Starting phenix.real_space_refine
on Wed Jul 30 00:01:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7u23_26306/07_2025/7u23_26306.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7u23_26306/07_2025/7u23_26306.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7u23_26306/07_2025/7u23_26306.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7u23_26306/07_2025/7u23_26306.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7u23_26306/07_2025/7u23_26306.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7u23_26306/07_2025/7u23_26306.cif"
  }
  resolution = 4.6
  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=   0.013
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      98      5.16       5
     C    7375      2.51       5
     N    2039      2.21       5
     O    2176      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 96 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11688
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "E"
      Number of atoms: 5380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 669, 5380
          Classifications: {'peptide': 669}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 633}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "F"
      Number of atoms: 5380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 669, 5380
          Classifications: {'peptide': 669}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 633}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 464
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 464
          Classifications: {'peptide': 62}
          Link IDs: {'PTRANS': 3, 'TRANS': 58}
    Chain: "D"
      Number of atoms: 464
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 464
          Classifications: {'peptide': 62}
          Link IDs: {'PTRANS': 3, 'TRANS': 58}
  Time building chain proxies: 7.68, per 1000 atoms: 0.66
  Number of scatterers: 11688
  At special positions: 0
  Unit cell: (107.06, 126.14, 149.46, 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      98     16.00
     O    2176      8.00
     N    2039      7.00
     C    7375      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=38, symmetry=0
    Simple disulfide: pdb=" SG  CYS E   3 " - pdb=" SG  CYS E  22 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 120 " - pdb=" SG  CYS E 148 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 152 " - pdb=" SG  CYS E 175 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 162 " - pdb=" SG  CYS E 181 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 185 " - pdb=" SG  CYS E 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 189 " - pdb=" SG  CYS E 200 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 201 " - pdb=" SG  CYS E 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 205 " - pdb=" SG  CYS E 218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 221 " - pdb=" SG  CYS E 230 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 234 " - pdb=" SG  CYS E 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 252 " - pdb=" SG  CYS E 273 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 277 " - pdb=" SG  CYS E 291 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 294 " - pdb=" SG  CYS E 298 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 302 " - pdb=" SG  CYS E 323 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 425 " - pdb=" SG  CYS E 458 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 776 " - pdb=" SG  CYS E 785 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F   3 " - pdb=" SG  CYS F  22 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 120 " - pdb=" SG  CYS F 148 " distance=2.02
    Simple disulfide: pdb=" SG  CYS F 152 " - pdb=" SG  CYS F 175 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 162 " - pdb=" SG  CYS F 181 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 185 " - pdb=" SG  CYS F 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 189 " - pdb=" SG  CYS F 200 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 201 " - pdb=" SG  CYS F 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 205 " - pdb=" SG  CYS F 218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 221 " - pdb=" SG  CYS F 230 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 234 " - pdb=" SG  CYS F 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 252 " - pdb=" SG  CYS F 273 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 277 " - pdb=" SG  CYS F 291 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 294 " - pdb=" SG  CYS F 298 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 302 " - pdb=" SG  CYS F 323 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 425 " - pdb=" SG  CYS F 458 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 776 " - pdb=" SG  CYS F 785 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C   7 " - pdb=" SG  CYS C  47 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  19 " - pdb=" SG  CYS C  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  46 " - pdb=" SG  CYS C  52 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D   7 " - pdb=" SG  CYS D  47 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  19 " - pdb=" SG  CYS D  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  46 " - pdb=" SG  CYS D  52 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.26
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2764

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 28 sheets defined
      15.6% alpha, 26.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.16
  Creating SS restraints...
    Processing helix  chain 'E' and resid 13 through 20
    Processing helix  chain 'E' and resid 65 through 69
    Processing helix  chain 'E' and resid 126 through 130
    Processing helix  chain 'E' and resid 133 through 137
    Processing helix  chain 'E' and resid 144 through 148
    Processing helix  chain 'E' and resid 249 through 253
    Processing helix  chain 'E' and resid 315 through 321
      removed outlier: 3.748A  pdb=" N   MET E 319 " --> pdb=" O   SER E 316 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 340 through 349
    Processing helix  chain 'E' and resid 425 through 437
      removed outlier: 3.783A  pdb=" N   ILE E 429 " --> pdb=" O   CYS E 425 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   GLU E 434 " --> pdb=" O   TYR E 430 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   VAL E 435 " --> pdb=" O   ARG E 431 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 685 through 701
      removed outlier: 3.760A  pdb=" N   PHE E 701 " --> pdb=" O   HIS E 697 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 779 through 784
    Processing helix  chain 'F' and resid 13 through 20
    Processing helix  chain 'F' and resid 65 through 69
    Processing helix  chain 'F' and resid 144 through 148
    Processing helix  chain 'F' and resid 249 through 253
    Processing helix  chain 'F' and resid 315 through 321
      removed outlier: 3.756A  pdb=" N   MET F 319 " --> pdb=" O   SER F 316 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 340 through 348
      removed outlier: 3.533A  pdb=" N   GLU F 345 " --> pdb=" O   ALA F 341 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ASN F 346 " --> pdb=" O   SER F 342 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 349 through 351
      No H-bonds generated for 'chain 'F' and resid 349 through 351'
    Processing helix  chain 'F' and resid 425 through 437
      removed outlier: 3.865A  pdb=" N   ILE F 429 " --> pdb=" O   CYS F 425 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   GLU F 434 " --> pdb=" O   TYR F 430 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   VAL F 435 " --> pdb=" O   ARG F 431 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 684 through 701
      removed outlier: 3.736A  pdb=" N   PHE F 701 " --> pdb=" O   HIS F 697 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 779 through 782
    Processing helix  chain 'C' and resid 7 through 20
      removed outlier: 3.572A  pdb=" N   VAL C  12 " --> pdb=" O   SER C   8 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 41 through 48
    Processing helix  chain 'C' and resid 53 through 61
    Processing helix  chain 'D' and resid 7 through 20
    Processing helix  chain 'D' and resid 21 through 23
      No H-bonds generated for 'chain 'D' and resid 21 through 23'
    Processing helix  chain 'D' and resid 41 through 48
      removed outlier: 3.717A  pdb=" N   CYS D  47 " --> pdb=" O   ALA D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 53 through 61
    Processing sheet with id=AA1, first strand: chain 'E' and resid 2 through 3
    Processing sheet with id=AA2, first strand: chain 'E' and resid 7 through 10
      removed outlier: 6.285A  pdb=" N   LEU E  29 " --> pdb=" O   LEU E  56 " (cutoff:3.500A)
      removed outlier: 7.913A  pdb=" N   PHE E  58 " --> pdb=" O   LEU E  29 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   ILE E  31 " --> pdb=" O   PHE E  58 " (cutoff:3.500A)
      removed outlier: 5.565A  pdb=" N   VAL E  60 " --> pdb=" O   ILE E  31 " (cutoff:3.500A)
      removed outlier: 7.474A  pdb=" N   LEU E  33 " --> pdb=" O   VAL E  60 " (cutoff:3.500A)
      removed outlier: 4.813A  pdb=" N   TYR E  85 " --> pdb=" O   ALA E 110 " (cutoff:3.500A)
      removed outlier: 7.440A  pdb=" N   ARG E 112 " --> pdb=" O   TYR E  85 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   LEU E  87 " --> pdb=" O   ARG E 112 " (cutoff:3.500A)
      removed outlier: 7.669A  pdb=" N   GLU E 114 " --> pdb=" O   LEU E  87 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   ILE E  89 " --> pdb=" O   GLU E 114 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   ILE E 111 " --> pdb=" O   TYR E 138 " (cutoff:3.500A)
      removed outlier: 7.667A  pdb=" N   VAL E 140 " --> pdb=" O   ILE E 111 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   ILE E 113 " --> pdb=" O   VAL E 140 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 164 through 167
      removed outlier: 3.724A  pdb=" N   THR E 165 " --> pdb=" O   ASN E 172 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 205 through 209
      removed outlier: 5.783A  pdb=" N   LEU E 206 " --> pdb=" O   CYS E 221 " (cutoff:3.500A)
      removed outlier: 4.992A  pdb=" N   CYS E 221 " --> pdb=" O   LEU E 206 " (cutoff:3.500A)
      removed outlier: 7.185A  pdb=" N   SER E 208 " --> pdb=" O   VAL E 219 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   VAL E 219 " --> pdb=" O   SER E 208 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'E' and resid 224 through 226
    Processing sheet with id=AA6, first strand: chain 'E' and resid 245 through 248
      removed outlier: 3.840A  pdb=" N   ARG E 245 " --> pdb=" O   PHE E 241 " (cutoff:3.500A)
      removed outlier: 7.832A  pdb=" N   CYS E 273 " --> pdb=" O   THR E 238 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   ARG E 240 " --> pdb=" O   CYS E 273 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 282 through 283
    Processing sheet with id=AA8, first strand: chain 'E' and resid 302 through 311
      removed outlier: 10.962A  pdb=" N   ILE E 325 " --> pdb=" O   GLU E 303 " (cutoff:3.500A)
      removed outlier: 11.563A  pdb=" N   GLU E 305 " --> pdb=" O   ILE E 325 " (cutoff:3.500A)
      removed outlier: 10.564A  pdb=" N   LYS E 327 " --> pdb=" O   GLU E 305 " (cutoff:3.500A)
      removed outlier: 7.259A  pdb=" N   LYS E 307 " --> pdb=" O   LYS E 327 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 302 through 311
      removed outlier: 10.962A  pdb=" N   ILE E 325 " --> pdb=" O   GLU E 303 " (cutoff:3.500A)
      removed outlier: 11.563A  pdb=" N   GLU E 305 " --> pdb=" O   ILE E 325 " (cutoff:3.500A)
      removed outlier: 10.564A  pdb=" N   LYS E 327 " --> pdb=" O   GLU E 305 " (cutoff:3.500A)
      removed outlier: 7.259A  pdb=" N   LYS E 307 " --> pdb=" O   LYS E 327 " (cutoff:3.500A)
      removed outlier: 7.758A  pdb=" N   TYR E 417 " --> pdb=" O   SER E 389 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   TYR E 391 " --> pdb=" O   TYR E 417 " (cutoff:3.500A)
      removed outlier: 8.098A  pdb=" N   ALA E 419 " --> pdb=" O   TYR E 391 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   LEU E 393 " --> pdb=" O   ALA E 419 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 461 through 462
      removed outlier: 5.589A  pdb=" N   ASP E 461 " --> pdb=" O   LYS E 568 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'E' and resid 465 through 470
      removed outlier: 6.653A  pdb=" N   THR E 478 " --> pdb=" O   THR E 466 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   THR E 468 " --> pdb=" O   ILE E 476 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   ILE E 476 " --> pdb=" O   THR E 468 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 520 through 525
    Processing sheet with id=AB4, first strand: chain 'E' and resid 585 through 590
      removed outlier: 4.522A  pdb=" N   VAL E 587 " --> pdb=" O   LYS E 600 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   LYS E 600 " --> pdb=" O   VAL E 587 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   SER E 589 " --> pdb=" O   ILE E 598 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   ILE E 598 " --> pdb=" O   SER E 589 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 747 through 752
      removed outlier: 4.279A  pdb=" N   TYR E 613 " --> pdb=" O   CYS E 776 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'F' and resid 2 through 3
    Processing sheet with id=AB7, first strand: chain 'F' and resid 6 through 10
      removed outlier: 6.325A  pdb=" N   LEU F  29 " --> pdb=" O   LEU F  56 " (cutoff:3.500A)
      removed outlier: 8.000A  pdb=" N   PHE F  58 " --> pdb=" O   LEU F  29 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   ILE F  31 " --> pdb=" O   PHE F  58 " (cutoff:3.500A)
      removed outlier: 5.506A  pdb=" N   VAL F  60 " --> pdb=" O   ILE F  31 " (cutoff:3.500A)
      removed outlier: 7.412A  pdb=" N   LEU F  33 " --> pdb=" O   VAL F  60 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   ARG F 112 " --> pdb=" O   ALA F  86 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   VAL F  88 " --> pdb=" O   ARG F 112 " (cutoff:3.500A)
      removed outlier: 7.383A  pdb=" N   GLU F 114 " --> pdb=" O   VAL F  88 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   PHE F  90 " --> pdb=" O   GLU F 114 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'F' and resid 164 through 167
      removed outlier: 3.749A  pdb=" N   THR F 165 " --> pdb=" O   ASN F 172 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'F' and resid 205 through 209
      removed outlier: 3.552A  pdb=" N   ALA F 220 " --> pdb=" O   LEU F 206 " (cutoff:3.500A)
      removed outlier: 7.562A  pdb=" N   SER F 208 " --> pdb=" O   CYS F 218 " (cutoff:3.500A)
      removed outlier: 5.518A  pdb=" N   CYS F 218 " --> pdb=" O   SER F 208 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'F' and resid 224 through 226
    Processing sheet with id=AC2, first strand: chain 'F' and resid 245 through 248
      removed outlier: 3.791A  pdb=" N   ARG F 245 " --> pdb=" O   PHE F 241 " (cutoff:3.500A)
      removed outlier: 7.849A  pdb=" N   CYS F 273 " --> pdb=" O   THR F 238 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   ARG F 240 " --> pdb=" O   CYS F 273 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'F' and resid 282 through 283
    Processing sheet with id=AC4, first strand: chain 'F' and resid 301 through 311
      removed outlier: 11.033A  pdb=" N   ILE F 325 " --> pdb=" O   GLU F 303 " (cutoff:3.500A)
      removed outlier: 11.594A  pdb=" N   GLU F 305 " --> pdb=" O   ILE F 325 " (cutoff:3.500A)
      removed outlier: 10.554A  pdb=" N   LYS F 327 " --> pdb=" O   GLU F 305 " (cutoff:3.500A)
      removed outlier: 7.348A  pdb=" N   LYS F 307 " --> pdb=" O   LYS F 327 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'F' and resid 301 through 311
      removed outlier: 11.033A  pdb=" N   ILE F 325 " --> pdb=" O   GLU F 303 " (cutoff:3.500A)
      removed outlier: 11.594A  pdb=" N   GLU F 305 " --> pdb=" O   ILE F 325 " (cutoff:3.500A)
      removed outlier: 10.554A  pdb=" N   LYS F 327 " --> pdb=" O   GLU F 305 " (cutoff:3.500A)
      removed outlier: 7.348A  pdb=" N   LYS F 307 " --> pdb=" O   LYS F 327 " (cutoff:3.500A)
      removed outlier: 5.449A  pdb=" N   LYS F 415 " --> pdb=" O   TYR F 388 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA F 419 " --> pdb=" O   VAL F 392 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'F' and resid 461 through 463
      removed outlier: 5.640A  pdb=" N   ASP F 461 " --> pdb=" O   LYS F 568 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC6
    Processing sheet with id=AC7, first strand: chain 'F' and resid 465 through 470
      removed outlier: 6.622A  pdb=" N   THR F 478 " --> pdb=" O   THR F 466 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   THR F 468 " --> pdb=" O   ILE F 476 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   ILE F 476 " --> pdb=" O   THR F 468 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'F' and resid 520 through 525
    Processing sheet with id=AC9, first strand: chain 'F' and resid 585 through 593
      removed outlier: 4.511A  pdb=" N   VAL F 587 " --> pdb=" O   LYS F 600 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   LYS F 600 " --> pdb=" O   VAL F 587 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   SER F 589 " --> pdb=" O   ILE F 598 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   ILE F 598 " --> pdb=" O   SER F 589 " (cutoff:3.500A)
      removed outlier: 4.976A  pdb=" N   SER F 591 " --> pdb=" O   GLN F 596 " (cutoff:3.500A)
      removed outlier: 7.608A  pdb=" N   GLN F 596 " --> pdb=" O   SER F 591 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'F' and resid 747 through 752
      removed outlier: 4.336A  pdb=" N   TYR F 613 " --> pdb=" O   CYS F 776 " (cutoff:3.500A)

    311 hydrogen bonds defined for protein.
    759 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: 4.43

  Time building geometry restraints manager: 2.75 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: 3846
        1.34 -     1.46: 2774
        1.46 -     1.58: 5204
        1.58 -     1.70: 0
        1.70 -     1.83: 120
  Bond restraints: 11944
  Sorted by residual:
  bond pdb=" N   SER E 579 "
       pdb=" CA  SER E 579 "
    ideal  model  delta    sigma   weight residual
    1.454  1.486 -0.032 1.15e-02 7.56e+03 7.57e+00
  bond pdb=" N   VAL E 580 "
       pdb=" CA  VAL E 580 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.23e-02 6.61e+03 6.80e+00
  bond pdb=" N   THR E 576 "
       pdb=" CA  THR E 576 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.032 1.25e-02 6.40e+03 6.45e+00
  bond pdb=" N   ASN E 577 "
       pdb=" CA  ASN E 577 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.031 1.31e-02 5.83e+03 5.51e+00
  bond pdb=" N   ALA E 578 "
       pdb=" CA  ALA E 578 "
    ideal  model  delta    sigma   weight residual
    1.457  1.481 -0.023 1.28e-02 6.10e+03 3.35e+00
  ... (remaining 11939 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.27: 15499
        1.27 -     2.54: 543
        2.54 -     3.81: 139
        3.81 -     5.08: 12
        5.08 -     6.35: 4
  Bond angle restraints: 16197
  Sorted by residual:
  angle pdb=" N   ARG D  26 "
        pdb=" CA  ARG D  26 "
        pdb=" C   ARG D  26 "
      ideal   model   delta    sigma   weight residual
     110.73  117.08   -6.35 1.55e+00 4.16e-01 1.68e+01
  angle pdb=" CA  ARG D  26 "
        pdb=" C   ARG D  26 "
        pdb=" N   PRO D  27 "
      ideal   model   delta    sigma   weight residual
     117.84  121.27   -3.43 9.70e-01 1.06e+00 1.25e+01
  angle pdb=" C   THR E 107 "
        pdb=" N   ARG E 108 "
        pdb=" CA  ARG E 108 "
      ideal   model   delta    sigma   weight residual
     122.17  117.41    4.76 1.54e+00 4.22e-01 9.56e+00
  angle pdb=" CA  THR E 576 "
        pdb=" C   THR E 576 "
        pdb=" O   THR E 576 "
      ideal   model   delta    sigma   weight residual
     121.44  118.21    3.23 1.08e+00 8.57e-01 8.95e+00
  angle pdb=" CA  SER E 579 "
        pdb=" C   SER E 579 "
        pdb=" O   SER E 579 "
      ideal   model   delta    sigma   weight residual
     121.66  118.31    3.35 1.22e+00 6.72e-01 7.53e+00
  ... (remaining 16192 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.40: 6649
       15.40 -    30.79: 479
       30.79 -    46.19: 134
       46.19 -    61.58: 42
       61.58 -    76.98: 9
  Dihedral angle restraints: 7313
    sinusoidal: 3033
      harmonic: 4280
  Sorted by residual:
  dihedral pdb=" CB  CYS C   7 "
           pdb=" SG  CYS C   7 "
           pdb=" SG  CYS C  47 "
           pdb=" CB  CYS C  47 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -156.41   70.41     1      1.00e+01 1.00e-02 6.38e+01
  dihedral pdb=" CB  CYS F 201 "
           pdb=" SG  CYS F 201 "
           pdb=" SG  CYS F 209 "
           pdb=" CB  CYS F 209 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  145.08  -52.08     1      1.00e+01 1.00e-02 3.70e+01
  dihedral pdb=" CB  CYS E 201 "
           pdb=" SG  CYS E 201 "
           pdb=" SG  CYS E 209 "
           pdb=" CB  CYS E 209 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  144.71  -51.71     1      1.00e+01 1.00e-02 3.65e+01
  ... (remaining 7310 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 1180
       0.033 -    0.067: 362
       0.067 -    0.100: 169
       0.100 -    0.133: 76
       0.133 -    0.166: 3
  Chirality restraints: 1790
  Sorted by residual:
  chirality pdb=" CA  VAL E 580 "
            pdb=" N   VAL E 580 "
            pdb=" C   VAL E 580 "
            pdb=" CB  VAL E 580 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 6.91e-01
  chirality pdb=" CA  VAL C  24 "
            pdb=" N   VAL C  24 "
            pdb=" C   VAL C  24 "
            pdb=" CB  VAL C  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.04e-01
  chirality pdb=" CA  PRO E 422 "
            pdb=" N   PRO E 422 "
            pdb=" C   PRO E 422 "
            pdb=" CB  PRO E 422 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.80e-01
  ... (remaining 1787 not shown)

  Planarity restraints: 2091
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY F   4 "   -0.047 5.00e-02 4.00e+02   7.14e-02 8.16e+00
        pdb=" N   PRO F   5 "    0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO F   5 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO F   5 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS F 143 "    0.038 5.00e-02 4.00e+02   5.72e-02 5.23e+00
        pdb=" N   PRO F 144 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO F 144 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO F 144 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS F 234 "   -0.026 5.00e-02 4.00e+02   3.98e-02 2.54e+00
        pdb=" N   PRO F 235 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO F 235 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO F 235 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 2088 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 924
        2.74 -     3.28: 11587
        3.28 -     3.82: 19134
        3.82 -     4.36: 23678
        4.36 -     4.90: 39111
  Nonbonded interactions: 94434
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP E 126 "
            pdb=" OG  SER E 128 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" O   LYS E 503 "
            pdb=" OH  TYR E 573 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" O   LYS F 503 "
            pdb=" OH  TYR F 573 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" O   PHE E 701 "
            pdb=" OH  TYR D  60 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OD1 ASN E 698 "
            pdb=" N   GLY D  41 "
     model   vdw
     2.234 3.120
  ... (remaining 94429 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}
ncs_group {
  reference = (chain 'E' and (resid 1 through 256 or resid 265 through 798))
  selection = (chain 'F' and (resid 1 through 624 or resid 684 through 798))
}

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:             3.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     28.920
  Find NCS groups from input model:        0.430
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6121
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11982  Z= 0.199
  Angle     :  0.594   6.353  16273  Z= 0.329
  Chirality :  0.043   0.166   1790
  Planarity :  0.004   0.071   2091
  Dihedral  : 11.885  76.976   4435
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 17.46
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  6.73 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  :  6.79 %
    Favored  : 90.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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: -1.99 (0.20), residues: 1426
  helix: -1.46 (0.36), residues: 153
  sheet: -0.75 (0.30), residues: 289
  loop : -1.56 (0.18), residues: 984

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E  79 
 HIS   0.004   0.001   HIS F 539 
 PHE   0.021   0.001   PHE F 692 
 TYR   0.012   0.001   TYR D  25 
 ARG   0.005   0.000   ARG D  26 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.26439 (  303)
  hydrogen bonds       : angle       9.94094 (  759)
  SS BOND              : bond        0.00276 (   38)
  SS BOND              : angle       0.92716 (   76)
  covalent geometry    : bond        0.00392 (11944)
  covalent geometry    : angle       0.59246 (16197)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 254
  time to evaluate  : 1.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    2 ILE cc_start: 0.7420 (mt) cc_final: 0.6854 (mt)
REVERT: E  100 LEU cc_start: 0.9170 (mt) cc_final: 0.8727 (mt)
REVERT: E  169 ASN cc_start: 0.9159 (m-40) cc_final: 0.8858 (p0)
REVERT: E  398 LEU cc_start: 0.8993 (tp) cc_final: 0.8741 (tp)
REVERT: E  446 ASP cc_start: 0.6518 (m-30) cc_final: 0.6309 (m-30)
REVERT: F   76 ILE cc_start: 0.9039 (mt) cc_final: 0.8718 (tt)
REVERT: F  353 VAL cc_start: 0.8866 (t) cc_final: 0.8555 (t)
REVERT: F  398 LEU cc_start: 0.9277 (tp) cc_final: 0.9043 (tp)
REVERT: F  416 MET cc_start: 0.7559 (mtm) cc_final: 0.7232 (ptt)
REVERT: F  432 MET cc_start: 0.9004 (ttt) cc_final: 0.8457 (tmm)
REVERT: F  436 THR cc_start: 0.7987 (m) cc_final: 0.7439 (m)
REVERT: F  448 ASN cc_start: 0.9172 (OUTLIER) cc_final: 0.8813 (t0)
REVERT: F  490 LEU cc_start: 0.9315 (tt) cc_final: 0.9048 (mm)
REVERT: D   21 ASN cc_start: 0.7465 (m-40) cc_final: 0.7261 (p0)
  outliers start: 35
  outliers final: 9
  residues processed: 281
  average time/residue: 0.2740
  time to fit residues: 104.7519
Evaluate side-chains
  135 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 125
  time to evaluate  : 1.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 121 optimal weight:   10.0000
   chunk 109 optimal weight:    0.4980
   chunk 60 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9990
   chunk 73 optimal weight:    7.9990
   chunk 58 optimal weight:    5.9990
   chunk 112 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 68 optimal weight:    0.5980
   chunk 84 optimal weight:   10.0000
   chunk 130 optimal weight:    6.9990
   overall best weight:    2.2186

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

Flipped N/Q/H residues before XYZ refinement:
E  15 GLN
E 136 ASN
** E 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 374 ASN
E 395 ASN
E 399 GLN
** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 694 ASN
** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 395 ASN
F 399 GLN
F 421 ASN
** F 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.082826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.063121 restraints weight = 90567.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.064641 restraints weight = 57213.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.065791 restraints weight = 40989.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7343
moved from start:          0.3235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  11982  Z= 0.221
  Angle     :  0.747  10.118  16273  Z= 0.392
  Chirality :  0.049   0.215   1790
  Planarity :  0.005   0.059   2091
  Dihedral  :  5.409  26.214   1610
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 16.55
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.26 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.13 %
    Favored  : 96.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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: -1.81 (0.20), residues: 1426
  helix: -1.31 (0.35), residues: 164
  sheet: -0.60 (0.30), residues: 292
  loop : -1.43 (0.18), residues: 970

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP E 402 
 HIS   0.007   0.001   HIS F 539 
 PHE   0.025   0.002   PHE E 493 
 TYR   0.028   0.002   TYR E 496 
 ARG   0.005   0.001   ARG E  44 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05404 (  303)
  hydrogen bonds       : angle       7.63043 (  759)
  SS BOND              : bond        0.00667 (   38)
  SS BOND              : angle       2.53885 (   76)
  covalent geometry    : bond        0.00478 (11944)
  covalent geometry    : angle       0.72801 (16197)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 158
  time to evaluate  : 1.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    2 ILE cc_start: 0.7752 (mt) cc_final: 0.7399 (mm)
REVERT: E  169 ASN cc_start: 0.9027 (m-40) cc_final: 0.8522 (p0)
REVERT: E  348 MET cc_start: 0.8794 (mpp) cc_final: 0.8501 (mpp)
REVERT: E  395 ASN cc_start: 0.8760 (m110) cc_final: 0.8485 (m-40)
REVERT: F   25 ILE cc_start: 0.9068 (tt) cc_final: 0.8837 (tp)
REVERT: F  432 MET cc_start: 0.9181 (ttt) cc_final: 0.8717 (tmm)
REVERT: F  436 THR cc_start: 0.8357 (m) cc_final: 0.7628 (m)
REVERT: F  473 ASN cc_start: 0.9060 (p0) cc_final: 0.8828 (p0)
REVERT: F  478 THR cc_start: 0.6353 (p) cc_final: 0.5976 (t)
REVERT: F  521 MET cc_start: 0.8064 (mmp) cc_final: 0.7747 (mmm)
REVERT: F  529 ASN cc_start: 0.8703 (t0) cc_final: 0.8278 (t0)
REVERT: F  790 PHE cc_start: 0.9055 (p90) cc_final: 0.8762 (p90)
REVERT: F  796 MET cc_start: 0.8201 (mmp) cc_final: 0.7960 (mmm)
REVERT: D   36 ARG cc_start: 0.7713 (tmt170) cc_final: 0.7341 (mmt180)
REVERT: D   37 ASN cc_start: 0.8809 (p0) cc_final: 0.8505 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 159
  average time/residue: 0.3349
  time to fit residues: 73.1862
Evaluate side-chains
  106 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 1.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 26 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 16 optimal weight:    7.9990
   chunk 71 optimal weight:   10.0000
   chunk 79 optimal weight:    0.4980
   chunk 84 optimal weight:    0.0470
   chunk 94 optimal weight:    8.9990
   chunk 31 optimal weight:    0.6980
   overall best weight:    1.0482

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

Flipped N/Q/H residues before XYZ refinement:
E 116 ASN
** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 621 GLN
C  37 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.082740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.063189 restraints weight = 92637.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.064926 restraints weight = 57982.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.066100 restraints weight = 41041.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7333
moved from start:          0.3777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  11982  Z= 0.144
  Angle     :  0.626   7.973  16273  Z= 0.333
  Chirality :  0.047   0.206   1790
  Planarity :  0.004   0.053   2091
  Dihedral  :  5.220  24.465   1610
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 14.60
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.98 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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: -1.47 (0.21), residues: 1426
  helix: -0.93 (0.37), residues: 164
  sheet: -0.37 (0.31), residues: 292
  loop : -1.22 (0.19), residues: 970

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 402 
 HIS   0.005   0.001   HIS F 539 
 PHE   0.018   0.001   PHE E 692 
 TYR   0.021   0.002   TYR F 496 
 ARG   0.003   0.000   ARG E 249 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04564 (  303)
  hydrogen bonds       : angle       7.14316 (  759)
  SS BOND              : bond        0.00392 (   38)
  SS BOND              : angle       1.82770 (   76)
  covalent geometry    : bond        0.00315 (11944)
  covalent geometry    : angle       0.61448 (16197)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 1.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   74 THR cc_start: 0.8594 (m) cc_final: 0.8361 (p)
REVERT: E  169 ASN cc_start: 0.8987 (m-40) cc_final: 0.8461 (p0)
REVERT: E  348 MET cc_start: 0.8776 (mpp) cc_final: 0.8449 (mpp)
REVERT: E  395 ASN cc_start: 0.8582 (m110) cc_final: 0.8269 (m-40)
REVERT: E  446 ASP cc_start: 0.6794 (m-30) cc_final: 0.6463 (m-30)
REVERT: F  344 LEU cc_start: 0.9745 (mt) cc_final: 0.9417 (mt)
REVERT: F  398 LEU cc_start: 0.9669 (mm) cc_final: 0.9357 (mm)
REVERT: F  400 GLN cc_start: 0.9001 (pm20) cc_final: 0.8634 (pm20)
REVERT: F  416 MET cc_start: 0.8041 (ptt) cc_final: 0.7830 (ptt)
REVERT: F  432 MET cc_start: 0.9017 (ttt) cc_final: 0.8756 (tmm)
REVERT: F  436 THR cc_start: 0.8394 (m) cc_final: 0.7431 (m)
REVERT: F  473 ASN cc_start: 0.8909 (p0) cc_final: 0.8692 (p0)
REVERT: F  529 ASN cc_start: 0.8754 (t0) cc_final: 0.8283 (t0)
REVERT: F  753 ASP cc_start: 0.8426 (t0) cc_final: 0.8216 (t0)
REVERT: F  790 PHE cc_start: 0.8999 (p90) cc_final: 0.8734 (p90)
REVERT: F  796 MET cc_start: 0.8196 (mmp) cc_final: 0.7968 (mmm)
REVERT: D   36 ARG cc_start: 0.7732 (tmt170) cc_final: 0.7352 (mmt180)
REVERT: D   37 ASN cc_start: 0.8842 (p0) cc_final: 0.8578 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.4100
  time to fit residues: 82.1931
Evaluate side-chains
  98 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 2.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 135 optimal weight:   10.0000
   chunk 123 optimal weight:   10.0000
   chunk 124 optimal weight:    3.9990
   chunk 116 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 105 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 36 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 127 optimal weight:    4.9990
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
E 116 ASN
** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 442 GLN ** 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 = 0.3999 r_free = 0.3999 target = 0.080090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.060352 restraints weight = 92669.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.061946 restraints weight = 58336.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.062966 restraints weight = 41883.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.4521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11982  Z= 0.201
  Angle     :  0.688   7.342  16273  Z= 0.358
  Chirality :  0.048   0.248   1790
  Planarity :  0.005   0.052   2091
  Dihedral  :  5.488  26.130   1610
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 16.94
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  6.24 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.89 %
    Favored  : 96.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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: -1.28 (0.22), residues: 1426
  helix: -0.34 (0.41), residues: 149
  sheet: -0.44 (0.30), residues: 304
  loop : -1.11 (0.20), residues: 973

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP E 402 
 HIS   0.008   0.001   HIS E 364 
 PHE   0.019   0.002   PHE E 692 
 TYR   0.018   0.002   TYR E 239 
 ARG   0.005   0.000   ARG C  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03986 (  303)
  hydrogen bonds       : angle       6.95008 (  759)
  SS BOND              : bond        0.00393 (   38)
  SS BOND              : angle       1.74250 (   76)
  covalent geometry    : bond        0.00442 (11944)
  covalent geometry    : angle       0.67950 (16197)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 131
  time to evaluate  : 1.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   53 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7233 (mt-10)
REVERT: E  169 ASN cc_start: 0.9042 (m-40) cc_final: 0.8456 (p0)
REVERT: E  274 MET cc_start: 0.8778 (mpp) cc_final: 0.8566 (mpp)
REVERT: E  348 MET cc_start: 0.8542 (mpp) cc_final: 0.8217 (mpp)
REVERT: E  398 LEU cc_start: 0.9128 (tp) cc_final: 0.8894 (tp)
REVERT: E  436 THR cc_start: 0.6582 (m) cc_final: 0.6023 (p)
REVERT: E  521 MET cc_start: 0.3910 (mmt) cc_final: 0.3642 (mmt)
REVERT: F  319 MET cc_start: 0.7960 (tmm) cc_final: 0.7495 (tmm)
REVERT: F  398 LEU cc_start: 0.9717 (mm) cc_final: 0.9421 (mm)
REVERT: F  402 TRP cc_start: 0.8140 (p-90) cc_final: 0.7745 (p-90)
REVERT: F  409 LEU cc_start: 0.8466 (mt) cc_final: 0.8017 (tp)
REVERT: F  432 MET cc_start: 0.8951 (ttt) cc_final: 0.8545 (tmm)
REVERT: F  436 THR cc_start: 0.8514 (m) cc_final: 0.7699 (m)
REVERT: F  473 ASN cc_start: 0.9047 (p0) cc_final: 0.8813 (p0)
REVERT: F  478 THR cc_start: 0.6473 (p) cc_final: 0.6027 (t)
REVERT: F  529 ASN cc_start: 0.8842 (t0) cc_final: 0.8313 (t0)
REVERT: F  753 ASP cc_start: 0.8457 (t0) cc_final: 0.8248 (t0)
REVERT: F  760 ILE cc_start: 0.8990 (mm) cc_final: 0.8743 (tp)
REVERT: F  790 PHE cc_start: 0.9069 (p90) cc_final: 0.8836 (p90)
REVERT: F  796 MET cc_start: 0.8412 (mmp) cc_final: 0.8169 (mmm)
  outliers start: 1
  outliers final: 1
  residues processed: 132
  average time/residue: 0.3637
  time to fit residues: 68.8500
Evaluate side-chains
  93 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 1.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 91 optimal weight:    6.9990
   chunk 102 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   chunk 61 optimal weight:    6.9990
   chunk 118 optimal weight:    0.0370
   chunk 130 optimal weight:    6.9990
   chunk 64 optimal weight:   50.0000
   chunk 72 optimal weight:    8.9990
   chunk 23 optimal weight:    0.0970
   chunk 73 optimal weight:    0.5980
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.7460

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

Flipped N/Q/H residues before XYZ refinement:
E 395 ASN
** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 442 GLN ** 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 = 0.4035 r_free = 0.4035 target = 0.081405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.062071 restraints weight = 92590.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.063739 restraints weight = 57725.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.064886 restraints weight = 40690.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.4749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11982  Z= 0.120
  Angle     :  0.612   8.202  16273  Z= 0.319
  Chirality :  0.047   0.270   1790
  Planarity :  0.004   0.051   2091
  Dihedral  :  5.184  24.754   1610
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 14.29
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.12 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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: -1.00 (0.22), residues: 1426
  helix:  0.26 (0.44), residues: 138
  sheet: -0.35 (0.30), residues: 305
  loop : -0.93 (0.20), residues: 983

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 404 
 HIS   0.004   0.001   HIS E  30 
 PHE   0.019   0.002   PHE F 418 
 TYR   0.014   0.001   TYR F 391 
 ARG   0.005   0.000   ARG F 617 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03640 (  303)
  hydrogen bonds       : angle       6.69416 (  759)
  SS BOND              : bond        0.00286 (   38)
  SS BOND              : angle       1.64869 (   76)
  covalent geometry    : bond        0.00272 (11944)
  covalent geometry    : angle       0.60324 (16197)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 1.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   53 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7348 (mt-10)
REVERT: E   74 THR cc_start: 0.8186 (m) cc_final: 0.7893 (p)
REVERT: E  169 ASN cc_start: 0.8958 (m-40) cc_final: 0.8397 (p0)
REVERT: E  274 MET cc_start: 0.8806 (mpp) cc_final: 0.8539 (mpp)
REVERT: E  348 MET cc_start: 0.8430 (mpp) cc_final: 0.8095 (mpp)
REVERT: E  398 LEU cc_start: 0.8959 (tp) cc_final: 0.8676 (tp)
REVERT: F  398 LEU cc_start: 0.9640 (mm) cc_final: 0.9406 (mm)
REVERT: F  432 MET cc_start: 0.8844 (ttt) cc_final: 0.8516 (tmm)
REVERT: F  436 THR cc_start: 0.8447 (m) cc_final: 0.7691 (m)
REVERT: F  529 ASN cc_start: 0.8819 (t0) cc_final: 0.8273 (t0)
REVERT: F  790 PHE cc_start: 0.9061 (p90) cc_final: 0.8857 (p90)
REVERT: F  796 MET cc_start: 0.8395 (mmp) cc_final: 0.8166 (mmm)
REVERT: D    5 ILE cc_start: 0.8254 (mp) cc_final: 0.8009 (mm)
REVERT: D   37 ASN cc_start: 0.8863 (p0) cc_final: 0.8652 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.3009
  time to fit residues: 55.0460
Evaluate side-chains
  91 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 1.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 101 optimal weight:    7.9990
   chunk 14 optimal weight:    0.0970
   chunk 3 optimal weight:    5.9990
   chunk 54 optimal weight:    5.9990
   chunk 64 optimal weight:   30.0000
   chunk 53 optimal weight:   10.0000
   chunk 1 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9990
   chunk 89 optimal weight:    1.9990
   chunk 141 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
E 395 ASN
** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 321 GLN
** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 442 GLN ** 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 = 0.3986 r_free = 0.3986 target = 0.078943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.058581 restraints weight = 89530.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.060366 restraints weight = 55452.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.061563 restraints weight = 39854.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.5183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11982  Z= 0.178
  Angle     :  0.649   8.269  16273  Z= 0.339
  Chirality :  0.047   0.219   1790
  Planarity :  0.004   0.046   2091
  Dihedral  :  5.434  26.310   1610
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 16.72
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.24 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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: -0.95 (0.22), residues: 1426
  helix:  0.19 (0.43), residues: 139
  sheet: -0.36 (0.30), residues: 302
  loop : -0.86 (0.20), residues: 985

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 618 
 HIS   0.008   0.001   HIS E 364 
 PHE   0.024   0.002   PHE E  70 
 TYR   0.015   0.002   TYR F  28 
 ARG   0.004   0.000   ARG E 336 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03713 (  303)
  hydrogen bonds       : angle       6.66382 (  759)
  SS BOND              : bond        0.00429 (   38)
  SS BOND              : angle       1.63739 (   76)
  covalent geometry    : bond        0.00386 (11944)
  covalent geometry    : angle       0.64067 (16197)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 1.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   53 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7182 (mt-10)
REVERT: E  274 MET cc_start: 0.8959 (mpp) cc_final: 0.8676 (mpp)
REVERT: E  348 MET cc_start: 0.8474 (mpp) cc_final: 0.8169 (mpp)
REVERT: E  366 LEU cc_start: 0.9205 (mt) cc_final: 0.8940 (mt)
REVERT: E  398 LEU cc_start: 0.8915 (tp) cc_final: 0.8683 (tp)
REVERT: E  436 THR cc_start: 0.6184 (m) cc_final: 0.5637 (p)
REVERT: F  398 LEU cc_start: 0.9667 (mm) cc_final: 0.9434 (mm)
REVERT: F  432 MET cc_start: 0.8853 (ttt) cc_final: 0.8537 (tmm)
REVERT: F  436 THR cc_start: 0.8522 (m) cc_final: 0.7819 (m)
REVERT: F  529 ASN cc_start: 0.8877 (t0) cc_final: 0.8309 (t0)
REVERT: F  760 ILE cc_start: 0.8928 (mm) cc_final: 0.8703 (tp)
REVERT: D   36 ARG cc_start: 0.7750 (tmt170) cc_final: 0.7374 (mmt-90)
REVERT: D   37 ASN cc_start: 0.8879 (p0) cc_final: 0.8575 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.2223
  time to fit residues: 40.1103
Evaluate side-chains
  85 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 1.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 44 optimal weight:    8.9990
   chunk 2 optimal weight:    0.5980
   chunk 112 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   chunk 58 optimal weight:    4.9990
   chunk 88 optimal weight:    3.9990
   chunk 84 optimal weight:    3.9990
   chunk 97 optimal weight:    6.9990
   chunk 142 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9980
   chunk 131 optimal weight:    8.9990
   overall best weight:    1.8784

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

Flipped N/Q/H residues before XYZ refinement:
E 395 ASN
** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 442 GLN ** 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 = 0.3931 r_free = 0.3931 target = 0.077845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.057077 restraints weight = 93448.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.058566 restraints weight = 61648.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.059562 restraints weight = 45533.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.5630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11982  Z= 0.175
  Angle     :  0.657   7.387  16273  Z= 0.343
  Chirality :  0.048   0.275   1790
  Planarity :  0.005   0.053   2091
  Dihedral  :  5.470  27.118   1610
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 17.46
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  5.82 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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: -1.02 (0.23), residues: 1426
  helix:  0.08 (0.43), residues: 142
  sheet: -0.56 (0.29), residues: 317
  loop : -0.83 (0.21), residues: 967

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F 479 
 HIS   0.006   0.001   HIS E 364 
 PHE   0.029   0.002   PHE E  90 
 TYR   0.018   0.002   TYR F 391 
 ARG   0.013   0.001   ARG C  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03608 (  303)
  hydrogen bonds       : angle       6.74691 (  759)
  SS BOND              : bond        0.00397 (   38)
  SS BOND              : angle       1.86594 (   76)
  covalent geometry    : bond        0.00385 (11944)
  covalent geometry    : angle       0.64607 (16197)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 1.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   74 THR cc_start: 0.8716 (m) cc_final: 0.8467 (p)
REVERT: E  274 MET cc_start: 0.8987 (mpp) cc_final: 0.8652 (mpp)
REVERT: E  348 MET cc_start: 0.8438 (mpp) cc_final: 0.8029 (mpp)
REVERT: E  366 LEU cc_start: 0.9240 (mt) cc_final: 0.8995 (mt)
REVERT: E  395 ASN cc_start: 0.8808 (m110) cc_final: 0.8603 (m-40)
REVERT: E  398 LEU cc_start: 0.8845 (tp) cc_final: 0.8618 (tp)
REVERT: F  348 MET cc_start: 0.8784 (mmp) cc_final: 0.8526 (mmm)
REVERT: F  398 LEU cc_start: 0.9650 (mm) cc_final: 0.9433 (mm)
REVERT: F  432 MET cc_start: 0.8868 (ttt) cc_final: 0.8562 (tmm)
REVERT: F  529 ASN cc_start: 0.8832 (t0) cc_final: 0.8296 (t0)
REVERT: F  760 ILE cc_start: 0.8833 (mm) cc_final: 0.8618 (tp)
REVERT: F  796 MET cc_start: 0.8632 (mmp) cc_final: 0.8343 (mmp)
REVERT: D   36 ARG cc_start: 0.7941 (tmt170) cc_final: 0.7355 (mmt-90)
REVERT: D   37 ASN cc_start: 0.8917 (p0) cc_final: 0.8596 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.2147
  time to fit residues: 36.4034
Evaluate side-chains
  83 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 1.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 100 optimal weight:    5.9990
   chunk 116 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0980
   chunk 87 optimal weight:    0.7980
   chunk 46 optimal weight:    6.9990
   chunk 98 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 66 optimal weight:   10.0000
   chunk 106 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 399 GLN
** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 102 ASN
F 374 ASN
** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.079377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.060548 restraints weight = 92401.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.061787 restraints weight = 64212.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.062188 restraints weight = 48832.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.5743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  11982  Z= 0.117
  Angle     :  0.615  10.815  16273  Z= 0.319
  Chirality :  0.048   0.329   1790
  Planarity :  0.005   0.088   2091
  Dihedral  :  5.286  24.477   1610
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.68 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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: -0.89 (0.23), residues: 1426
  helix:  0.05 (0.44), residues: 142
  sheet: -0.44 (0.30), residues: 313
  loop : -0.74 (0.21), residues: 971

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 404 
 HIS   0.003   0.001   HIS E 364 
 PHE   0.017   0.001   PHE E  90 
 TYR   0.015   0.001   TYR F 391 
 ARG   0.006   0.000   ARG E  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03388 (  303)
  hydrogen bonds       : angle       6.53414 (  759)
  SS BOND              : bond        0.00238 (   38)
  SS BOND              : angle       1.62029 (   76)
  covalent geometry    : bond        0.00271 (11944)
  covalent geometry    : angle       0.60656 (16197)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 1.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   53 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7970 (mt-10)
REVERT: E   74 THR cc_start: 0.8647 (m) cc_final: 0.8394 (p)
REVERT: E  348 MET cc_start: 0.8481 (mpp) cc_final: 0.8104 (mpp)
REVERT: E  366 LEU cc_start: 0.9156 (mt) cc_final: 0.8930 (mt)
REVERT: E  398 LEU cc_start: 0.8801 (tp) cc_final: 0.8554 (tp)
REVERT: E  558 MET cc_start: 0.4270 (tpt) cc_final: 0.3586 (pmm)
REVERT: F  184 MET cc_start: 0.4106 (mtm) cc_final: 0.3773 (mtt)
REVERT: F  331 LEU cc_start: 0.9223 (tt) cc_final: 0.8936 (mt)
REVERT: F  348 MET cc_start: 0.8799 (mmp) cc_final: 0.8541 (mmm)
REVERT: F  398 LEU cc_start: 0.9646 (mm) cc_final: 0.9427 (mm)
REVERT: F  432 MET cc_start: 0.8810 (ttt) cc_final: 0.8417 (tmm)
REVERT: F  436 THR cc_start: 0.8530 (m) cc_final: 0.7213 (m)
REVERT: F  796 MET cc_start: 0.8729 (mmp) cc_final: 0.8482 (mmp)
REVERT: D    5 ILE cc_start: 0.8295 (mp) cc_final: 0.8066 (mm)
REVERT: D   36 ARG cc_start: 0.8039 (tmt170) cc_final: 0.7370 (mmt-90)
REVERT: D   37 ASN cc_start: 0.8898 (p0) cc_final: 0.8568 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.2107
  time to fit residues: 36.3740
Evaluate side-chains
  83 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 1.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 86 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0170
   chunk 81 optimal weight:    0.0020
   chunk 122 optimal weight:    7.9990
   chunk 6 optimal weight:    0.2980
   chunk 120 optimal weight:    0.8980
   chunk 143 optimal weight:    5.9990
   chunk 106 optimal weight:    0.9980
   chunk 108 optimal weight:    0.9980
   chunk 76 optimal weight:   10.0000
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.4226

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

Flipped N/Q/H residues before XYZ refinement:
** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 374 ASN
F 397 ASN
** F 442 GLN ** 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 = 0.3968 r_free = 0.3968 target = 0.079463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.061043 restraints weight = 92914.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.062220 restraints weight = 67658.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.062307 restraints weight = 48702.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.5869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  11982  Z= 0.111
  Angle     :  0.616  10.129  16273  Z= 0.320
  Chirality :  0.048   0.309   1790
  Planarity :  0.005   0.070   2091
  Dihedral  :  5.197  23.557   1610
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 13.12
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  5.61 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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: -0.77 (0.23), residues: 1426
  helix:  0.12 (0.43), residues: 141
  sheet: -0.15 (0.31), residues: 298
  loop : -0.73 (0.21), residues: 987

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 404 
 HIS   0.004   0.001   HIS E 364 
 PHE   0.014   0.001   PHE F 418 
 TYR   0.014   0.001   TYR F 391 
 ARG   0.005   0.000   ARG E  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03339 (  303)
  hydrogen bonds       : angle       6.49963 (  759)
  SS BOND              : bond        0.00224 (   38)
  SS BOND              : angle       1.45951 (   76)
  covalent geometry    : bond        0.00257 (11944)
  covalent geometry    : angle       0.60935 (16197)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 1.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   53 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6994 (mt-10)
REVERT: E   74 THR cc_start: 0.8508 (m) cc_final: 0.8281 (p)
REVERT: E  348 MET cc_start: 0.8418 (mpp) cc_final: 0.8072 (mpp)
REVERT: E  521 MET cc_start: 0.3752 (mmp) cc_final: 0.3159 (mmp)
REVERT: E  558 MET cc_start: 0.4316 (tpt) cc_final: 0.3604 (pmm)
REVERT: F  184 MET cc_start: 0.4555 (mtm) cc_final: 0.4160 (mtt)
REVERT: F  331 LEU cc_start: 0.9242 (tt) cc_final: 0.8947 (mt)
REVERT: F  398 LEU cc_start: 0.9599 (mm) cc_final: 0.9354 (mm)
REVERT: F  432 MET cc_start: 0.8782 (ttt) cc_final: 0.8427 (tmm)
REVERT: F  436 THR cc_start: 0.8518 (m) cc_final: 0.7217 (m)
REVERT: F  454 GLU cc_start: 0.9056 (pm20) cc_final: 0.8627 (pm20)
REVERT: F  529 ASN cc_start: 0.8433 (t0) cc_final: 0.8030 (t0)
REVERT: F  796 MET cc_start: 0.8750 (mmp) cc_final: 0.8494 (mmp)
REVERT: D    5 ILE cc_start: 0.8234 (mp) cc_final: 0.7992 (mm)
REVERT: D   36 ARG cc_start: 0.8133 (tmt170) cc_final: 0.7408 (mmt-90)
REVERT: D   37 ASN cc_start: 0.8921 (p0) cc_final: 0.8571 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.2167
  time to fit residues: 35.5607
Evaluate side-chains
  83 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 1.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 135 optimal weight:    0.0770
   chunk 45 optimal weight:    0.9990
   chunk 97 optimal weight:    7.9990
   chunk 22 optimal weight:    1.9990
   chunk 71 optimal weight:   10.0000
   chunk 31 optimal weight:    0.5980
   chunk 84 optimal weight:    4.9990
   chunk 139 optimal weight:    7.9990
   chunk 23 optimal weight:    1.9990
   chunk 130 optimal weight:    3.9990
   overall best weight:    1.1344

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

Flipped N/Q/H residues before XYZ refinement:
E 395 ASN
** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 374 ASN
** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 698 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 = 0.3933 r_free = 0.3933 target = 0.077718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.056297 restraints weight = 86809.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.058094 restraints weight = 53782.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.059321 restraints weight = 38784.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.6090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11982  Z= 0.133
  Angle     :  0.611   7.923  16273  Z= 0.321
  Chirality :  0.047   0.280   1790
  Planarity :  0.005   0.062   2091
  Dihedral  :  5.216  24.400   1610
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 14.42
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.96 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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: -0.77 (0.23), residues: 1426
  helix:  0.10 (0.43), residues: 141
  sheet: -0.21 (0.31), residues: 298
  loop : -0.70 (0.21), residues: 987

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 244 
 HIS   0.007   0.001   HIS E 364 
 PHE   0.013   0.002   PHE E  70 
 TYR   0.015   0.001   TYR F 391 
 ARG   0.007   0.000   ARG E  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03308 (  303)
  hydrogen bonds       : angle       6.53706 (  759)
  SS BOND              : bond        0.00271 (   38)
  SS BOND              : angle       1.44920 (   76)
  covalent geometry    : bond        0.00302 (11944)
  covalent geometry    : angle       0.60482 (16197)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 1.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   53 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7970 (mt-10)
REVERT: E   74 THR cc_start: 0.8590 (m) cc_final: 0.8364 (p)
REVERT: E  348 MET cc_start: 0.8415 (mpp) cc_final: 0.8055 (mpp)
REVERT: E  521 MET cc_start: 0.4101 (mmp) cc_final: 0.3512 (mmp)
REVERT: F  184 MET cc_start: 0.4623 (mtm) cc_final: 0.4131 (mtt)
REVERT: F  331 LEU cc_start: 0.9206 (tt) cc_final: 0.8922 (mt)
REVERT: F  398 LEU cc_start: 0.9574 (mm) cc_final: 0.9311 (mm)
REVERT: F  432 MET cc_start: 0.8782 (ttt) cc_final: 0.8450 (tmm)
REVERT: F  436 THR cc_start: 0.8529 (m) cc_final: 0.7285 (m)
REVERT: F  454 GLU cc_start: 0.9026 (pm20) cc_final: 0.8426 (pm20)
REVERT: F  529 ASN cc_start: 0.8845 (t0) cc_final: 0.8281 (t0)
REVERT: F  796 MET cc_start: 0.8696 (mmp) cc_final: 0.8429 (mmp)
REVERT: D    5 ILE cc_start: 0.8228 (mp) cc_final: 0.7968 (mm)
REVERT: D   36 ARG cc_start: 0.7968 (tmt170) cc_final: 0.7329 (mmt-90)
REVERT: D   37 ASN cc_start: 0.8880 (p0) cc_final: 0.8564 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.2131
  time to fit residues: 35.2277
Evaluate side-chains
  76 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 1.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 107 optimal weight:    0.6980
   chunk 102 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 125 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 80 optimal weight:    0.8980
   chunk 66 optimal weight:   10.0000
   chunk 138 optimal weight:    9.9990
   chunk 136 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 374 ASN
** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 698 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.078846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.060027 restraints weight = 92400.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.061479 restraints weight = 64250.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.061857 restraints weight = 46418.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.6237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11982  Z= 0.114
  Angle     :  0.600   8.992  16273  Z= 0.312
  Chirality :  0.047   0.255   1790
  Planarity :  0.004   0.053   2091
  Dihedral  :  5.076  22.648   1610
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.19 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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: -0.72 (0.23), residues: 1426
  helix:  0.20 (0.43), residues: 141
  sheet: -0.21 (0.31), residues: 300
  loop : -0.66 (0.21), residues: 985

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP E 544 
 HIS   0.006   0.001   HIS F 697 
 PHE   0.012   0.001   PHE E  70 
 TYR   0.014   0.001   TYR F 391 
 ARG   0.006   0.000   ARG E  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03221 (  303)
  hydrogen bonds       : angle       6.45629 (  759)
  SS BOND              : bond        0.00234 (   38)
  SS BOND              : angle       1.36556 (   76)
  covalent geometry    : bond        0.00260 (11944)
  covalent geometry    : angle       0.59442 (16197)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4762.67 seconds
wall clock time: 86 minutes 55.20 seconds (5215.20 seconds total)