Starting phenix.real_space_refine
on Thu Sep 18 07:32:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lng_63235/09_2025/9lng_63235.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lng_63235/09_2025/9lng_63235.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.45
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lng_63235/09_2025/9lng_63235.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lng_63235/09_2025/9lng_63235.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lng_63235/09_2025/9lng_63235.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lng_63235/09_2025/9lng_63235.map"
  }
  resolution = 2.45
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.104
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      93      5.16       5
     C    9561      2.51       5
     N    2499      2.21       5
     O    2988      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15141
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "B"
      Number of atoms: 3358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 437, 3358
          Classifications: {'peptide': 437}
          Link IDs: {'PTRANS': 15, 'TRANS': 421}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 903
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 903
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 4, 'TRANS': 112}
    Chain: "L"
      Number of atoms: 786
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 786
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 4, 'TRANS': 100}
    Chain: "A"
      Number of atoms: 3358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 437, 3358
          Classifications: {'peptide': 437}
          Link IDs: {'PTRANS': 15, 'TRANS': 421}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 903
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 903
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 4, 'TRANS': 112}
    Chain: "F"
      Number of atoms: 786
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 786
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 4, 'TRANS': 100}
    Chain: "C"
      Number of atoms: 3358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 437, 3358
          Classifications: {'peptide': 437}
          Link IDs: {'PTRANS': 15, 'TRANS': 421}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 903
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 903
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 4, 'TRANS': 112}
    Chain: "G"
      Number of atoms: 786
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 786
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 4, 'TRANS': 100}
  Time building chain proxies: 3.50, per 1000 atoms: 0.23
  Number of scatterers: 15141
  At special positions: 0
  Unit cell: (126.99, 136.12, 102.92, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      93     16.00
     O    2988      8.00
     N    2499      7.00
     C    9561      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=21, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  71 " - pdb=" SG  CYS B 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 331 " - pdb=" SG  CYS B 340 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 355 " - pdb=" SG  CYS B 363 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 387 " - pdb=" SG  CYS B 392 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 394 " - pdb=" SG  CYS B 417 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  71 " - pdb=" SG  CYS A 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 331 " - pdb=" SG  CYS A 340 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 355 " - pdb=" SG  CYS A 363 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 387 " - pdb=" SG  CYS A 392 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 394 " - pdb=" SG  CYS A 417 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  23 " - pdb=" SG  CYS F  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  71 " - pdb=" SG  CYS C 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 331 " - pdb=" SG  CYS C 340 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 355 " - pdb=" SG  CYS C 363 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 387 " - pdb=" SG  CYS C 392 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 394 " - pdb=" SG  CYS C 417 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  23 " - pdb=" SG  CYS G  88 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.08
  Conformation dependent library (CDL) restraints added in 709.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3672

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 21 sheets defined
      30.2% alpha, 23.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'B' and resid 29 through 36
    Processing helix  chain 'B' and resid 65 through 72
      removed outlier: 3.709A  pdb=" N   SER B  69 " --> pdb=" O   SER B  66 " (cutoff:3.500A)
      removed outlier: 5.796A  pdb=" N   GLN B  70 " --> pdb=" O   ASN B  67 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   CYS B  71 " --> pdb=" O   MET B  68 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   THR B  72 " --> pdb=" O   SER B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 99
      Proline residue:  B  89  - end of helix
      removed outlier: 3.888A  pdb=" N   TYR B  97 " --> pdb=" O   ALA B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 121
    Processing helix  chain 'B' and resid 125 through 137
    Processing helix  chain 'B' and resid 137 through 146
    Processing helix  chain 'B' and resid 147 through 153
    Processing helix  chain 'B' and resid 175 through 183
    Processing helix  chain 'B' and resid 184 through 187
      removed outlier: 3.551A  pdb=" N   ILE B 187 " --> pdb=" O   VAL B 184 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 184 through 187'
    Processing helix  chain 'B' and resid 191 through 215
      removed outlier: 4.223A  pdb=" N   PHE B 212 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   VAL B 213 " --> pdb=" O   ASP B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 232
    Processing helix  chain 'B' and resid 233 through 236
    Processing helix  chain 'B' and resid 238 through 247
    Processing helix  chain 'B' and resid 252 through 259
    Processing helix  chain 'B' and resid 328 through 331
    Processing helix  chain 'B' and resid 349 through 357
    Processing helix  chain 'B' and resid 359 through 363
    Processing helix  chain 'B' and resid 437 through 441
    Processing helix  chain 'B' and resid 452 through 470
    Processing helix  chain 'H' and resid 62 through 65
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.709A  pdb=" N   VAL L  83 " --> pdb=" O   PRO L  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 29 through 36
    Processing helix  chain 'A' and resid 65 through 72
      removed outlier: 3.731A  pdb=" N   SER A  69 " --> pdb=" O   SER A  66 " (cutoff:3.500A)
      removed outlier: 5.806A  pdb=" N   GLN A  70 " --> pdb=" O   ASN A  67 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   CYS A  71 " --> pdb=" O   MET A  68 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   THR A  72 " --> pdb=" O   SER A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 99
      Proline residue:  A  89  - end of helix
      removed outlier: 3.904A  pdb=" N   TYR A  97 " --> pdb=" O   ALA A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 121
    Processing helix  chain 'A' and resid 125 through 137
    Processing helix  chain 'A' and resid 137 through 146
    Processing helix  chain 'A' and resid 147 through 153
    Processing helix  chain 'A' and resid 175 through 183
    Processing helix  chain 'A' and resid 184 through 187
      removed outlier: 3.524A  pdb=" N   ILE A 187 " --> pdb=" O   VAL A 184 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 184 through 187'
    Processing helix  chain 'A' and resid 191 through 215
      removed outlier: 4.200A  pdb=" N   PHE A 212 " --> pdb=" O   SER A 208 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   VAL A 213 " --> pdb=" O   ASP A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 232
    Processing helix  chain 'A' and resid 233 through 236
    Processing helix  chain 'A' and resid 238 through 247
    Processing helix  chain 'A' and resid 252 through 259
    Processing helix  chain 'A' and resid 328 through 331
    Processing helix  chain 'A' and resid 349 through 357
    Processing helix  chain 'A' and resid 359 through 363
    Processing helix  chain 'A' and resid 437 through 441
    Processing helix  chain 'A' and resid 452 through 470
    Processing helix  chain 'D' and resid 62 through 65
    Processing helix  chain 'D' and resid 87 through 91
    Processing helix  chain 'F' and resid 79 through 83
      removed outlier: 3.568A  pdb=" N   ASP F  82 " --> pdb=" O   HIS F  79 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   VAL F  83 " --> pdb=" O   PRO F  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 79 through 83'
    Processing helix  chain 'C' and resid 29 through 36
    Processing helix  chain 'C' and resid 65 through 72
      removed outlier: 3.713A  pdb=" N   SER C  69 " --> pdb=" O   SER C  66 " (cutoff:3.500A)
      removed outlier: 5.869A  pdb=" N   GLN C  70 " --> pdb=" O   ASN C  67 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   CYS C  71 " --> pdb=" O   MET C  68 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   THR C  72 " --> pdb=" O   SER C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 99
      Proline residue:  C  89  - end of helix
      removed outlier: 3.881A  pdb=" N   TYR C  97 " --> pdb=" O   ALA C  93 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 117 through 121
    Processing helix  chain 'C' and resid 125 through 137
    Processing helix  chain 'C' and resid 137 through 146
    Processing helix  chain 'C' and resid 147 through 153
    Processing helix  chain 'C' and resid 175 through 183
    Processing helix  chain 'C' and resid 184 through 187
      removed outlier: 3.565A  pdb=" N   ILE C 187 " --> pdb=" O   VAL C 184 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 184 through 187'
    Processing helix  chain 'C' and resid 191 through 215
      removed outlier: 4.207A  pdb=" N   PHE C 212 " --> pdb=" O   SER C 208 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   VAL C 213 " --> pdb=" O   ASP C 209 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 227 through 232
    Processing helix  chain 'C' and resid 233 through 236
    Processing helix  chain 'C' and resid 238 through 247
    Processing helix  chain 'C' and resid 252 through 259
    Processing helix  chain 'C' and resid 328 through 331
    Processing helix  chain 'C' and resid 349 through 357
    Processing helix  chain 'C' and resid 359 through 363
    Processing helix  chain 'C' and resid 437 through 441
    Processing helix  chain 'C' and resid 452 through 470
    Processing helix  chain 'E' and resid 62 through 65
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'G' and resid 79 through 83
      removed outlier: 3.728A  pdb=" N   VAL G  83 " --> pdb=" O   PRO G  80 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 38 through 60
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 38 through 60
    current: chain 'B' and resid 168 through 173
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 168 through 173
    current: chain 'B' and resid 275 through 298
      removed outlier: 6.646A  pdb=" N   PHE B 315 " --> pdb=" O   ILE B 326 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   ILE B 326 " --> pdb=" O   PHE B 315 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 322 through 326
    current: chain 'B' and resid 337 through 340
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 337 through 340
    current: chain 'H' and resid 44 through 52
  WARNING: can't find start of bonding for strands!
    previous: chain 'H' and resid 57 through 60
    current: chain 'H' and resid 106 through 107
    Processing sheet with id=AA2, first strand: chain 'B' and resid 101 through 102
      removed outlier: 3.639A  pdb=" N   VAL A 425 " --> pdb=" O   LEU A 422 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 123 through 124
    Processing sheet with id=AA4, first strand: chain 'B' and resid 301 through 303
      removed outlier: 6.261A  pdb=" N   ARG B 365 " --> pdb=" O   VAL B 449 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 410 through 412
    Processing sheet with id=AA6, first strand: chain 'B' and resid 392 through 394
      removed outlier: 3.589A  pdb=" N   VAL B 425 " --> pdb=" O   LEU B 422 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 6
      removed outlier: 3.911A  pdb=" N   GLN L  70 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.823A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 4.932A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 38 through 60
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 38 through 60
    current: chain 'A' and resid 168 through 173
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 168 through 173
    current: chain 'A' and resid 275 through 298
      removed outlier: 6.607A  pdb=" N   PHE A 315 " --> pdb=" O   ILE A 326 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   ILE A 326 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 322 through 326
    current: chain 'A' and resid 337 through 340
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 337 through 340
    current: chain 'D' and resid 44 through 52
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 57 through 60
    current: chain 'D' and resid 106 through 107
    Processing sheet with id=AB2, first strand: chain 'A' and resid 101 through 102
      removed outlier: 6.426A  pdb=" N   MET A 115 " --> pdb=" O   SER C 428 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   VAL C 425 " --> pdb=" O   LEU C 422 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 123 through 124
    Processing sheet with id=AB4, first strand: chain 'A' and resid 301 through 303
      removed outlier: 6.275A  pdb=" N   ARG A 365 " --> pdb=" O   VAL A 449 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 3 through 6
    Processing sheet with id=AB6, first strand: chain 'F' and resid 4 through 6
      removed outlier: 3.921A  pdb=" N   GLN F  70 " --> pdb=" O   SER F  67 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 10 through 12
      removed outlier: 6.831A  pdb=" N   LEU F  33 " --> pdb=" O   TYR F  49 " (cutoff:3.500A)
      removed outlier: 4.910A  pdb=" N   TYR F  49 " --> pdb=" O   LEU F  33 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   TRP F  35 " --> pdb=" O   LEU F  47 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 38 through 60
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 38 through 60
    current: chain 'C' and resid 168 through 173
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 168 through 173
    current: chain 'C' and resid 275 through 298
      removed outlier: 6.573A  pdb=" N   PHE C 315 " --> pdb=" O   ILE C 326 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   ILE C 326 " --> pdb=" O   PHE C 315 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 322 through 326
    current: chain 'C' and resid 337 through 340
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 337 through 340
    current: chain 'E' and resid 44 through 52
  WARNING: can't find start of bonding for strands!
    previous: chain 'E' and resid 57 through 60
    current: chain 'E' and resid 106 through 107
    Processing sheet with id=AB9, first strand: chain 'C' and resid 301 through 303
      removed outlier: 6.250A  pdb=" N   ARG C 365 " --> pdb=" O   VAL C 449 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'E' and resid 3 through 6
    Processing sheet with id=AC2, first strand: chain 'G' and resid 4 through 6
      removed outlier: 3.877A  pdb=" N   GLN G  70 " --> pdb=" O   SER G  67 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'G' and resid 10 through 12
      removed outlier: 6.831A  pdb=" N   LEU G  33 " --> pdb=" O   TYR G  49 " (cutoff:3.500A)
      removed outlier: 4.945A  pdb=" N   TYR G  49 " --> pdb=" O   LEU G  33 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   TRP G  35 " --> pdb=" O   LEU G  47 " (cutoff:3.500A)

    552 hydrogen bonds defined for protein.
    1416 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.00

  Time building geometry restraints manager: 1.42 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: 4381
        1.33 -     1.46: 2979
        1.46 -     1.58: 7889
        1.58 -     1.70: 0
        1.70 -     1.82: 144
  Bond restraints: 15393
  Sorted by residual:
  bond pdb=" C   GLY A 423 "
       pdb=" O   GLY A 423 "
    ideal  model  delta    sigma   weight residual
    1.235  1.211  0.024 1.35e-02 5.49e+03 3.09e+00
  bond pdb=" N   ASN C 424 "
       pdb=" CA  ASN C 424 "
    ideal  model  delta    sigma   weight residual
    1.454  1.473 -0.020 1.42e-02 4.96e+03 1.90e+00
  bond pdb=" N   HIS L  79 "
       pdb=" CA  HIS L  79 "
    ideal  model  delta    sigma   weight residual
    1.456  1.442  0.014 1.04e-02 9.25e+03 1.78e+00
  bond pdb=" N   ASN B 424 "
       pdb=" CA  ASN B 424 "
    ideal  model  delta    sigma   weight residual
    1.454  1.472 -0.018 1.42e-02 4.96e+03 1.64e+00
  bond pdb=" N   HIS F  79 "
       pdb=" CA  HIS F  79 "
    ideal  model  delta    sigma   weight residual
    1.456  1.443  0.013 1.04e-02 9.25e+03 1.58e+00
  ... (remaining 15388 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 20349
        1.54 -     3.08: 447
        3.08 -     4.62: 68
        4.62 -     6.16: 22
        6.16 -     7.70: 3
  Bond angle restraints: 20889
  Sorted by residual:
  angle pdb=" CA  ASN C 424 "
        pdb=" CB  ASN C 424 "
        pdb=" CG  ASN C 424 "
      ideal   model   delta    sigma   weight residual
     112.60  116.97   -4.37 1.00e+00 1.00e+00 1.91e+01
  angle pdb=" N   HIS F  79 "
        pdb=" CA  HIS F  79 "
        pdb=" C   HIS F  79 "
      ideal   model   delta    sigma   weight residual
     108.11  102.95    5.16 1.29e+00 6.01e-01 1.60e+01
  angle pdb=" N   ASN B 424 "
        pdb=" CA  ASN B 424 "
        pdb=" C   ASN B 424 "
      ideal   model   delta    sigma   weight residual
     114.12  108.83    5.29 1.39e+00 5.18e-01 1.45e+01
  angle pdb=" N   HIS L  79 "
        pdb=" CA  HIS L  79 "
        pdb=" C   HIS L  79 "
      ideal   model   delta    sigma   weight residual
     108.11  103.37    4.74 1.29e+00 6.01e-01 1.35e+01
  angle pdb=" N   GLY A 423 "
        pdb=" CA  GLY A 423 "
        pdb=" C   GLY A 423 "
      ideal   model   delta    sigma   weight residual
     113.18  105.48    7.70 2.37e+00 1.78e-01 1.05e+01
  ... (remaining 20884 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 8590
       17.94 -    35.87: 583
       35.87 -    53.81: 122
       53.81 -    71.75: 43
       71.75 -    89.68: 13
  Dihedral angle restraints: 9351
    sinusoidal: 3621
      harmonic: 5730
  Sorted by residual:
  dihedral pdb=" CB  CYS A  71 "
           pdb=" SG  CYS A  71 "
           pdb=" SG  CYS A 192 "
           pdb=" CB  CYS A 192 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   43.12   49.88     1      1.00e+01 1.00e-02 3.41e+01
  dihedral pdb=" CB  CYS C  71 "
           pdb=" SG  CYS C  71 "
           pdb=" SG  CYS C 192 "
           pdb=" CB  CYS C 192 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   46.00   47.00     1      1.00e+01 1.00e-02 3.05e+01
  dihedral pdb=" CB  CYS B  71 "
           pdb=" SG  CYS B  71 "
           pdb=" SG  CYS B 192 "
           pdb=" CB  CYS B 192 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   47.20   45.80     1      1.00e+01 1.00e-02 2.91e+01
  ... (remaining 9348 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1431
       0.030 -    0.060: 678
       0.060 -    0.090: 191
       0.090 -    0.120: 144
       0.120 -    0.150: 22
  Chirality restraints: 2466
  Sorted by residual:
  chirality pdb=" CA  VAL B 312 "
            pdb=" N   VAL B 312 "
            pdb=" C   VAL B 312 "
            pdb=" CB  VAL B 312 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.64e-01
  chirality pdb=" CA  VAL C 312 "
            pdb=" N   VAL C 312 "
            pdb=" C   VAL C 312 "
            pdb=" CB  VAL C 312 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.58e-01
  chirality pdb=" CA  THR G  94 "
            pdb=" N   THR G  94 "
            pdb=" C   THR G  94 "
            pdb=" CB  THR G  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.15 2.00e-01 2.50e+01 5.45e-01
  ... (remaining 2463 not shown)

  Planarity restraints: 2649
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 423 "   -0.010 2.00e-02 2.50e+03   2.08e-02 4.33e+00
        pdb=" C   GLY A 423 "    0.036 2.00e-02 2.50e+03
        pdb=" O   GLY A 423 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ASN A 424 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 373 "   -0.031 5.00e-02 4.00e+02   4.70e-02 3.53e+00
        pdb=" N   PRO A 374 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A 374 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 374 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 373 "   -0.031 5.00e-02 4.00e+02   4.69e-02 3.52e+00
        pdb=" N   PRO C 374 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO C 374 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO C 374 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 2646 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 340
        2.67 -     3.22: 14896
        3.22 -     3.78: 25892
        3.78 -     4.34: 37104
        4.34 -     4.90: 58790
  Nonbonded interactions: 137022
  Sorted by model distance:
  nonbonded pdb=" O   MET B  61 "
            pdb=" OH  TYR B  79 "
     model   vdw
     2.108 3.040
  nonbonded pdb=" O   MET A  61 "
            pdb=" OH  TYR A  79 "
     model   vdw
     2.128 3.040
  nonbonded pdb=" O   MET C  61 "
            pdb=" OH  TYR C  79 "
     model   vdw
     2.147 3.040
  nonbonded pdb=" OG  SER G  26 "
            pdb=" OE1 GLU G  27 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" OG  SER L  26 "
            pdb=" OE1 GLU L  27 "
     model   vdw
     2.235 3.040
  ... (remaining 137017 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'G'
  selection = chain 'L'
}

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 individual isotropic
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:             2.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.790
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  15414  Z= 0.151
  Angle     :  0.595   7.697  20931  Z= 0.332
  Chirality :  0.044   0.150   2466
  Planarity :  0.004   0.047   2649
  Dihedral  : 13.392  89.685   5616
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.17 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.48 (0.19), residues: 1953
  helix:  1.02 (0.25), residues: 429
  sheet: -0.58 (0.20), residues: 615
  loop : -0.67 (0.21), residues: 909

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H 102 
 TYR   0.020   0.002   TYR H  27 
 PHE   0.010   0.001   PHE A 301 
 TRP   0.013   0.002   TRP H  47 
 HIS   0.002   0.001   HIS B 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (15393)
  covalent geometry    : angle       0.58953 (20889)
  SS BOND              : bond        0.00240 (   21)
  SS BOND              : angle       1.88993 (   42)
  hydrogen bonds       : bond        0.18809 (  552)
  hydrogen bonds       : angle       7.24132 ( 1416)

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

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

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  340 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 337
  time to evaluate  : 0.636 
Fit side-chains
REVERT: B  258 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6878 (mm-30)
REVERT: A  136 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7343 (mm-30)
REVERT: A  258 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6827 (mm-30)
REVERT: A  424 ASN cc_start: 0.6527 (p0) cc_final: 0.6224 (p0)
REVERT: D   19 LYS cc_start: 0.7412 (ttmt) cc_final: 0.7054 (ttpp)
  outliers start: 3
  outliers final: 2
  residues processed: 338
  average time/residue: 0.6237
  time to fit residues: 232.3660
Evaluate side-chains
  299 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 297
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  103 ASP
Chi-restraints excluded: chain C residue  103 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    0.1980
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   chunk 149 optimal weight:    1.9990
   overall best weight:    1.6388

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

Flipped N/Q/H residues before XYZ refinement:
B 127 GLN
H   3 GLN
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   6 GLN
** L  79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 314 ASN
D   3 GLN
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F   6 GLN
** E   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G   6 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.172276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.151288 restraints weight = 16129.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3886 rms_B_bonded: 1.35
r_work: 0.3810 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.3715 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.1153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  15414  Z= 0.219
  Angle     :  0.618   8.351  20931  Z= 0.323
  Chirality :  0.046   0.161   2466
  Planarity :  0.004   0.050   2649
  Dihedral  :  5.485  85.868   2110
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  :  9.44 %
    Favored  : 88.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.39 (0.19), residues: 1953
  helix:  1.15 (0.25), residues: 432
  sheet: -0.69 (0.21), residues: 558
  loop : -0.55 (0.20), residues: 963

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H 102 
 TYR   0.019   0.002   TYR B 438 
 PHE   0.013   0.002   PHE B 212 
 TRP   0.009   0.002   TRP D  47 
 HIS   0.004   0.001   HIS F  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 (15393)
  covalent geometry    : angle       0.61407 (20889)
  SS BOND              : bond        0.00405 (   21)
  SS BOND              : angle       1.71216 (   42)
  hydrogen bonds       : bond        0.04382 (  552)
  hydrogen bonds       : angle       5.74929 ( 1416)

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

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

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  355 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 325
  time to evaluate  : 0.641 
Fit side-chains
REVERT: B  139 LYS cc_start: 0.8032 (mptp) cc_final: 0.7775 (mptp)
REVERT: B  258 GLU cc_start: 0.7318 (mm-30) cc_final: 0.6933 (mm-30)
REVERT: B  287 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7445 (tm-30)
REVERT: H   82 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.6808 (tm-30)
REVERT: L   81 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7739 (t0)
REVERT: L   82 ASP cc_start: 0.7374 (p0) cc_final: 0.7138 (p0)
REVERT: A  258 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7126 (mm-30)
REVERT: A  424 ASN cc_start: 0.6797 (p0) cc_final: 0.6594 (p0)
REVERT: D   19 LYS cc_start: 0.7581 (ttmt) cc_final: 0.7207 (ttpp)
REVERT: D   67 LYS cc_start: 0.7395 (tttt) cc_final: 0.7106 (ttmm)
REVERT: C  139 LYS cc_start: 0.8110 (mptp) cc_final: 0.7892 (mptp)
REVERT: C  152 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7018 (tm-30)
  outliers start: 30
  outliers final: 9
  residues processed: 335
  average time/residue: 0.5947
  time to fit residues: 220.3774
Evaluate side-chains
  319 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 307
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  287 GLU
Chi-restraints excluded: chain B residue  336 ARG
Chi-restraints excluded: chain H residue   17 SER
Chi-restraints excluded: chain H residue   82 GLU
Chi-restraints excluded: chain L residue   81 ASP
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain C residue   67 ASN
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  287 GLU
Chi-restraints excluded: chain C residue  391 THR
Chi-restraints excluded: chain C residue  427 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 132 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 111 optimal weight:    1.9990
   chunk 171 optimal weight:    4.9990
   chunk 67 optimal weight:    3.9990
   chunk 186 optimal weight:    6.9990
   chunk 178 optimal weight:    5.9990
   chunk 97 optimal weight:    1.9990
   chunk 166 optimal weight:    2.9990
   chunk 157 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
B 314 ASN
H   3 GLN
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 314 ASN
A 351 ASN
D   3 GLN
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 302 ASN
E   5 GLN
** E   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  41 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.172290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.151076 restraints weight = 16266.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3887 rms_B_bonded: 1.37
r_work: 0.3811 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.3717 rms_B_bonded: 3.01 restraints_weight: 0.2500
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.1462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  15414  Z= 0.188
  Angle     :  0.582   6.845  20931  Z= 0.302
  Chirality :  0.045   0.154   2466
  Planarity :  0.004   0.052   2649
  Dihedral  :  4.945  22.341   2106
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 11.60 %
    Favored  : 86.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.37 (0.19), residues: 1953
  helix:  1.23 (0.25), residues: 432
  sheet: -0.74 (0.20), residues: 588
  loop : -0.50 (0.20), residues: 933

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  38 
 TYR   0.017   0.002   TYR H  94 
 PHE   0.020   0.002   PHE C 212 
 TRP   0.010   0.001   TRP D  47 
 HIS   0.004   0.001   HIS F  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 (15393)
  covalent geometry    : angle       0.57937 (20889)
  SS BOND              : bond        0.00364 (   21)
  SS BOND              : angle       1.33431 (   42)
  hydrogen bonds       : bond        0.03848 (  552)
  hydrogen bonds       : angle       5.46930 ( 1416)

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

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

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  356 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 315
  time to evaluate  : 0.998 
Fit side-chains
REVERT: B  139 LYS cc_start: 0.8030 (mptp) cc_final: 0.7743 (mptp)
REVERT: B  258 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6875 (mm-30)
REVERT: B  287 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7461 (tm-30)
REVERT: L   81 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7852 (t0)
REVERT: A  115 MET cc_start: 0.8265 (mtm) cc_final: 0.8004 (mtm)
REVERT: A  258 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7124 (mm-30)
REVERT: A  424 ASN cc_start: 0.6902 (p0) cc_final: 0.6673 (p0)
REVERT: D   19 LYS cc_start: 0.7629 (ttmt) cc_final: 0.7213 (ttpp)
REVERT: C  152 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7021 (tm-30)
REVERT: C  463 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.7418 (mtm)
REVERT: E   19 LYS cc_start: 0.7778 (tttt) cc_final: 0.7409 (ttpp)
  outliers start: 41
  outliers final: 18
  residues processed: 335
  average time/residue: 0.6079
  time to fit residues: 225.7237
Evaluate side-chains
  324 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 303
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 ASN
Chi-restraints excluded: chain B residue  287 GLU
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  336 ARG
Chi-restraints excluded: chain B residue  355 CYS
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain L residue   74 LYS
Chi-restraints excluded: chain L residue   81 ASP
Chi-restraints excluded: chain L residue   91 VAL
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain C residue  287 GLU
Chi-restraints excluded: chain C residue  355 CYS
Chi-restraints excluded: chain C residue  391 THR
Chi-restraints excluded: chain C residue  427 ILE
Chi-restraints excluded: chain C residue  463 MET
Chi-restraints excluded: chain E residue   30 THR
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   84 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 106 optimal weight:    4.9990
   chunk 153 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 144 optimal weight:    6.9990
   chunk 58 optimal weight:    0.0770
   chunk 115 optimal weight:    0.9990
   chunk 183 optimal weight:    8.9990
   chunk 59 optimal weight:    0.9990
   chunk 171 optimal weight:    0.3980
   chunk 35 optimal weight:    3.9990
   chunk 172 optimal weight:    3.9990
   overall best weight:    0.6542

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 314 ASN
D   3 GLN
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 162 GLN
E   5 GLN
** E   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  41 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.175971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.154976 restraints weight = 16185.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3931 rms_B_bonded: 1.37
r_work: 0.3856 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.3763 rms_B_bonded: 3.04 restraints_weight: 0.2500
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.1637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15414  Z= 0.131
  Angle     :  0.531   6.740  20931  Z= 0.274
  Chirality :  0.044   0.149   2466
  Planarity :  0.004   0.051   2649
  Dihedral  :  4.643  21.058   2106
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 13.23 %
    Favored  : 84.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.22 (0.19), residues: 1953
  helix:  1.48 (0.25), residues: 432
  sheet: -0.70 (0.20), residues: 591
  loop : -0.44 (0.20), residues: 930

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  38 
 TYR   0.019   0.001   TYR D  27 
 PHE   0.022   0.001   PHE C 212 
 TRP   0.011   0.001   TRP H  47 
 HIS   0.002   0.001   HIS F  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (15393)
  covalent geometry    : angle       0.52905 (20889)
  SS BOND              : bond        0.00285 (   21)
  SS BOND              : angle       1.06876 (   42)
  hydrogen bonds       : bond        0.03265 (  552)
  hydrogen bonds       : angle       5.13968 ( 1416)

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

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

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  367 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 323
  time to evaluate  : 0.598 
Fit side-chains
REVERT: B  139 LYS cc_start: 0.7942 (mptp) cc_final: 0.7712 (mptp)
REVERT: B  258 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6839 (mm-30)
REVERT: H    5 GLN cc_start: 0.8206 (mt0) cc_final: 0.7532 (mp10)
REVERT: A   61 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7787 (mmm)
REVERT: A  189 LYS cc_start: 0.8204 (mmtt) cc_final: 0.7672 (mttm)
REVERT: A  258 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7154 (mm-30)
REVERT: A  287 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7091 (tm-30)
REVERT: A  424 ASN cc_start: 0.6770 (p0) cc_final: 0.6542 (p0)
REVERT: D   19 LYS cc_start: 0.7577 (ttmt) cc_final: 0.7075 (ttpp)
REVERT: D   37 VAL cc_start: 0.8481 (OUTLIER) cc_final: 0.8251 (t)
REVERT: C  152 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7040 (tm-30)
REVERT: E   19 LYS cc_start: 0.7706 (tttt) cc_final: 0.7334 (ttpp)
  outliers start: 44
  outliers final: 18
  residues processed: 343
  average time/residue: 0.5716
  time to fit residues: 217.8853
Evaluate side-chains
  328 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 307
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  336 ARG
Chi-restraints excluded: chain B residue  355 CYS
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain L residue   74 LYS
Chi-restraints excluded: chain L residue   91 VAL
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  192 CYS
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain C residue   67 ASN
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  355 CYS
Chi-restraints excluded: chain C residue  391 THR
Chi-restraints excluded: chain C residue  427 ILE
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   30 THR
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   84 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 142 optimal weight:    0.9980
   chunk 170 optimal weight:    0.6980
   chunk 107 optimal weight:    0.0870
   chunk 145 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9990
   chunk 152 optimal weight:    0.8980
   chunk 122 optimal weight:    3.9990
   chunk 27 optimal weight:    0.4980
   chunk 76 optimal weight:    0.4980
   chunk 154 optimal weight:    0.4980
   overall best weight:    0.4558

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

Flipped N/Q/H residues before XYZ refinement:
B 100 ASN
** L  79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  84 ASN
A 314 ASN
D   3 GLN
C 100 ASN
E   3 GLN
E   5 GLN
E  41 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.177519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.156814 restraints weight = 15985.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.3955 rms_B_bonded: 1.34
r_work: 0.3881 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.3788 rms_B_bonded: 3.01 restraints_weight: 0.2500
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.1849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  15414  Z= 0.115
  Angle     :  0.511   6.532  20931  Z= 0.264
  Chirality :  0.043   0.143   2466
  Planarity :  0.004   0.051   2649
  Dihedral  :  4.458  19.952   2106
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 14.98 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.08 (0.19), residues: 1953
  helix:  1.60 (0.25), residues: 432
  sheet: -0.63 (0.21), residues: 576
  loop : -0.36 (0.21), residues: 945

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  38 
 TYR   0.021   0.001   TYR E  27 
 PHE   0.015   0.001   PHE B 212 
 TRP   0.010   0.001   TRP H  47 
 HIS   0.002   0.001   HIS A 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (15393)
  covalent geometry    : angle       0.50964 (20889)
  SS BOND              : bond        0.00259 (   21)
  SS BOND              : angle       0.97448 (   42)
  hydrogen bonds       : bond        0.03055 (  552)
  hydrogen bonds       : angle       4.98900 ( 1416)

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

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

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  375 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 333
  time to evaluate  : 0.682 
Fit side-chains
REVERT: B   27 ILE cc_start: 0.6635 (tp) cc_final: 0.5936 (tp)
REVERT: B  139 LYS cc_start: 0.7893 (mptp) cc_final: 0.7664 (mptp)
REVERT: B  258 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6767 (mm-30)
REVERT: B  287 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7309 (tm-30)
REVERT: H    5 GLN cc_start: 0.8166 (mt0) cc_final: 0.7484 (mp10)
REVERT: A   61 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7808 (mmm)
REVERT: A  135 TYR cc_start: 0.8304 (t80) cc_final: 0.7714 (t80)
REVERT: A  189 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7668 (mttm)
REVERT: A  258 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7015 (mm-30)
REVERT: A  287 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7023 (tm-30)
REVERT: A  424 ASN cc_start: 0.6570 (p0) cc_final: 0.6345 (p0)
REVERT: D   19 LYS cc_start: 0.7463 (ttmt) cc_final: 0.7023 (ttpp)
REVERT: C  152 GLU cc_start: 0.7286 (mt-10) cc_final: 0.7015 (tm-30)
REVERT: E   19 LYS cc_start: 0.7639 (tttt) cc_final: 0.7278 (ttpp)
REVERT: G   74 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7482 (tppp)
  outliers start: 42
  outliers final: 15
  residues processed: 349
  average time/residue: 0.5533
  time to fit residues: 214.1232
Evaluate side-chains
  336 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 317
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 ASN
Chi-restraints excluded: chain B residue  287 GLU
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain L residue   74 LYS
Chi-restraints excluded: chain L residue   91 VAL
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain C residue   67 ASN
Chi-restraints excluded: chain C residue  355 CYS
Chi-restraints excluded: chain C residue  391 THR
Chi-restraints excluded: chain C residue  427 ILE
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   30 THR
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   84 LEU
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain G residue   85 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 136 optimal weight:    0.0070
   chunk 130 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0040
   chunk 131 optimal weight:    0.0970
   chunk 103 optimal weight:    5.9990
   chunk 92 optimal weight:    0.6980
   chunk 141 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 173 optimal weight:    2.9990
   chunk 122 optimal weight:    3.9990
   chunk 163 optimal weight:    2.9990
   overall best weight:    0.3408

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

Flipped N/Q/H residues before XYZ refinement:
B  84 ASN
B 351 ASN
H   3 GLN
** L  79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  84 ASN
A 314 ASN
D   3 GLN
C  84 ASN
C 194 GLN
E   3 GLN
E  41 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.179418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.158892 restraints weight = 16027.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3980 rms_B_bonded: 1.34
r_work: 0.3906 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.3814 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.2040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  15414  Z= 0.107
  Angle     :  0.510   6.529  20931  Z= 0.263
  Chirality :  0.043   0.141   2466
  Planarity :  0.004   0.050   2649
  Dihedral  :  4.359  18.912   2106
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 16.49 %
    Favored  : 81.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.03 (0.19), residues: 1953
  helix:  1.72 (0.25), residues: 432
  sheet: -0.59 (0.21), residues: 561
  loop : -0.28 (0.21), residues: 960

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  38 
 TYR   0.018   0.001   TYR E  27 
 PHE   0.024   0.001   PHE C 212 
 TRP   0.010   0.001   TRP D  47 
 HIS   0.002   0.000   HIS F  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (15393)
  covalent geometry    : angle       0.50760 (20889)
  SS BOND              : bond        0.00212 (   21)
  SS BOND              : angle       1.31105 (   42)
  hydrogen bonds       : bond        0.02927 (  552)
  hydrogen bonds       : angle       4.84702 ( 1416)

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

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

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  368 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 330
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
REVERT: B  136 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7372 (mt-10)
REVERT: B  139 LYS cc_start: 0.7808 (mptp) cc_final: 0.7602 (mptp)
REVERT: B  258 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6822 (mm-30)
REVERT: H    5 GLN cc_start: 0.8105 (mt0) cc_final: 0.7435 (mp10)
REVERT: A   61 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7715 (mmm)
REVERT: A  189 LYS cc_start: 0.8146 (mmtt) cc_final: 0.7684 (mttm)
REVERT: A  258 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7024 (mm-30)
REVERT: A  287 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7050 (tm-30)
REVERT: A  424 ASN cc_start: 0.6502 (p0) cc_final: 0.6283 (p0)
REVERT: C  152 GLU cc_start: 0.7263 (mt-10) cc_final: 0.7018 (tm-30)
REVERT: C  258 GLU cc_start: 0.7331 (mm-30) cc_final: 0.7111 (mm-30)
REVERT: E   67 LYS cc_start: 0.7183 (tttt) cc_final: 0.6854 (ttmm)
  outliers start: 38
  outliers final: 14
  residues processed: 350
  average time/residue: 0.5354
  time to fit residues: 208.8935
Evaluate side-chains
  339 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 323
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain H residue   17 SER
Chi-restraints excluded: chain H residue   72 VAL
Chi-restraints excluded: chain H residue   84 LEU
Chi-restraints excluded: chain L residue   74 LYS
Chi-restraints excluded: chain L residue   85 THR
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain C residue   67 ASN
Chi-restraints excluded: chain C residue  355 CYS
Chi-restraints excluded: chain C residue  391 THR
Chi-restraints excluded: chain C residue  427 ILE
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   84 LEU
Chi-restraints excluded: chain G residue   85 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 186 optimal weight:    0.9990
   chunk 172 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 48 optimal weight:    5.9990
   chunk 151 optimal weight:    0.3980
   chunk 95 optimal weight:    0.9980
   chunk 177 optimal weight:    0.6980
   chunk 55 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0870
   chunk 14 optimal weight:    3.9990
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  41 HIS
** L  79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  84 ASN
A 100 ASN
A 294 GLN
A 314 ASN
D   3 GLN
C  84 ASN
E   3 GLN
E  41 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.178534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.157875 restraints weight = 15869.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.3966 rms_B_bonded: 1.33
r_work: 0.3890 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.3796 rms_B_bonded: 3.06 restraints_weight: 0.2500
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066  15414  Z= 0.126
  Angle     :  0.525   6.970  20931  Z= 0.270
  Chirality :  0.044   0.139   2466
  Planarity :  0.004   0.048   2649
  Dihedral  :  4.411  19.044   2106
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 16.78 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.19), residues: 1953
  helix:  1.74 (0.25), residues: 432
  sheet: -0.59 (0.21), residues: 561
  loop : -0.24 (0.21), residues: 960

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  38 
 TYR   0.014   0.001   TYR E  27 
 PHE   0.025   0.001   PHE A 212 
 TRP   0.008   0.001   TRP D  47 
 HIS   0.002   0.001   HIS F  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (15393)
  covalent geometry    : angle       0.52069 (20889)
  SS BOND              : bond        0.00239 (   21)
  SS BOND              : angle       1.52054 (   42)
  hydrogen bonds       : bond        0.03010 (  552)
  hydrogen bonds       : angle       4.84922 ( 1416)

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

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

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  364 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 324
  time to evaluate  : 0.589 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  258 GLU cc_start: 0.7358 (mm-30) cc_final: 0.6941 (mm-30)
REVERT: B  287 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7368 (tm-30)
REVERT: H    5 GLN cc_start: 0.8151 (mt0) cc_final: 0.7558 (mp10)
REVERT: A   61 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7655 (mmm)
REVERT: A  135 TYR cc_start: 0.8372 (t80) cc_final: 0.7870 (t80)
REVERT: A  189 LYS cc_start: 0.8155 (mmtt) cc_final: 0.7746 (mttm)
REVERT: A  258 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7093 (mm-30)
REVERT: A  287 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7040 (tm-30)
REVERT: A  350 ASN cc_start: 0.7777 (t0) cc_final: 0.7508 (m-40)
REVERT: A  424 ASN cc_start: 0.6462 (p0) cc_final: 0.6250 (p0)
REVERT: D  102 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.6997 (tpp80)
REVERT: C  136 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7573 (mm-30)
REVERT: C  152 GLU cc_start: 0.7291 (mt-10) cc_final: 0.7084 (tm-30)
REVERT: E    5 GLN cc_start: 0.8126 (mt0) cc_final: 0.7499 (mp-120)
  outliers start: 40
  outliers final: 21
  residues processed: 342
  average time/residue: 0.5801
  time to fit residues: 220.2450
Evaluate side-chains
  341 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 316
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  287 GLU
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   17 SER
Chi-restraints excluded: chain H residue   72 VAL
Chi-restraints excluded: chain H residue   84 LEU
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   74 LYS
Chi-restraints excluded: chain L residue   85 THR
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   72 VAL
Chi-restraints excluded: chain D residue  102 ARG
Chi-restraints excluded: chain F residue   85 THR
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain C residue   67 ASN
Chi-restraints excluded: chain C residue  192 CYS
Chi-restraints excluded: chain C residue  355 CYS
Chi-restraints excluded: chain C residue  391 THR
Chi-restraints excluded: chain C residue  427 ILE
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   84 LEU
Chi-restraints excluded: chain G residue   85 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 123 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 136 optimal weight:    0.3980
   chunk 103 optimal weight:    5.9990
   chunk 99 optimal weight:    2.9990
   chunk 49 optimal weight:    6.9990
   chunk 190 optimal weight:    8.9990
   chunk 125 optimal weight:    9.9990
   chunk 95 optimal weight:    2.9990
   overall best weight:    2.2788

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

Flipped N/Q/H residues before XYZ refinement:
B 217 ASN
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 314 ASN
D   3 GLN
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 194 GLN
E   3 GLN
** E   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  41 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.170394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.148883 restraints weight = 16223.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3856 rms_B_bonded: 1.36
r_work: 0.3777 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.3680 rms_B_bonded: 3.06 restraints_weight: 0.2500
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.1935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061  15414  Z= 0.265
  Angle     :  0.660   7.962  20931  Z= 0.342
  Chirality :  0.048   0.227   2466
  Planarity :  0.004   0.047   2649
  Dihedral  :  5.072  22.654   2106
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 17.02 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.23 (0.19), residues: 1953
  helix:  1.39 (0.24), residues: 432
  sheet: -0.73 (0.21), residues: 555
  loop : -0.40 (0.20), residues: 966

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F  38 
 TYR   0.019   0.003   TYR A 438 
 PHE   0.029   0.002   PHE C 212 
 TRP   0.008   0.002   TRP E 107 
 HIS   0.004   0.001   HIS F  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00619 (15393)
  covalent geometry    : angle       0.65380 (20889)
  SS BOND              : bond        0.00514 (   21)
  SS BOND              : angle       2.15242 (   42)
  hydrogen bonds       : bond        0.03954 (  552)
  hydrogen bonds       : angle       5.39709 ( 1416)

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

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

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  351 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 305
  time to evaluate  : 0.623 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  258 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6852 (mm-30)
REVERT: B  287 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7557 (tm-30)
REVERT: H    5 GLN cc_start: 0.8309 (mt0) cc_final: 0.7532 (mp10)
REVERT: A  135 TYR cc_start: 0.8415 (t80) cc_final: 0.7996 (t80)
REVERT: A  189 LYS cc_start: 0.8262 (mmtt) cc_final: 0.7715 (mttm)
REVERT: A  258 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7104 (mm-30)
REVERT: A  287 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7108 (tm-30)
REVERT: A  350 ASN cc_start: 0.7888 (t0) cc_final: 0.7609 (m-40)
REVERT: A  424 ASN cc_start: 0.6709 (p0) cc_final: 0.6500 (p0)
REVERT: D  102 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.7488 (tpp80)
REVERT: C  152 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7060 (tm-30)
  outliers start: 46
  outliers final: 25
  residues processed: 327
  average time/residue: 0.5812
  time to fit residues: 210.8496
Evaluate side-chains
  325 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 297
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 ASN
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  287 GLU
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   17 SER
Chi-restraints excluded: chain H residue   72 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   74 LYS
Chi-restraints excluded: chain L residue   91 VAL
Chi-restraints excluded: chain A residue  192 CYS
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue  102 ARG
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain C residue   67 ASN
Chi-restraints excluded: chain C residue  103 ASP
Chi-restraints excluded: chain C residue  192 CYS
Chi-restraints excluded: chain C residue  287 GLU
Chi-restraints excluded: chain C residue  355 CYS
Chi-restraints excluded: chain C residue  391 THR
Chi-restraints excluded: chain C residue  422 LEU
Chi-restraints excluded: chain C residue  427 ILE
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   84 LEU
Chi-restraints excluded: chain G residue   91 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0870
   chunk 21 optimal weight:    0.8980
   chunk 117 optimal weight:    0.7980
   chunk 182 optimal weight:    6.9990
   chunk 139 optimal weight:    0.6980
   chunk 114 optimal weight:    6.9990
   chunk 102 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  84 ASN
A 100 ASN
A 314 ASN
D   3 GLN
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84 ASN
C 100 ASN
E   3 GLN
E   5 GLN
** E   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.175402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.154435 restraints weight = 15910.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.3928 rms_B_bonded: 1.34
r_work: 0.3852 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.3762 rms_B_bonded: 2.97 restraints_weight: 0.2500
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  15414  Z= 0.140
  Angle     :  0.561   7.683  20931  Z= 0.289
  Chirality :  0.045   0.168   2466
  Planarity :  0.004   0.048   2649
  Dihedral  :  4.737  21.283   2106
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 17.42 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.10 (0.19), residues: 1953
  helix:  1.56 (0.25), residues: 432
  sheet: -0.71 (0.20), residues: 585
  loop : -0.29 (0.21), residues: 936

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  38 
 TYR   0.014   0.002   TYR C 438 
 PHE   0.029   0.001   PHE A 212 
 TRP   0.009   0.001   TRP H  47 
 HIS   0.005   0.001   HIS C 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (15393)
  covalent geometry    : angle       0.55790 (20889)
  SS BOND              : bond        0.00430 (   21)
  SS BOND              : angle       1.37694 (   42)
  hydrogen bonds       : bond        0.03231 (  552)
  hydrogen bonds       : angle       5.08388 ( 1416)

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

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

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  348 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 315
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
REVERT: B   61 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7371 (mmm)
REVERT: B  197 LEU cc_start: 0.8257 (mt) cc_final: 0.7243 (tp)
REVERT: B  226 MET cc_start: 0.7459 (ptt) cc_final: 0.7160 (ppp)
REVERT: B  258 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6841 (mm-30)
REVERT: B  287 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7450 (tm-30)
REVERT: H    5 GLN cc_start: 0.8235 (mt0) cc_final: 0.7520 (mp10)
REVERT: A  135 TYR cc_start: 0.8367 (t80) cc_final: 0.7880 (t80)
REVERT: A  189 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7719 (mttm)
REVERT: A  258 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7004 (mm-30)
REVERT: A  287 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7034 (tm-30)
REVERT: A  350 ASN cc_start: 0.7783 (t0) cc_final: 0.7542 (m-40)
REVERT: A  424 ASN cc_start: 0.6631 (p0) cc_final: 0.6408 (OUTLIER)
REVERT: D   18 MET cc_start: 0.8177 (ppp) cc_final: 0.7913 (tmm)
REVERT: D  102 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7204 (tpp80)
REVERT: C  152 GLU cc_start: 0.7332 (mt-10) cc_final: 0.7025 (tm-30)
REVERT: E    5 GLN cc_start: 0.8216 (mt0) cc_final: 0.7581 (mp-120)
REVERT: E   19 LYS cc_start: 0.7692 (tttt) cc_final: 0.7240 (ttpp)
  outliers start: 33
  outliers final: 21
  residues processed: 334
  average time/residue: 0.5568
  time to fit residues: 206.6287
Evaluate side-chains
  327 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 303
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  103 ASP
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  192 CYS
Chi-restraints excluded: chain B residue  287 GLU
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   17 SER
Chi-restraints excluded: chain H residue   72 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue  102 ARG
Chi-restraints excluded: chain C residue   67 ASN
Chi-restraints excluded: chain C residue  287 GLU
Chi-restraints excluded: chain C residue  328 ILE
Chi-restraints excluded: chain C residue  355 CYS
Chi-restraints excluded: chain C residue  391 THR
Chi-restraints excluded: chain C residue  422 LEU
Chi-restraints excluded: chain C residue  427 ILE
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   84 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 110 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 180 optimal weight:    0.9980
   chunk 188 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 68 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 181 optimal weight:    0.7980
   chunk 158 optimal weight:    0.2980
   chunk 122 optimal weight:    8.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 100 ASN
A 314 ASN
D   3 GLN
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84 ASN
E   3 GLN
** E   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.174355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.153043 restraints weight = 16189.859|
|-----------------------------------------------------------------------------|
r_work (start): 0.3912 rms_B_bonded: 1.36
r_work: 0.3836 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.3742 rms_B_bonded: 3.03 restraints_weight: 0.2500
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.1975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  15414  Z= 0.175
  Angle     :  0.596   9.229  20931  Z= 0.307
  Chirality :  0.046   0.258   2466
  Planarity :  0.004   0.050   2649
  Dihedral  :  4.796  21.302   2106
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 18.47 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.09 (0.19), residues: 1953
  helix:  1.58 (0.25), residues: 432
  sheet: -0.71 (0.21), residues: 555
  loop : -0.31 (0.21), residues: 966

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F  38 
 TYR   0.016   0.002   TYR A 438 
 PHE   0.026   0.002   PHE C 212 
 TRP   0.008   0.001   TRP D 107 
 HIS   0.002   0.001   HIS B 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 (15393)
  covalent geometry    : angle       0.59010 (20889)
  SS BOND              : bond        0.00331 (   21)
  SS BOND              : angle       1.94122 (   42)
  hydrogen bonds       : bond        0.03402 (  552)
  hydrogen bonds       : angle       5.12567 ( 1416)

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

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

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 296
  time to evaluate  : 0.660 
Fit side-chains
   revert: symmetry clash
REVERT: B   61 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.7390 (mmm)
REVERT: B  197 LEU cc_start: 0.8354 (mt) cc_final: 0.7203 (tp)
REVERT: B  258 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6849 (mm-30)
REVERT: B  287 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7504 (tm-30)
REVERT: H    5 GLN cc_start: 0.8239 (mt0) cc_final: 0.7498 (mp10)
REVERT: H   18 MET cc_start: 0.8210 (ppp) cc_final: 0.7920 (ppp)
REVERT: A  135 TYR cc_start: 0.8356 (t80) cc_final: 0.7859 (t80)
REVERT: A  189 LYS cc_start: 0.8229 (mmtt) cc_final: 0.7705 (mttm)
REVERT: A  258 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7025 (mm-30)
REVERT: A  287 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7062 (tm-30)
REVERT: A  350 ASN cc_start: 0.7813 (t0) cc_final: 0.7564 (m-40)
REVERT: A  424 ASN cc_start: 0.6637 (p0) cc_final: 0.6418 (OUTLIER)
REVERT: D   18 MET cc_start: 0.8179 (ppp) cc_final: 0.7961 (tmm)
REVERT: D  102 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7839 (tpp80)
REVERT: C  152 GLU cc_start: 0.7342 (mt-10) cc_final: 0.7014 (tm-30)
REVERT: E    5 GLN cc_start: 0.8212 (mt0) cc_final: 0.7559 (mp-120)
REVERT: E   19 LYS cc_start: 0.7696 (tttt) cc_final: 0.7262 (ttpp)
REVERT: E   67 LYS cc_start: 0.7269 (tttt) cc_final: 0.6942 (ttmm)
  outliers start: 29
  outliers final: 22
  residues processed: 313
  average time/residue: 0.5733
  time to fit residues: 198.9012
Evaluate side-chains
  319 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 294
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  192 CYS
Chi-restraints excluded: chain B residue  287 GLU
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   17 SER
Chi-restraints excluded: chain H residue   72 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  192 CYS
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue  102 ARG
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain C residue   67 ASN
Chi-restraints excluded: chain C residue  287 GLU
Chi-restraints excluded: chain C residue  328 ILE
Chi-restraints excluded: chain C residue  355 CYS
Chi-restraints excluded: chain C residue  391 THR
Chi-restraints excluded: chain C residue  422 LEU
Chi-restraints excluded: chain C residue  427 ILE
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   84 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 115 optimal weight:    3.9990
   chunk 26 optimal weight:    0.5980
   chunk 60 optimal weight:    6.9990
   chunk 121 optimal weight:    4.9990
   chunk 15 optimal weight:    0.0980
   chunk 89 optimal weight:    4.9990
   chunk 152 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 189 optimal weight:    5.9990
   chunk 160 optimal weight:    0.0030
   overall best weight:    1.1394

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 314 ASN
D   3 GLN
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   3 GLN
** E   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.174577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.153426 restraints weight = 16076.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3914 rms_B_bonded: 1.35
r_work: 0.3838 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.3743 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.2009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  15414  Z= 0.169
  Angle     :  0.591   8.773  20931  Z= 0.305
  Chirality :  0.046   0.236   2466
  Planarity :  0.004   0.050   2649
  Dihedral  :  4.789  21.157   2106
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 18.30 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.19), residues: 1953
  helix:  1.59 (0.25), residues: 432
  sheet: -0.71 (0.21), residues: 552
  loop : -0.29 (0.20), residues: 969

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F  38 
 TYR   0.016   0.002   TYR H  94 
 PHE   0.010   0.001   PHE B 376 
 TRP   0.008   0.001   TRP D 107 
 HIS   0.002   0.001   HIS B 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 (15393)
  covalent geometry    : angle       0.58542 (20889)
  SS BOND              : bond        0.00421 (   21)
  SS BOND              : angle       1.85184 (   42)
  hydrogen bonds       : bond        0.03401 (  552)
  hydrogen bonds       : angle       5.11956 ( 1416)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6294.43 seconds
wall clock time: 108 minutes 12.94 seconds (6492.94 seconds total)