  : 1.729 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 ASP cc_start: 0.7670 (t70) cc_final: 0.7160 (m-30)
REVERT: A  332 PHE cc_start: 0.8621 (m-80) cc_final: 0.8149 (m-10)
REVERT: A  352 ASP cc_start: 0.6331 (p0) cc_final: 0.4812 (t0)
REVERT: A  395 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7552 (ppp)
REVERT: B   92 THR cc_start: 0.8707 (m) cc_final: 0.8359 (p)
REVERT: B  254 TRP cc_start: 0.9457 (m100) cc_final: 0.8906 (m100)
REVERT: B  303 MET cc_start: 0.8572 (tmm) cc_final: 0.8086 (tmm)
REVERT: B  435 MET cc_start: 0.4637 (mmt) cc_final: 0.4118 (mmm)
REVERT: B  470 CYS cc_start: 0.7846 (t) cc_final: 0.7109 (p)
REVERT: C  155 GLN cc_start: 0.7140 (OUTLIER) cc_final: 0.6866 (pm20)
REVERT: C  156 GLN cc_start: 0.6139 (OUTLIER) cc_final: 0.5851 (pt0)
REVERT: C  193 MET cc_start: 0.7094 (ttt) cc_final: 0.6347 (tmm)
REVERT: C  309 MET cc_start: 0.8357 (tpp) cc_final: 0.8047 (tpp)
REVERT: D   56 TYR cc_start: 0.8872 (t80) cc_final: 0.8660 (t80)
REVERT: D   78 PHE cc_start: 0.8370 (t80) cc_final: 0.7959 (t80)
REVERT: D   86 TRP cc_start: 0.8274 (t60) cc_final: 0.8023 (t60)
REVERT: D  303 MET cc_start: 0.8689 (tmm) cc_final: 0.8460 (tmm)
REVERT: D  309 ASP cc_start: 0.8491 (p0) cc_final: 0.8261 (p0)
REVERT: D  466 ASN cc_start: 0.8705 (t0) cc_final: 0.8378 (t0)
REVERT: D  481 ARG cc_start: 0.7740 (ttm-80) cc_final: 0.7406 (ttm-80)
  outliers start: 47
  outliers final: 34
  residues processed: 175
  average time/residue: 0.2353
  time to fit residues: 65.4980
Evaluate side-chains
  170 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 133
  time to evaluate  : 1.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  215 CYS
Chi-restraints excluded: chain A residue  395 MET
Chi-restraints excluded: chain B residue   25 ASP
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   83 ASP
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  205 GLN
Chi-restraints excluded: chain B residue  207 HIS
Chi-restraints excluded: chain B residue  223 ILE
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  360 HIS
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  501 LEU
Chi-restraints excluded: chain C residue   40 ASP
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue   87 GLN
Chi-restraints excluded: chain C residue  155 GLN
Chi-restraints excluded: chain C residue  156 GLN
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  192 TRP
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   12 ILE
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   59 HIS
Chi-restraints excluded: chain D residue   60 ILE
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain D residue  223 ILE
Chi-restraints excluded: chain D residue  365 PHE
Chi-restraints excluded: chain D residue  374 LEU
Chi-restraints excluded: chain D residue  391 THR
Chi-restraints excluded: chain D residue  463 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 105 optimal weight:    4.9990
   chunk 98 optimal weight:    2.9990
   chunk 57 optimal weight:   20.0000
   chunk 168 optimal weight:    0.0170
   chunk 141 optimal weight:    2.9990
   chunk 54 optimal weight:    7.9990
   chunk 127 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 47 optimal weight:    0.0270
   chunk 84 optimal weight:    3.9990
   overall best weight:    1.1680

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 360 HIS
D  59 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.100046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.077717 restraints weight = 67065.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.079817 restraints weight = 41742.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.080709 restraints weight = 29920.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.4971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  16533  Z= 0.143
  Angle     :  0.677  10.262  22631  Z= 0.344
  Chirality :  0.043   0.278   2484
  Planarity :  0.004   0.061   2620
  Dihedral  : 17.261 172.074   2932
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 13.31
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  4.80 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 18.52 %
    Favored  : 79.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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 (0.20), residues: 1770
  helix:  1.02 (0.21), residues: 594
  sheet: -0.69 (0.30), residues: 296
  loop : -1.09 (0.21), residues: 880

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.002   TRP A  46 
 HIS   0.018   0.001   HIS D  59 
 PHE   0.018   0.001   PHE C 273 
 TYR   0.022   0.001   TYR C 293 
 ARG   0.007   0.001   ARG A  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03971 (  599)
  hydrogen bonds       : angle       5.24457 ( 1625)
  covalent geometry    : bond        0.00324 (16533)
  covalent geometry    : angle       0.67732 (22631)

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

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

  3540 Ramachandran restraints generated.
    1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3540 Ramachandran restraints generated.
    1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 140
  time to evaluate  : 1.659 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 ARG cc_start: 0.5424 (tpt90) cc_final: 0.3182 (mpt180)
REVERT: A  279 ASP cc_start: 0.7729 (t70) cc_final: 0.7206 (m-30)
REVERT: A  332 PHE cc_start: 0.8535 (m-80) cc_final: 0.8044 (m-10)
REVERT: A  352 ASP cc_start: 0.6508 (p0) cc_final: 0.5168 (t0)
REVERT: A  395 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7760 (ppp)
REVERT: B   92 THR cc_start: 0.8709 (m) cc_final: 0.8364 (p)
REVERT: B  254 TRP cc_start: 0.9432 (m100) cc_final: 0.8888 (m100)
REVERT: B  303 MET cc_start: 0.8591 (tmm) cc_final: 0.8124 (tmm)
REVERT: B  360 HIS cc_start: 0.8212 (OUTLIER) cc_final: 0.7926 (m170)
REVERT: B  435 MET cc_start: 0.4836 (mmt) cc_final: 0.4337 (mmm)
REVERT: B  470 CYS cc_start: 0.7732 (t) cc_final: 0.6967 (p)
REVERT: C  155 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.6794 (pm20)
REVERT: C  156 GLN cc_start: 0.5996 (OUTLIER) cc_final: 0.5568 (pt0)
REVERT: C  193 MET cc_start: 0.7216 (ttt) cc_final: 0.6408 (tmm)
REVERT: C  287 MET cc_start: 0.7700 (tpt) cc_final: 0.7151 (tpt)
REVERT: C  309 MET cc_start: 0.8315 (tpp) cc_final: 0.8060 (tpp)
REVERT: D   78 PHE cc_start: 0.8314 (t80) cc_final: 0.8037 (t80)
REVERT: D  303 MET cc_start: 0.8668 (tmm) cc_final: 0.8419 (tmm)
REVERT: D  309 ASP cc_start: 0.8456 (p0) cc_final: 0.8238 (p0)
REVERT: D  466 ASN cc_start: 0.8714 (t0) cc_final: 0.8367 (t0)
REVERT: D  476 GLU cc_start: 0.8054 (pm20) cc_final: 0.7246 (pm20)
REVERT: D  481 ARG cc_start: 0.7801 (ttm-80) cc_final: 0.7353 (ttm-80)
  outliers start: 39
  outliers final: 30
  residues processed: 168
  average time/residue: 0.2339
  time to fit residues: 62.8860
Evaluate side-chains
  167 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 133
  time to evaluate  : 1.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ASP
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  215 CYS
Chi-restraints excluded: chain A residue  395 MET
Chi-restraints excluded: chain B residue   25 ASP
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   83 ASP
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  223 ILE
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  360 HIS
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  501 LEU
Chi-restraints excluded: chain C residue   40 ASP
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue   87 GLN
Chi-restraints excluded: chain C residue  155 GLN
Chi-restraints excluded: chain C residue  156 GLN
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  192 TRP
Chi-restraints excluded: chain C residue  329 LEU
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   12 ILE
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain D residue  223 ILE
Chi-restraints excluded: chain D residue  365 PHE
Chi-restraints excluded: chain D residue  374 LEU
Chi-restraints excluded: chain D residue  390 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 71 optimal weight:    5.9990
   chunk 10 optimal weight:    7.9990
   chunk 132 optimal weight:    6.9990
   chunk 75 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 106 optimal weight:    8.9990
   chunk 3 optimal weight:    6.9990
   chunk 130 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 166 optimal weight:    1.9990
   chunk 127 optimal weight:    9.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 364 GLN
B 207 HIS
B 360 HIS
D  59 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.098105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.076277 restraints weight = 66912.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.078361 restraints weight = 40893.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.079523 restraints weight = 29095.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.5279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  16533  Z= 0.183
  Angle     :  0.701  10.398  22631  Z= 0.359
  Chirality :  0.044   0.285   2484
  Planarity :  0.005   0.061   2620
  Dihedral  : 17.214 171.043   2932
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 15.39
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  5.76 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 18.96 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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: -0.55 (0.20), residues: 1770
  helix:  0.98 (0.21), residues: 588
  sheet: -0.91 (0.29), residues: 318
  loop : -1.07 (0.21), residues: 864

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.002   TRP A  46 
 HIS   0.009   0.001   HIS D  59 
 PHE   0.016   0.002   PHE C 273 
 TYR   0.028   0.001   TYR C 293 
 ARG   0.007   0.001   ARG A 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04256 (  599)
  hydrogen bonds       : angle       5.33316 ( 1625)
  covalent geometry    : bond        0.00409 (16533)
  covalent geometry    : angle       0.70066 (22631)

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

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

  3540 Ramachandran restraints generated.
    1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3540 Ramachandran restraints generated.
    1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 132
  time to evaluate  : 1.655 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  274 GLU cc_start: 0.7629 (tt0) cc_final: 0.7392 (tp30)
REVERT: A  277 MET cc_start: 0.6157 (ptp) cc_final: 0.5921 (ptp)
REVERT: A  279 ASP cc_start: 0.7732 (t70) cc_final: 0.7206 (m-30)
REVERT: A  352 ASP cc_start: 0.6698 (p0) cc_final: 0.5488 (t0)
REVERT: A  395 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7721 (ppp)
REVERT: B   92 THR cc_start: 0.8709 (m) cc_final: 0.8359 (p)
REVERT: B  254 TRP cc_start: 0.9480 (m100) cc_final: 0.8979 (m100)
REVERT: B  303 MET cc_start: 0.8607 (tmm) cc_final: 0.8289 (tmm)
REVERT: B  435 MET cc_start: 0.4667 (mmt) cc_final: 0.4320 (mmp)
REVERT: B  470 CYS cc_start: 0.7691 (t) cc_final: 0.7186 (p)
REVERT: C  155 GLN cc_start: 0.7055 (OUTLIER) cc_final: 0.6810 (pm20)
REVERT: C  287 MET cc_start: 0.7906 (tpt) cc_final: 0.7653 (tpt)
REVERT: C  309 MET cc_start: 0.8389 (tpp) cc_final: 0.8133 (tpp)
REVERT: D  303 MET cc_start: 0.8685 (tmm) cc_final: 0.8419 (tmm)
REVERT: D  309 ASP cc_start: 0.8503 (p0) cc_final: 0.8280 (p0)
REVERT: D  481 ARG cc_start: 0.7777 (ttm-80) cc_final: 0.7434 (ttm-80)
  outliers start: 36
  outliers final: 32
  residues processed: 161
  average time/residue: 0.2434
  time to fit residues: 62.0112
Evaluate side-chains
  160 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 126
  time to evaluate  : 1.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ASP
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue  215 CYS
Chi-restraints excluded: chain A residue  395 MET
Chi-restraints excluded: chain B residue   25 ASP
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   83 ASP
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  205 GLN
Chi-restraints excluded: chain B residue  207 HIS
Chi-restraints excluded: chain B residue  223 ILE
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  489 ILE
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  501 LEU
Chi-restraints excluded: chain C residue   40 ASP
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue   87 GLN
Chi-restraints excluded: chain C residue  155 GLN
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  192 TRP
Chi-restraints excluded: chain C residue  329 LEU
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   12 ILE
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain D residue  223 ILE
Chi-restraints excluded: chain D residue  365 PHE
Chi-restraints excluded: chain D residue  374 LEU
Chi-restraints excluded: chain D residue  390 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 118 optimal weight:    0.7980
   chunk 76 optimal weight:    0.8980
   chunk 65 optimal weight:    0.0270
   chunk 109 optimal weight:    1.9990
   chunk 119 optimal weight:    1.9990
   chunk 92 optimal weight:   10.0000
   chunk 173 optimal weight:    5.9990
   chunk 30 optimal weight:    9.9990
   chunk 136 optimal weight:    1.9990
   chunk 28 optimal weight:    9.9990
   chunk 60 optimal weight:    0.3980
   overall best weight:    0.8240

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 357 GLN
B 207 HIS
B 360 HIS
D  59 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.100233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.078748 restraints weight = 66221.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.080711 restraints weight = 41024.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.081865 restraints weight = 29761.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.5306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  16533  Z= 0.131
  Angle     :  0.674  10.977  22631  Z= 0.340
  Chirality :  0.043   0.273   2484
  Planarity :  0.004   0.060   2620
  Dihedral  : 17.085 170.485   2932
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 13.00
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  4.75 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 19.34 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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: -0.45 (0.20), residues: 1770
  helix:  1.08 (0.21), residues: 584
  sheet: -0.82 (0.30), residues: 290
  loop : -1.03 (0.21), residues: 896

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.002   TRP A  46 
 HIS   0.008   0.001   HIS D  59 
 PHE   0.014   0.001   PHE A 273 
 TYR   0.022   0.001   TYR C 293 
 ARG   0.007   0.001   ARG A  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03884 (  599)
  hydrogen bonds       : angle       5.17261 ( 1625)
  covalent geometry    : bond        0.00299 (16533)
  covalent geometry    : angle       0.67414 (22631)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4873.72 seconds
wall clock time: 87 minutes 46.42 seconds (5266.42 seconds total)