Starting phenix.real_space_refine
on Mon Jul 28 09:13:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bw9_44962/07_2025/9bw9_44962.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bw9_44962/07_2025/9bw9_44962.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bw9_44962/07_2025/9bw9_44962.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bw9_44962/07_2025/9bw9_44962.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bw9_44962/07_2025/9bw9_44962.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bw9_44962/07_2025/9bw9_44962.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    6502      2.51       5
     N    1818      2.21       5
     O    1864      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10238
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "E"
      Number of atoms: 632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 632
          Classifications: {'peptide': 77}
          Link IDs: {'TRANS': 76}
    Chain: "F"
      Number of atoms: 632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 632
          Classifications: {'peptide': 77}
          Link IDs: {'TRANS': 76}
    Chain: "A"
      Number of atoms: 1897
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 240, 1897
          Classifications: {'peptide': 240}
          Link IDs: {'PTRANS': 8, 'TRANS': 231}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 1958
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 247, 1958
          Classifications: {'peptide': 247}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 238}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
  Restraints were copied for chains:
    C, D, G, H
  Time building chain proxies: 7.35, per 1000 atoms: 0.72
  Number of scatterers: 10238
  At special positions: 0
  Unit cell: (146.28, 129.72, 81.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      54     16.00
     O    1864      8.00
     N    1818      7.00
     C    6502      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.64
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2432

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 8 sheets defined
      57.3% alpha, 12.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.15
  Creating SS restraints...
    Processing helix  chain 'G' and resid 348 through 362
      removed outlier: 3.675A  pdb=" N   GLU G 358 " --> pdb=" O   ARG G 354 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ILE G 359 " --> pdb=" O   ILE G 355 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 369 through 381
      removed outlier: 3.601A  pdb=" N   CYS G 373 " --> pdb=" O   ASP G 369 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   ILE G 374 " --> pdb=" O   VAL G 370 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 386 through 393
      removed outlier: 3.954A  pdb=" N   HIS G 393 " --> pdb=" O   GLN G 389 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 394 through 404
    Processing helix  chain 'G' and resid 411 through 424
      removed outlier: 3.572A  pdb=" N   LEU G 419 " --> pdb=" O   LYS G 415 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 349 through 363
    Processing helix  chain 'H' and resid 369 through 383
      removed outlier: 4.020A  pdb=" N   CYS H 373 " --> pdb=" O   ASP H 369 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 386 through 393
    Processing helix  chain 'H' and resid 394 through 403
    Processing helix  chain 'H' and resid 404 through 406
      No H-bonds generated for 'chain 'H' and resid 404 through 406'
    Processing helix  chain 'H' and resid 409 through 424
      removed outlier: 4.265A  pdb=" N   MET H 413 " --> pdb=" O   SER H 409 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   GLU H 414 " --> pdb=" O   GLN H 410 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LYS H 424 " --> pdb=" O   TYR H 420 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 3 through 15
    Processing helix  chain 'C' and resid 18 through 26
      removed outlier: 3.945A  pdb=" N   MET C  22 " --> pdb=" O   ASN C  18 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   SER C  24 " --> pdb=" O   ARG C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 39
      removed outlier: 3.689A  pdb=" N   GLU C  35 " --> pdb=" O   VAL C  31 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   VAL C  37 " --> pdb=" O   ALA C  33 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   ALA C  38 " --> pdb=" O   LYS C  34 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 93 through 106
      removed outlier: 4.191A  pdb=" N   THR C  97 " --> pdb=" O   THR C  93 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ALA C  98 " --> pdb=" O   GLY C  94 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   GLY C 106 " --> pdb=" O   LEU C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 123 through 133
      removed outlier: 3.931A  pdb=" N   ALA C 133 " --> pdb=" O   ALA C 129 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 150 through 166
      removed outlier: 3.566A  pdb=" N   LYS C 156 " --> pdb=" O   GLU C 152 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLU C 157 " --> pdb=" O   SER C 153 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 167 through 169
      No H-bonds generated for 'chain 'C' and resid 167 through 169'
    Processing helix  chain 'C' and resid 175 through 185
    Processing helix  chain 'C' and resid 198 through 222
      removed outlier: 3.844A  pdb=" N   GLN C 216 " --> pdb=" O   GLU C 212 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   GLN C 221 " --> pdb=" O   ILE C 217 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 2 through 15
      removed outlier: 3.755A  pdb=" N   GLU D  11 " --> pdb=" O   LYS D   7 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   HIS D  12 " --> pdb=" O   ALA D   8 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   GLU D  13 " --> pdb=" O   GLN D   9 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   LYS D  14 " --> pdb=" O   GLU D  10 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 18 through 26
      removed outlier: 3.713A  pdb=" N   ASP D  25 " --> pdb=" O   ALA D  21 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   PHE D  26 " --> pdb=" O   MET D  22 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 40
    Processing helix  chain 'D' and resid 41 through 45
    Processing helix  chain 'D' and resid 93 through 107
      removed outlier: 3.864A  pdb=" N   GLY D 106 " --> pdb=" O   LEU D 102 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   ARG D 107 " --> pdb=" O   LYS D 103 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 123 through 133
      removed outlier: 3.526A  pdb=" N   LYS D 127 " --> pdb=" O   SER D 123 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 150 through 167
      removed outlier: 4.267A  pdb=" N   ASP D 167 " --> pdb=" O   GLY D 163 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 171 through 174
    Processing helix  chain 'D' and resid 175 through 185
    Processing helix  chain 'D' and resid 195 through 221
      removed outlier: 3.628A  pdb=" N   VAL D 201 " --> pdb=" O   GLY D 197 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 349 through 362
      removed outlier: 3.674A  pdb=" N   GLU E 358 " --> pdb=" O   ARG E 354 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ILE E 359 " --> pdb=" O   ILE E 355 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 369 through 381
      removed outlier: 3.600A  pdb=" N   CYS E 373 " --> pdb=" O   ASP E 369 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   ILE E 374 " --> pdb=" O   VAL E 370 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 386 through 393
      removed outlier: 3.954A  pdb=" N   HIS E 393 " --> pdb=" O   GLN E 389 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 394 through 404
    Processing helix  chain 'E' and resid 411 through 424
      removed outlier: 3.571A  pdb=" N   LEU E 419 " --> pdb=" O   LYS E 415 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 349 through 363
    Processing helix  chain 'F' and resid 369 through 383
      removed outlier: 4.021A  pdb=" N   CYS F 373 " --> pdb=" O   ASP F 369 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 386 through 393
    Processing helix  chain 'F' and resid 394 through 403
    Processing helix  chain 'F' and resid 404 through 406
      No H-bonds generated for 'chain 'F' and resid 404 through 406'
    Processing helix  chain 'F' and resid 409 through 424
      removed outlier: 4.265A  pdb=" N   MET F 413 " --> pdb=" O   SER F 409 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   GLU F 414 " --> pdb=" O   GLN F 410 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LYS F 424 " --> pdb=" O   TYR F 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3 through 15
    Processing helix  chain 'A' and resid 18 through 26
      removed outlier: 3.943A  pdb=" N   MET A  22 " --> pdb=" O   ASN A  18 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   SER A  24 " --> pdb=" O   ARG A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 29 through 39
      removed outlier: 3.688A  pdb=" N   GLU A  35 " --> pdb=" O   VAL A  31 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   VAL A  37 " --> pdb=" O   ALA A  33 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   ALA A  38 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 106
      removed outlier: 4.190A  pdb=" N   THR A  97 " --> pdb=" O   THR A  93 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ALA A  98 " --> pdb=" O   GLY A  94 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLY A 106 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 133
      removed outlier: 3.932A  pdb=" N   ALA A 133 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 166
      removed outlier: 3.567A  pdb=" N   LYS A 156 " --> pdb=" O   GLU A 152 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   GLU A 157 " --> pdb=" O   SER A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 169
      No H-bonds generated for 'chain 'A' and resid 167 through 169'
    Processing helix  chain 'A' and resid 175 through 185
    Processing helix  chain 'A' and resid 198 through 222
      removed outlier: 3.844A  pdb=" N   GLN A 216 " --> pdb=" O   GLU A 212 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   GLN A 221 " --> pdb=" O   ILE A 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 15
      removed outlier: 3.755A  pdb=" N   GLU B  11 " --> pdb=" O   LYS B   7 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   HIS B  12 " --> pdb=" O   ALA B   8 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   GLU B  13 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   LYS B  14 " --> pdb=" O   GLU B  10 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 26
      removed outlier: 3.712A  pdb=" N   ASP B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   PHE B  26 " --> pdb=" O   MET B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 40
    Processing helix  chain 'B' and resid 41 through 45
    Processing helix  chain 'B' and resid 93 through 107
      removed outlier: 3.864A  pdb=" N   GLY B 106 " --> pdb=" O   LEU B 102 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   ARG B 107 " --> pdb=" O   LYS B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 133
      removed outlier: 3.527A  pdb=" N   LYS B 127 " --> pdb=" O   SER B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 150 through 167
      removed outlier: 4.267A  pdb=" N   ASP B 167 " --> pdb=" O   GLY B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 174
    Processing helix  chain 'B' and resid 175 through 185
    Processing helix  chain 'B' and resid 195 through 221
      removed outlier: 3.628A  pdb=" N   VAL B 201 " --> pdb=" O   GLY B 197 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 84 through 89
      removed outlier: 3.618A  pdb=" N   GLU C  87 " --> pdb=" O   LEU C  74 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   LEU C  74 " --> pdb=" O   GLU C  87 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   ILE C  89 " --> pdb=" O   VAL C  72 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   VAL C  72 " --> pdb=" O   ILE C  89 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 240 through 243
      removed outlier: 3.989A  pdb=" N   LYS C 240 " --> pdb=" O   GLN C 252 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU C 242 " --> pdb=" O   VAL C 250 " (cutoff:3.500A)
      removed outlier: 7.240A  pdb=" N   VAL C 250 " --> pdb=" O   LEU C 242 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 84 through 88
      removed outlier: 3.616A  pdb=" N   LEU D  74 " --> pdb=" O   GLU D  87 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   HIS D 114 " --> pdb=" O   TRP D  61 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LEU D  63 " --> pdb=" O   HIS D 114 " (cutoff:3.500A)
      removed outlier: 5.702A  pdb=" N   VAL D 113 " --> pdb=" O   GLU D 138 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 256 through 261
      removed outlier: 7.081A  pdb=" N   ALA D 248 " --> pdb=" O   LYS D 244 " (cutoff:3.500A)
      removed outlier: 5.243A  pdb=" N   LYS D 244 " --> pdb=" O   ALA D 248 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   VAL D 250 " --> pdb=" O   LEU D 242 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   GLN D 252 " --> pdb=" O   LYS D 240 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   LYS D 240 " --> pdb=" O   GLN D 252 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 89
      removed outlier: 3.618A  pdb=" N   GLU A  87 " --> pdb=" O   LEU A  74 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   LEU A  74 " --> pdb=" O   GLU A  87 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   ILE A  89 " --> pdb=" O   VAL A  72 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   VAL A  72 " --> pdb=" O   ILE A  89 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 240 through 243
      removed outlier: 3.989A  pdb=" N   LYS A 240 " --> pdb=" O   GLN A 252 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU A 242 " --> pdb=" O   VAL A 250 " (cutoff:3.500A)
      removed outlier: 7.240A  pdb=" N   VAL A 250 " --> pdb=" O   LEU A 242 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 84 through 88
      removed outlier: 3.616A  pdb=" N   LEU B  74 " --> pdb=" O   GLU B  87 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   HIS B 114 " --> pdb=" O   TRP B  61 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LEU B  63 " --> pdb=" O   HIS B 114 " (cutoff:3.500A)
      removed outlier: 5.702A  pdb=" N   VAL B 113 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 256 through 261
      removed outlier: 7.080A  pdb=" N   ALA B 248 " --> pdb=" O   LYS B 244 " (cutoff:3.500A)
      removed outlier: 5.243A  pdb=" N   LYS B 244 " --> pdb=" O   ALA B 248 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   VAL B 250 " --> pdb=" O   LEU B 242 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLN B 252 " --> pdb=" O   LYS B 240 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   LYS B 240 " --> pdb=" O   GLN B 252 " (cutoff:3.500A)

    517 hydrogen bonds defined for protein.
    1503 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.74

  Time building geometry restraints manager: 3.09 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3322
        1.34 -     1.46: 1183
        1.46 -     1.57: 5817
        1.57 -     1.69: 0
        1.69 -     1.81: 86
  Bond restraints: 10408
  Sorted by residual:
  bond pdb=" N   ILE A  36 "
       pdb=" CA  ILE A  36 "
    ideal  model  delta    sigma   weight residual
    1.462  1.497 -0.035 1.14e-02 7.69e+03 9.59e+00
  bond pdb=" N   ILE C  36 "
       pdb=" CA  ILE C  36 "
    ideal  model  delta    sigma   weight residual
    1.462  1.497 -0.035 1.14e-02 7.69e+03 9.32e+00
  bond pdb=" N   VAL C  37 "
       pdb=" CA  VAL C  37 "
    ideal  model  delta    sigma   weight residual
    1.462  1.497 -0.035 1.14e-02 7.69e+03 9.18e+00
  bond pdb=" N   VAL A  37 "
       pdb=" CA  VAL A  37 "
    ideal  model  delta    sigma   weight residual
    1.462  1.496 -0.034 1.14e-02 7.69e+03 9.00e+00
  bond pdb=" N   ILE C 251 "
       pdb=" CA  ILE C 251 "
    ideal  model  delta    sigma   weight residual
    1.454  1.492 -0.038 1.28e-02 6.10e+03 8.88e+00
  ... (remaining 10403 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 13610
        1.67 -     3.34: 337
        3.34 -     5.01: 45
        5.01 -     6.68: 10
        6.68 -     8.35: 2
  Bond angle restraints: 14004
  Sorted by residual:
  angle pdb=" O   GLY A 237 "
        pdb=" C   GLY A 237 "
        pdb=" N   PRO A 238 "
      ideal   model   delta    sigma   weight residual
     121.77  117.31    4.46 1.00e+00 1.00e+00 1.99e+01
  angle pdb=" O   GLY C 237 "
        pdb=" C   GLY C 237 "
        pdb=" N   PRO C 238 "
      ideal   model   delta    sigma   weight residual
     121.77  117.33    4.44 1.00e+00 1.00e+00 1.98e+01
  angle pdb=" CA  ILE A 251 "
        pdb=" C   ILE A 251 "
        pdb=" O   ILE A 251 "
      ideal   model   delta    sigma   weight residual
     121.72  118.19    3.53 9.60e-01 1.09e+00 1.35e+01
  angle pdb=" CA  ILE C 251 "
        pdb=" C   ILE C 251 "
        pdb=" O   ILE C 251 "
      ideal   model   delta    sigma   weight residual
     121.72  118.21    3.51 9.60e-01 1.09e+00 1.33e+01
  angle pdb=" CA  ILE A  36 "
        pdb=" C   ILE A  36 "
        pdb=" O   ILE A  36 "
      ideal   model   delta    sigma   weight residual
     121.27  117.55    3.72 1.04e+00 9.25e-01 1.28e+01
  ... (remaining 13999 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.30: 5649
       17.30 -    34.61: 567
       34.61 -    51.91: 104
       51.91 -    69.22: 22
       69.22 -    86.52: 6
  Dihedral angle restraints: 6348
    sinusoidal: 2628
      harmonic: 3720
  Sorted by residual:
  dihedral pdb=" CA  LYS F 407 "
           pdb=" C   LYS F 407 "
           pdb=" N   VAL F 408 "
           pdb=" CA  VAL F 408 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.00   16.00     0      5.00e+00 4.00e-02 1.02e+01
  dihedral pdb=" CA  LYS H 407 "
           pdb=" C   LYS H 407 "
           pdb=" N   VAL H 408 "
           pdb=" CA  VAL H 408 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.09   15.91     0      5.00e+00 4.00e-02 1.01e+01
  dihedral pdb=" CB  GLU A  92 "
           pdb=" CG  GLU A  92 "
           pdb=" CD  GLU A  92 "
           pdb=" OE1 GLU A  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.52  -86.52     1      3.00e+01 1.11e-03 1.00e+01
  ... (remaining 6345 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 1159
       0.043 -    0.085: 313
       0.085 -    0.128: 84
       0.128 -    0.171: 15
       0.171 -    0.213: 13
  Chirality restraints: 1584
  Sorted by residual:
  chirality pdb=" CA  LYS C 240 "
            pdb=" N   LYS C 240 "
            pdb=" C   LYS C 240 "
            pdb=" CB  LYS C 240 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.14e+00
  chirality pdb=" CA  LYS A 240 "
            pdb=" N   LYS A 240 "
            pdb=" C   LYS A 240 "
            pdb=" CB  LYS A 240 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CA  ILE C 251 "
            pdb=" N   ILE C 251 "
            pdb=" C   ILE C 251 "
            pdb=" CB  ILE C 251 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.11e+00
  ... (remaining 1581 not shown)

  Planarity restraints: 1760
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 180 "   -0.009 2.00e-02 2.50e+03   1.84e-02 3.38e+00
        pdb=" C   VAL C 180 "    0.032 2.00e-02 2.50e+03
        pdb=" O   VAL C 180 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   PHE C 181 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 180 "    0.009 2.00e-02 2.50e+03   1.83e-02 3.35e+00
        pdb=" C   VAL A 180 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   VAL A 180 "    0.012 2.00e-02 2.50e+03
        pdb=" N   PHE A 181 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO C  30 "    0.006 2.00e-02 2.50e+03   1.16e-02 1.33e+00
        pdb=" C   PRO C  30 "   -0.020 2.00e-02 2.50e+03
        pdb=" O   PRO C  30 "    0.008 2.00e-02 2.50e+03
        pdb=" N   VAL C  31 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1757 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1869
        2.77 -     3.30: 10471
        3.30 -     3.84: 16453
        3.84 -     4.37: 18473
        4.37 -     4.90: 30963
  Nonbonded interactions: 78229
  Sorted by model distance:
  nonbonded pdb=" O   GLY D 118 "
            pdb=" OG1 THR D 122 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" O   GLY B 118 "
            pdb=" OG1 THR B 122 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" O   VAL C 150 "
            pdb=" OG  SER C 153 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   VAL A 150 "
            pdb=" OG  SER A 153 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" OE2 GLU A  87 "
            pdb=" OH  TYR B  99 "
     model   vdw
     2.271 3.040
  ... (remaining 78224 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' and (resid 1 through 126 or (resid 127 through 129 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 130 through 189 or resid 196 thr \ 
ough 267))
  selection = (chain 'B' and (resid 1 through 41 or resid 56 through 193 or resid 196 through  \ 
267))
  selection = (chain 'C' and (resid 1 through 126 or (resid 127 through 129 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 130 through 189 or resid 196 thr \ 
ough 267))
  selection = (chain 'D' and (resid 1 through 41 or resid 56 through 193 or resid 196 through  \ 
267))
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.130
  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:             0.000
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     26.750
  Find NCS groups from input model:        0.460
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
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   0.046  10408  Z= 0.214
  Angle     :  0.595   8.350  14004  Z= 0.358
  Chirality :  0.046   0.213   1584
  Planarity :  0.003   0.028   1760
  Dihedral  : 14.330  86.522   3916
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  0.00 %
    Favored  : 98.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.23), residues: 1242
  helix: -0.07 (0.20), residues: 646
  sheet:  0.43 (0.43), residues: 152
  loop : -1.61 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 131 
 HIS   0.005   0.001   HIS A 171 
 PHE   0.015   0.001   PHE E 423 
 TYR   0.012   0.001   TYR A  83 
 ARG   0.003   0.000   ARG A 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.23900 (  517)
  hydrogen bonds       : angle       7.49572 ( 1503)
  covalent geometry    : bond        0.00334 (10408)
  covalent geometry    : angle       0.59507 (14004)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 242
  time to evaluate  : 1.125 
Fit side-chains
REVERT: C    9 GLN cc_start: 0.7909 (pp30) cc_final: 0.7257 (pp30)
REVERT: A    9 GLN cc_start: 0.7928 (pp30) cc_final: 0.7339 (pp30)
REVERT: A  251 ILE cc_start: 0.7697 (OUTLIER) cc_final: 0.7473 (tp)
REVERT: B  154 MET cc_start: 0.7191 (mmt) cc_final: 0.6967 (mmt)
  outliers start: 16
  outliers final: 2
  residues processed: 252
  average time/residue: 0.2576
  time to fit residues: 86.7692
Evaluate side-chains
  193 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 190
  time to evaluate  : 1.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    6.9990
   chunk 93 optimal weight:    0.9980
   chunk 52 optimal weight:    0.1980
   chunk 32 optimal weight:    1.9990
   chunk 63 optimal weight:    9.9990
   chunk 50 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   chunk 37 optimal weight:   10.0000
   chunk 59 optimal weight:    9.9990
   chunk 72 optimal weight:    7.9990
   chunk 112 optimal weight:    2.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
C 117 ASN
C 171 HIS
** D  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 117 ASN
A 171 HIS
** B  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.199473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.151310 restraints weight = 17836.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.148072 restraints weight = 19969.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.149426 restraints weight = 18492.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.3810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7170
moved from start:          0.1562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  10408  Z= 0.183
  Angle     :  0.600   5.969  14004  Z= 0.323
  Chirality :  0.044   0.154   1584
  Planarity :  0.004   0.040   1760
  Dihedral  :  3.979  17.691   1350
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  7.12 %
    Favored  : 92.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.23), residues: 1242
  helix:  0.42 (0.20), residues: 656
  sheet:  0.45 (0.40), residues: 156
  loop : -1.70 (0.27), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 131 
 HIS   0.005   0.001   HIS A 171 
 PHE   0.009   0.001   PHE G 423 
 TYR   0.019   0.001   TYR C  83 
 ARG   0.004   0.000   ARG C 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04394 (  517)
  hydrogen bonds       : angle       4.82009 ( 1503)
  covalent geometry    : bond        0.00418 (10408)
  covalent geometry    : angle       0.60001 (14004)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 239
  time to evaluate  : 1.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  371 ASN cc_start: 0.8848 (m-40) cc_final: 0.8263 (p0)
REVERT: C    9 GLN cc_start: 0.7844 (pp30) cc_final: 0.7447 (pp30)
REVERT: C   10 GLU cc_start: 0.8578 (tp30) cc_final: 0.7917 (tp30)
REVERT: C   18 ASN cc_start: 0.8238 (p0) cc_final: 0.8032 (p0)
REVERT: C  117 ASN cc_start: 0.8365 (m-40) cc_final: 0.7626 (p0)
REVERT: C  214 GLN cc_start: 0.6771 (mm-40) cc_final: 0.6386 (tm-30)
REVERT: D  242 LEU cc_start: 0.9001 (mm) cc_final: 0.8743 (mm)
REVERT: F  371 ASN cc_start: 0.8886 (m-40) cc_final: 0.8279 (p0)
REVERT: A    9 GLN cc_start: 0.7807 (pp30) cc_final: 0.7449 (pp30)
REVERT: A   10 GLU cc_start: 0.8563 (tp30) cc_final: 0.7871 (tp30)
REVERT: A   35 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8256 (mp0)
REVERT: A  117 ASN cc_start: 0.8346 (m-40) cc_final: 0.7605 (p0)
REVERT: B  242 LEU cc_start: 0.9019 (mm) cc_final: 0.8767 (mm)
  outliers start: 3
  outliers final: 0
  residues processed: 242
  average time/residue: 0.2496
  time to fit residues: 82.0589
Evaluate side-chains
  202 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 201
  time to evaluate  : 1.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 107 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 58 optimal weight:    8.9990
   chunk 82 optimal weight:    1.9990
   chunk 54 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
G 367 ASN
C  95 GLN
C 171 HIS
** D  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 367 ASN
A  95 GLN
A 171 HIS
** B  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.208805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.151916 restraints weight = 17927.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.148660 restraints weight = 13175.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.150329 restraints weight = 10308.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7323
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10408  Z= 0.124
  Angle     :  0.557   6.286  14004  Z= 0.297
  Chirality :  0.042   0.137   1584
  Planarity :  0.003   0.029   1760
  Dihedral  :  3.971  16.857   1350
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  2.79 %
    Favored  : 96.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.23), residues: 1242
  helix:  0.58 (0.20), residues: 668
  sheet:  0.61 (0.40), residues: 156
  loop : -1.63 (0.28), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 131 
 HIS   0.003   0.001   HIS B  78 
 PHE   0.013   0.001   PHE A 181 
 TYR   0.006   0.001   TYR C  83 
 ARG   0.003   0.000   ARG C 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03729 (  517)
  hydrogen bonds       : angle       4.49491 ( 1503)
  covalent geometry    : bond        0.00280 (10408)
  covalent geometry    : angle       0.55719 (14004)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 236
  time to evaluate  : 1.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  348 MET cc_start: 0.5583 (ttt) cc_final: 0.4640 (tmm)
REVERT: C    9 GLN cc_start: 0.7733 (pp30) cc_final: 0.7349 (pp30)
REVERT: C   10 GLU cc_start: 0.8563 (tp30) cc_final: 0.7989 (tp30)
REVERT: C   96 GLU cc_start: 0.8639 (pp20) cc_final: 0.8317 (pp20)
REVERT: C  117 ASN cc_start: 0.8172 (m-40) cc_final: 0.7461 (p0)
REVERT: D  178 MET cc_start: 0.8430 (ttm) cc_final: 0.8056 (ttm)
REVERT: F  348 MET cc_start: 0.5401 (ttt) cc_final: 0.4532 (tmm)
REVERT: A   11 GLU cc_start: 0.8482 (tp30) cc_final: 0.8091 (tp30)
REVERT: A   96 GLU cc_start: 0.8614 (pp20) cc_final: 0.8296 (pp20)
REVERT: A  117 ASN cc_start: 0.8201 (m-40) cc_final: 0.7486 (p0)
REVERT: B   22 MET cc_start: 0.6359 (ptt) cc_final: 0.5610 (ppp)
REVERT: B  178 MET cc_start: 0.8470 (ttm) cc_final: 0.8131 (ttm)
  outliers start: 5
  outliers final: 1
  residues processed: 241
  average time/residue: 0.2593
  time to fit residues: 84.5994
Evaluate side-chains
  193 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 192
  time to evaluate  : 1.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 86 optimal weight:    9.9990
   chunk 53 optimal weight:    0.4980
   chunk 60 optimal weight:    2.9990
   chunk 115 optimal weight:    0.0970
   chunk 106 optimal weight:    0.6980
   chunk 40 optimal weight:   20.0000
   chunk 107 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 89 optimal weight:    0.1980
   chunk 100 optimal weight:    7.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
G 367 ASN
C  95 GLN
** D  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 367 ASN
A  95 GLN
** B  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.211171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.166176 restraints weight = 17611.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.164327 restraints weight = 20836.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.166087 restraints weight = 18727.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.4054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7027
moved from start:          0.2159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  10408  Z= 0.106
  Angle     :  0.542   6.827  14004  Z= 0.283
  Chirality :  0.042   0.130   1584
  Planarity :  0.003   0.030   1760
  Dihedral  :  3.893  16.259   1350
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  3.42 %
    Favored  : 96.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.23), residues: 1242
  helix:  0.75 (0.20), residues: 676
  sheet:  0.84 (0.41), residues: 156
  loop : -1.60 (0.29), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C 131 
 HIS   0.002   0.001   HIS B  78 
 PHE   0.019   0.001   PHE G 423 
 TYR   0.011   0.001   TYR C  15 
 ARG   0.003   0.000   ARG B  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03169 (  517)
  hydrogen bonds       : angle       4.22508 ( 1503)
  covalent geometry    : bond        0.00233 (10408)
  covalent geometry    : angle       0.54203 (14004)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 240
  time to evaluate  : 1.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  348 MET cc_start: 0.5603 (ttt) cc_final: 0.4574 (tmm)
REVERT: H  373 CYS cc_start: 0.8068 (m) cc_final: 0.7852 (m)
REVERT: C   11 GLU cc_start: 0.8457 (tp30) cc_final: 0.8051 (tp30)
REVERT: C   15 TYR cc_start: 0.7731 (m-10) cc_final: 0.7471 (m-10)
REVERT: C   96 GLU cc_start: 0.8657 (pp20) cc_final: 0.8453 (pp20)
REVERT: D  266 LYS cc_start: 0.5761 (mtmt) cc_final: 0.5212 (mmtt)
REVERT: E  348 MET cc_start: 0.7369 (tpt) cc_final: 0.7126 (tpp)
REVERT: F  348 MET cc_start: 0.5502 (ttt) cc_final: 0.4562 (tmm)
REVERT: A    9 GLN cc_start: 0.7775 (pp30) cc_final: 0.7384 (pp30)
REVERT: A   10 GLU cc_start: 0.8403 (tp30) cc_final: 0.8186 (tp30)
REVERT: A   11 GLU cc_start: 0.8467 (tp30) cc_final: 0.8209 (tp30)
REVERT: B   15 TYR cc_start: 0.7552 (m-10) cc_final: 0.7302 (m-10)
REVERT: B   22 MET cc_start: 0.5549 (ptt) cc_final: 0.5176 (ppp)
REVERT: B  266 LYS cc_start: 0.5579 (mtmt) cc_final: 0.5058 (tptp)
  outliers start: 4
  outliers final: 0
  residues processed: 244
  average time/residue: 0.2476
  time to fit residues: 82.1106
Evaluate side-chains
  206 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 1.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 67 optimal weight:    6.9990
   chunk 92 optimal weight:    0.0070
   chunk 109 optimal weight:    1.9990
   chunk 55 optimal weight:    0.4980
   chunk 82 optimal weight:    0.9980
   chunk 23 optimal weight:    0.3980
   chunk 93 optimal weight:    0.7980
   chunk 43 optimal weight:    0.0070
   chunk 16 optimal weight:    0.0870
   chunk 50 optimal weight:    2.9990
   chunk 91 optimal weight:    0.6980
   overall best weight:    0.1994

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

Flipped N/Q/H residues before XYZ refinement:
C  95 GLN
C 117 ASN
** D  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  95 GLN
A 117 ASN
** B  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4546 r_free = 0.4546 target = 0.213083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.165415 restraints weight = 17660.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.162824 restraints weight = 18366.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.164641 restraints weight = 17635.013|
|-----------------------------------------------------------------------------|
r_work (final): 0.4043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7031
moved from start:          0.2345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10408  Z= 0.102
  Angle     :  0.545   6.713  14004  Z= 0.285
  Chirality :  0.042   0.140   1584
  Planarity :  0.003   0.036   1760
  Dihedral  :  3.887  15.451   1350
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  2.88 %
    Favored  : 96.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.23), residues: 1242
  helix:  0.81 (0.20), residues: 678
  sheet:  0.74 (0.41), residues: 160
  loop : -1.51 (0.29), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 131 
 HIS   0.003   0.001   HIS D  12 
 PHE   0.015   0.001   PHE E 406 
 TYR   0.006   0.001   TYR C  15 
 ARG   0.003   0.000   ARG B 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03044 (  517)
  hydrogen bonds       : angle       4.16735 ( 1503)
  covalent geometry    : bond        0.00216 (10408)
  covalent geometry    : angle       0.54489 (14004)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 262
  time to evaluate  : 1.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  348 MET cc_start: 0.5595 (ttt) cc_final: 0.5380 (ttm)
REVERT: H  371 ASN cc_start: 0.8951 (m-40) cc_final: 0.8303 (p0)
REVERT: C    6 ASP cc_start: 0.7169 (m-30) cc_final: 0.6543 (t70)
REVERT: C   10 GLU cc_start: 0.8446 (tp30) cc_final: 0.8227 (tp30)
REVERT: C   11 GLU cc_start: 0.8535 (tp30) cc_final: 0.8225 (tp30)
REVERT: C   15 TYR cc_start: 0.7635 (m-10) cc_final: 0.7373 (m-10)
REVERT: C   64 ASP cc_start: 0.7838 (t0) cc_final: 0.7480 (t70)
REVERT: C  117 ASN cc_start: 0.8141 (m-40) cc_final: 0.7516 (p0)
REVERT: C  154 MET cc_start: 0.7395 (tpt) cc_final: 0.7061 (tpt)
REVERT: C  229 ASP cc_start: 0.6381 (t0) cc_final: 0.6148 (t0)
REVERT: D   15 TYR cc_start: 0.7506 (m-10) cc_final: 0.7285 (m-10)
REVERT: D  178 MET cc_start: 0.8929 (ttm) cc_final: 0.8224 (ttm)
REVERT: D  266 LYS cc_start: 0.5845 (mtmt) cc_final: 0.5287 (mmtt)
REVERT: E  348 MET cc_start: 0.7440 (tpt) cc_final: 0.7176 (tpp)
REVERT: F  348 MET cc_start: 0.5571 (ttt) cc_final: 0.4558 (tmm)
REVERT: F  371 ASN cc_start: 0.8938 (m-40) cc_final: 0.8277 (p0)
REVERT: A    6 ASP cc_start: 0.7103 (m-30) cc_final: 0.6498 (t70)
REVERT: A   10 GLU cc_start: 0.8448 (tp30) cc_final: 0.8141 (tp30)
REVERT: A   11 GLU cc_start: 0.8567 (tp30) cc_final: 0.8216 (tp30)
REVERT: A   15 TYR cc_start: 0.7609 (m-10) cc_final: 0.7288 (m-10)
REVERT: A   31 VAL cc_start: 0.8804 (p) cc_final: 0.8511 (m)
REVERT: A   64 ASP cc_start: 0.7842 (t0) cc_final: 0.7470 (t70)
REVERT: A  117 ASN cc_start: 0.8132 (m-40) cc_final: 0.7502 (p0)
REVERT: A  154 MET cc_start: 0.7377 (tpt) cc_final: 0.7059 (tpt)
REVERT: B   15 TYR cc_start: 0.7550 (m-10) cc_final: 0.7234 (m-10)
REVERT: B   22 MET cc_start: 0.5793 (ptt) cc_final: 0.5359 (ppp)
REVERT: B  178 MET cc_start: 0.8923 (ttm) cc_final: 0.8219 (ttm)
REVERT: B  266 LYS cc_start: 0.5685 (mtmt) cc_final: 0.5121 (mmtt)
  outliers start: 2
  outliers final: 1
  residues processed: 264
  average time/residue: 0.2337
  time to fit residues: 84.1250
Evaluate side-chains
  210 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 209
  time to evaluate  : 1.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 38 optimal weight:    0.3980
   chunk 44 optimal weight:    0.5980
   chunk 101 optimal weight:    1.9990
   chunk 114 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 27 optimal weight:    4.9990
   chunk 97 optimal weight:    2.9990
   chunk 79 optimal weight:    8.9990
   chunk 111 optimal weight:    5.9990
   chunk 108 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
H 393 HIS
** D  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.211644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.153554 restraints weight = 17859.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.151315 restraints weight = 11731.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.152669 restraints weight = 10010.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.2446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10408  Z= 0.119
  Angle     :  0.561   7.000  14004  Z= 0.294
  Chirality :  0.042   0.130   1584
  Planarity :  0.003   0.037   1760
  Dihedral  :  3.863  16.450   1350
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.24), residues: 1242
  helix:  0.79 (0.20), residues: 678
  sheet:  0.76 (0.42), residues: 160
  loop : -1.52 (0.29), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 131 
 HIS   0.002   0.001   HIS A  12 
 PHE   0.017   0.001   PHE G 406 
 TYR   0.008   0.001   TYR A  83 
 ARG   0.003   0.000   ARG B 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03084 (  517)
  hydrogen bonds       : angle       4.07123 ( 1503)
  covalent geometry    : bond        0.00277 (10408)
  covalent geometry    : angle       0.56121 (14004)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 260
  time to evaluate  : 1.104 
Fit side-chains
   revert: symmetry clash
REVERT: H  348 MET cc_start: 0.5751 (ttt) cc_final: 0.5320 (ttm)
REVERT: H  395 GLU cc_start: 0.8076 (tp30) cc_final: 0.7861 (tp30)
REVERT: C    6 ASP cc_start: 0.7183 (m-30) cc_final: 0.6657 (t70)
REVERT: C   11 GLU cc_start: 0.8654 (tp30) cc_final: 0.8263 (tp30)
REVERT: C   15 TYR cc_start: 0.7570 (m-10) cc_final: 0.7306 (m-10)
REVERT: C   96 GLU cc_start: 0.8766 (pp20) cc_final: 0.8549 (pp20)
REVERT: C  117 ASN cc_start: 0.8177 (m-40) cc_final: 0.7489 (p0)
REVERT: D   15 TYR cc_start: 0.7685 (m-10) cc_final: 0.7391 (m-10)
REVERT: D  242 LEU cc_start: 0.8859 (mm) cc_final: 0.8576 (mt)
REVERT: D  266 LYS cc_start: 0.6027 (mtmt) cc_final: 0.5368 (mmtt)
REVERT: E  348 MET cc_start: 0.7481 (tpt) cc_final: 0.7262 (tpp)
REVERT: A    9 GLN cc_start: 0.7673 (pp30) cc_final: 0.7383 (pp30)
REVERT: A   11 GLU cc_start: 0.8583 (tp30) cc_final: 0.8216 (tp30)
REVERT: A  117 ASN cc_start: 0.8177 (m-40) cc_final: 0.7412 (p0)
REVERT: B   15 TYR cc_start: 0.7683 (m-10) cc_final: 0.7347 (m-10)
REVERT: B   22 MET cc_start: 0.6262 (ptt) cc_final: 0.5604 (ppp)
REVERT: B  242 LEU cc_start: 0.8896 (mm) cc_final: 0.8627 (mt)
REVERT: B  266 LYS cc_start: 0.5913 (mtmt) cc_final: 0.5252 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 260
  average time/residue: 0.2401
  time to fit residues: 86.1256
Evaluate side-chains
  202 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 43 optimal weight:    0.4980
   chunk 29 optimal weight:    0.5980
   chunk 17 optimal weight:    7.9990
   chunk 120 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 108 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 57 optimal weight:    0.0170
   chunk 19 optimal weight:    2.9990
   chunk 91 optimal weight:    0.7980
   chunk 60 optimal weight:    3.9990
   overall best weight:    0.5818

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

Flipped N/Q/H residues before XYZ refinement:
H 393 HIS
C  95 GLN
** D  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  95 GLN
** B  18 ASN ** 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 = 0.4538 r_free = 0.4538 target = 0.212389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.146578 restraints weight = 18028.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.150282 restraints weight = 11241.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.152888 restraints weight = 8693.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.3891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
moved from start:          0.2542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10408  Z= 0.114
  Angle     :  0.575   7.214  14004  Z= 0.300
  Chirality :  0.043   0.129   1584
  Planarity :  0.003   0.036   1760
  Dihedral  :  3.875  18.070   1350
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.53 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.23), residues: 1242
  helix:  0.77 (0.20), residues: 678
  sheet:  0.77 (0.43), residues: 160
  loop : -1.51 (0.29), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 131 
 HIS   0.002   0.001   HIS F 393 
 PHE   0.016   0.001   PHE E 423 
 TYR   0.006   0.001   TYR C  83 
 ARG   0.003   0.000   ARG B 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03017 (  517)
  hydrogen bonds       : angle       4.08659 ( 1503)
  covalent geometry    : bond        0.00259 (10408)
  covalent geometry    : angle       0.57543 (14004)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 255
  time to evaluate  : 1.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  348 MET cc_start: 0.5839 (ttt) cc_final: 0.5344 (ttm)
REVERT: H  360 LYS cc_start: 0.8707 (tptt) cc_final: 0.8446 (ptmt)
REVERT: H  371 ASN cc_start: 0.8929 (m-40) cc_final: 0.8287 (p0)
REVERT: H  395 GLU cc_start: 0.8118 (tp30) cc_final: 0.7897 (tp30)
REVERT: C   11 GLU cc_start: 0.8592 (tp30) cc_final: 0.8231 (tp30)
REVERT: C  117 ASN cc_start: 0.8072 (m-40) cc_final: 0.7329 (p0)
REVERT: D   15 TYR cc_start: 0.7629 (m-10) cc_final: 0.7325 (m-10)
REVERT: D   22 MET cc_start: 0.6080 (ppp) cc_final: 0.5605 (ptt)
REVERT: D  266 LYS cc_start: 0.5825 (mtmt) cc_final: 0.5290 (mmtt)
REVERT: E  348 MET cc_start: 0.7461 (tpt) cc_final: 0.7227 (tpp)
REVERT: F  360 LYS cc_start: 0.8747 (tptt) cc_final: 0.8353 (ptmt)
REVERT: F  371 ASN cc_start: 0.8924 (m-40) cc_final: 0.8273 (p0)
REVERT: A   11 GLU cc_start: 0.8512 (tp30) cc_final: 0.8120 (tp30)
REVERT: A   64 ASP cc_start: 0.7742 (t0) cc_final: 0.7480 (t0)
REVERT: A  117 ASN cc_start: 0.8049 (m-40) cc_final: 0.7375 (p0)
REVERT: B   15 TYR cc_start: 0.7628 (m-10) cc_final: 0.7289 (m-10)
REVERT: B   22 MET cc_start: 0.6039 (ptt) cc_final: 0.5446 (ppp)
REVERT: B  266 LYS cc_start: 0.5756 (mtmt) cc_final: 0.5198 (mmtt)
  outliers start: 2
  outliers final: 1
  residues processed: 257
  average time/residue: 0.2331
  time to fit residues: 82.1814
Evaluate side-chains
  209 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 208
  time to evaluate  : 1.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 114 optimal weight:    0.8980
   chunk 91 optimal weight:    0.6980
   chunk 85 optimal weight:    0.0040
   chunk 98 optimal weight:    2.9990
   chunk 54 optimal weight:    0.5980
   chunk 89 optimal weight:    3.9990
   chunk 59 optimal weight:    6.9990
   chunk 123 optimal weight:    0.7980
   overall best weight:    0.5592

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

Flipped N/Q/H residues before XYZ refinement:
H 393 HIS
** C  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.212446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.166295 restraints weight = 18030.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.164777 restraints weight = 19058.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.166404 restraints weight = 18249.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.4059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7022
moved from start:          0.2675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10408  Z= 0.118
  Angle     :  0.598   7.327  14004  Z= 0.312
  Chirality :  0.043   0.195   1584
  Planarity :  0.003   0.034   1760
  Dihedral  :  3.879  17.662   1350
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.00 (0.23), residues: 1242
  helix:  0.73 (0.20), residues: 678
  sheet:  0.77 (0.43), residues: 160
  loop : -1.53 (0.28), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 131 
 HIS   0.002   0.001   HIS B  78 
 PHE   0.017   0.001   PHE G 406 
 TYR   0.007   0.001   TYR A  99 
 ARG   0.004   0.000   ARG B 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03085 (  517)
  hydrogen bonds       : angle       4.15078 ( 1503)
  covalent geometry    : bond        0.00275 (10408)
  covalent geometry    : angle       0.59839 (14004)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 245
  time to evaluate  : 1.102 
Fit side-chains
REVERT: H  348 MET cc_start: 0.5941 (ttt) cc_final: 0.5371 (ttm)
REVERT: H  360 LYS cc_start: 0.8648 (tptt) cc_final: 0.8424 (ptmt)
REVERT: C   11 GLU cc_start: 0.8519 (tp30) cc_final: 0.8104 (tp30)
REVERT: C   15 TYR cc_start: 0.7643 (m-10) cc_final: 0.7323 (m-10)
REVERT: D   15 TYR cc_start: 0.7470 (m-10) cc_final: 0.7200 (m-10)
REVERT: D   22 MET cc_start: 0.5809 (ppp) cc_final: 0.5365 (ptt)
REVERT: D  266 LYS cc_start: 0.5787 (mtmt) cc_final: 0.5373 (tmtt)
REVERT: E  348 MET cc_start: 0.7232 (tpt) cc_final: 0.7016 (tpp)
REVERT: F  348 MET cc_start: 0.6506 (ttt) cc_final: 0.6196 (ttm)
REVERT: F  360 LYS cc_start: 0.8690 (tptt) cc_final: 0.8374 (ptmt)
REVERT: A    9 GLN cc_start: 0.7724 (pp30) cc_final: 0.7472 (pp30)
REVERT: A   15 TYR cc_start: 0.7576 (m-10) cc_final: 0.7358 (m-10)
REVERT: A   64 ASP cc_start: 0.7856 (t0) cc_final: 0.7649 (t0)
REVERT: B   15 TYR cc_start: 0.7509 (m-10) cc_final: 0.7228 (m-10)
REVERT: B   22 MET cc_start: 0.5700 (ptt) cc_final: 0.5139 (ppp)
REVERT: B   87 GLU cc_start: 0.8442 (tp30) cc_final: 0.8154 (mm-30)
REVERT: B  242 LEU cc_start: 0.8903 (mt) cc_final: 0.8551 (mp)
REVERT: B  266 LYS cc_start: 0.5733 (mtmt) cc_final: 0.5209 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 245
  average time/residue: 0.2210
  time to fit residues: 74.9117
Evaluate side-chains
  194 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 1.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   chunk 113 optimal weight:    0.0870
   chunk 9 optimal weight:   10.0000
   chunk 55 optimal weight:    0.7980
   chunk 4 optimal weight:    8.9990
   chunk 88 optimal weight:    0.2980
   chunk 117 optimal weight:    0.8980
   chunk 75 optimal weight:    3.9990
   chunk 51 optimal weight:    0.5980
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
** C  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 117 ASN
** D  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 393 HIS
** A  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 117 ASN
** B  18 ASN ** 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 = 0.4535 r_free = 0.4535 target = 0.212008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.156078 restraints weight = 17932.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.153272 restraints weight = 13351.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.154403 restraints weight = 10675.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7234
moved from start:          0.2700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10408  Z= 0.116
  Angle     :  0.604   7.671  14004  Z= 0.313
  Chirality :  0.044   0.174   1584
  Planarity :  0.003   0.039   1760
  Dihedral  :  3.871  17.236   1350
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.23), residues: 1242
  helix:  0.70 (0.20), residues: 672
  sheet:  0.68 (0.43), residues: 160
  loop : -1.45 (0.28), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 131 
 HIS   0.005   0.001   HIS F 393 
 PHE   0.017   0.001   PHE G 423 
 TYR   0.006   0.001   TYR C  83 
 ARG   0.005   0.000   ARG B 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03132 (  517)
  hydrogen bonds       : angle       4.13505 ( 1503)
  covalent geometry    : bond        0.00267 (10408)
  covalent geometry    : angle       0.60394 (14004)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 1.153 
Fit side-chains
REVERT: H  348 MET cc_start: 0.5926 (ttt) cc_final: 0.5422 (ttm)
REVERT: H  360 LYS cc_start: 0.8774 (tptt) cc_final: 0.8468 (ptmt)
REVERT: H  371 ASN cc_start: 0.8917 (m-40) cc_final: 0.8202 (p0)
REVERT: C  117 ASN cc_start: 0.8157 (m-40) cc_final: 0.7350 (p0)
REVERT: C  165 VAL cc_start: 0.9693 (m) cc_final: 0.9429 (t)
REVERT: D   15 TYR cc_start: 0.7665 (m-10) cc_final: 0.7318 (m-10)
REVERT: D   22 MET cc_start: 0.6198 (ppp) cc_final: 0.5753 (ptt)
REVERT: D  266 LYS cc_start: 0.5911 (mtmt) cc_final: 0.5414 (tmtt)
REVERT: F  348 MET cc_start: 0.6346 (ttt) cc_final: 0.6114 (ttm)
REVERT: F  360 LYS cc_start: 0.8660 (tptt) cc_final: 0.8303 (ptmt)
REVERT: F  371 ASN cc_start: 0.8922 (m-40) cc_final: 0.8297 (p0)
REVERT: A  117 ASN cc_start: 0.8153 (m-40) cc_final: 0.7426 (p0)
REVERT: B   15 TYR cc_start: 0.7643 (m-10) cc_final: 0.7314 (m-10)
REVERT: B   22 MET cc_start: 0.6215 (ptt) cc_final: 0.5499 (ppp)
REVERT: B   87 GLU cc_start: 0.8446 (tp30) cc_final: 0.8228 (mm-30)
REVERT: B  266 LYS cc_start: 0.5798 (mtmt) cc_final: 0.5201 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 240
  average time/residue: 0.2287
  time to fit residues: 76.5843
Evaluate side-chains
  196 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 23 optimal weight:    0.0470
   chunk 95 optimal weight:    0.5980
   chunk 4 optimal weight:    7.9990
   chunk 122 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 14 optimal weight:    5.9990
   chunk 104 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   chunk 1 optimal weight:    0.0050
   chunk 97 optimal weight:   20.0000
   overall best weight:    0.7094

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

Flipped N/Q/H residues before XYZ refinement:
** C  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 389 GLN
** A  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4533 r_free = 0.4533 target = 0.211841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.155454 restraints weight = 18477.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.158879 restraints weight = 15471.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.159317 restraints weight = 9593.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7192
moved from start:          0.2829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10408  Z= 0.124
  Angle     :  0.606   7.903  14004  Z= 0.315
  Chirality :  0.044   0.155   1584
  Planarity :  0.003   0.038   1760
  Dihedral  :  3.876  17.862   1350
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.23), residues: 1242
  helix:  0.72 (0.20), residues: 672
  sheet:  0.70 (0.43), residues: 160
  loop : -1.46 (0.28), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 132 
 HIS   0.002   0.001   HIS D  78 
 PHE   0.010   0.001   PHE A 181 
 TYR   0.008   0.001   TYR C  83 
 ARG   0.002   0.000   ARG A 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03116 (  517)
  hydrogen bonds       : angle       4.10718 ( 1503)
  covalent geometry    : bond        0.00293 (10408)
  covalent geometry    : angle       0.60628 (14004)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 1.072 
Fit side-chains
REVERT: H  348 MET cc_start: 0.5966 (ttt) cc_final: 0.5421 (ttm)
REVERT: H  360 LYS cc_start: 0.8720 (tptt) cc_final: 0.8473 (ptmt)
REVERT: H  361 ASN cc_start: 0.8822 (m-40) cc_final: 0.8456 (m-40)
REVERT: C  117 ASN cc_start: 0.7941 (m-40) cc_final: 0.7137 (p0)
REVERT: C  165 VAL cc_start: 0.9657 (m) cc_final: 0.9432 (t)
REVERT: D   15 TYR cc_start: 0.7583 (m-10) cc_final: 0.7301 (m-10)
REVERT: D   22 MET cc_start: 0.5772 (ppp) cc_final: 0.5349 (ptt)
REVERT: D  266 LYS cc_start: 0.5782 (mtmt) cc_final: 0.5362 (tmtt)
REVERT: F  348 MET cc_start: 0.6397 (ttt) cc_final: 0.6097 (ttm)
REVERT: F  360 LYS cc_start: 0.8662 (tptt) cc_final: 0.8394 (ptmt)
REVERT: A   11 GLU cc_start: 0.8540 (tp30) cc_final: 0.8098 (tp30)
REVERT: B   15 TYR cc_start: 0.7575 (m-10) cc_final: 0.7301 (m-10)
REVERT: B   22 MET cc_start: 0.5715 (ptt) cc_final: 0.5127 (ppp)
REVERT: B   87 GLU cc_start: 0.8380 (tp30) cc_final: 0.8125 (mm-30)
REVERT: B  266 LYS cc_start: 0.5608 (mtmt) cc_final: 0.5121 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 237
  average time/residue: 0.2209
  time to fit residues: 72.4825
Evaluate side-chains
  195 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 1.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 119 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 107 optimal weight:    0.7980
   chunk 59 optimal weight:    6.9990
   chunk 68 optimal weight:    0.7980
   chunk 76 optimal weight:    8.9990
   chunk 99 optimal weight:    0.9980
   chunk 55 optimal weight:    0.2980
   chunk 61 optimal weight:    0.8980
   chunk 40 optimal weight:    5.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** C  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 393 HIS
** A  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 117 ASN
** B  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4532 r_free = 0.4532 target = 0.211673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.167079 restraints weight = 17991.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.165243 restraints weight = 21377.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.166846 restraints weight = 19510.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.4047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
moved from start:          0.2828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10408  Z= 0.123
  Angle     :  0.599   7.893  14004  Z= 0.312
  Chirality :  0.044   0.154   1584
  Planarity :  0.003   0.037   1760
  Dihedral  :  3.911  17.008   1350
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.63 %
    Favored  : 99.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.23), residues: 1242
  helix:  0.72 (0.20), residues: 672
  sheet:  0.66 (0.43), residues: 160
  loop : -1.45 (0.29), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 132 
 HIS   0.002   0.001   HIS D  78 
 PHE   0.022   0.001   PHE G 406 
 TYR   0.008   0.001   TYR A  83 
 ARG   0.002   0.000   ARG A 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03028 (  517)
  hydrogen bonds       : angle       4.08501 ( 1503)
  covalent geometry    : bond        0.00294 (10408)
  covalent geometry    : angle       0.59919 (14004)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3572.80 seconds
wall clock time: 62 minutes 45.95 seconds (3765.95 seconds total)