Starting phenix.real_space_refine
on Sat Jun 14 23:26:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7a5s_11647/06_2025/7a5s_11647.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7a5s_11647/06_2025/7a5s_11647.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7a5s_11647/06_2025/7a5s_11647.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7a5s_11647/06_2025/7a5s_11647.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7a5s_11647/06_2025/7a5s_11647.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7a5s_11647/06_2025/7a5s_11647.cif"
  }
  resolution = 3.9
  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=   0.002 sd=   0.027
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      68      5.16       5
     C   10580      2.51       5
     N    2748      2.21       5
     O    3212      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 168 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 16608
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4948
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 624, 4948
          Classifications: {'peptide': 624}
          Link IDs: {'PTRANS': 31, 'TRANS': 592}
          Chain breaks: 2
    Chain: "M"
      Number of atoms: 1694
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1694
          Classifications: {'peptide': 218}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206}
    Chain: "I"
      Number of atoms: 1634
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1634
          Classifications: {'peptide': 220}
          Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 205}
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Restraints were copied for chains:
    G, H, B, L
  Time building chain proxies: 14.47, per 1000 atoms: 0.87
  Number of scatterers: 16608
  At special positions: 0
  Unit cell: (183.703, 190.225, 94.569, 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      68     16.00
     O    3212      8.00
     N    2748      7.00
     C   10580      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG G   1 " - " NAG G   2 "
    NAG-ASN
      " NAG D   1 " - " ASN A 343 "
      " NAG G   1 " - " ASN B 343 "
  Time building additional restraints: 4.25
  Conformation dependent library (CDL) restraints added in 2.3 seconds
  

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3932

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 40 sheets defined
      5.8% alpha, 34.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.72
  Creating SS restraints...
    Processing helix  chain 'H' and resid 160 through 162
      No H-bonds generated for 'chain 'H' and resid 160 through 162'
    Processing helix  chain 'L' and resid 127 through 134
      removed outlier: 3.689A  pdb=" N   LEU L 131 " --> pdb=" O   SER L 127 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LYS L 132 " --> pdb=" O   ASP L 128 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   SER L 133 " --> pdb=" O   GLU L 129 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLY L 134 " --> pdb=" O   GLN L 130 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 127 through 134'
    Processing helix  chain 'L' and resid 189 through 193
    Processing helix  chain 'A' and resid 294 through 304
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 365 through 369
      removed outlier: 3.964A  pdb=" N   LEU A 368 " --> pdb=" O   TYR A 365 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   TYR A 369 " --> pdb=" O   SER A 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 365 through 369'
    Processing helix  chain 'A' and resid 383 through 388
      removed outlier: 4.237A  pdb=" N   ASN A 388 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 3.759A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 422
    Processing helix  chain 'A' and resid 438 through 443
      removed outlier: 3.783A  pdb=" N   ASP A 442 " --> pdb=" O   SER A 438 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 127 through 134
      removed outlier: 3.690A  pdb=" N   LEU M 131 " --> pdb=" O   SER M 127 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LYS M 132 " --> pdb=" O   ASP M 128 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   SER M 133 " --> pdb=" O   GLU M 129 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLY M 134 " --> pdb=" O   GLN M 130 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'M' and resid 127 through 134'
    Processing helix  chain 'M' and resid 189 through 193
    Processing helix  chain 'B' and resid 294 through 304
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 365 through 369
      removed outlier: 3.965A  pdb=" N   LEU B 368 " --> pdb=" O   TYR B 365 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   TYR B 369 " --> pdb=" O   SER B 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 365 through 369'
    Processing helix  chain 'B' and resid 383 through 388
      removed outlier: 4.237A  pdb=" N   ASN B 388 " --> pdb=" O   PRO B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 3.759A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.783A  pdb=" N   ASP B 442 " --> pdb=" O   SER B 438 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 160 through 162
      No H-bonds generated for 'chain 'I' and resid 160 through 162'
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11
      removed outlier: 3.749A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 114 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   THR H 116 " --> pdb=" O   GLU H  10 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.556A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 11
      removed outlier: 3.749A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 114 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   THR H 116 " --> pdb=" O   GLU H  10 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   VAL H 108 " --> pdb=" O   GLY H  98 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 124 through 128
      removed outlier: 4.342A  pdb=" N   GLY H 143 " --> pdb=" O   LEU H 128 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   CYS H 144 " --> pdb=" O   SER H 184 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   SER H 184 " --> pdb=" O   CYS H 144 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ASP H 148 " --> pdb=" O   TYR H 180 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   TYR H 180 " --> pdb=" O   ASP H 148 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 155 through 158
      removed outlier: 4.747A  pdb=" N   TYR H 198 " --> pdb=" O   VAL H 215 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.247A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 111 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   TRP L  41 " --> pdb=" O   LEU L  53 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 30 through 31
      removed outlier: 3.772A  pdb=" N   LYS L  36 " --> pdb=" O   TYR L  31 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 120 through 124
      removed outlier: 3.879A  pdb=" N   SER L 120 " --> pdb=" O   ASN L 143 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ASN L 143 " --> pdb=" O   SER L 120 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 159 through 160
      removed outlier: 3.637A  pdb=" N   TYR L 198 " --> pdb=" O   PHE L 215 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 49 through 55
      removed outlier: 3.512A  pdb=" N   HIS A  49 " --> pdb=" O   LEU A 277 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU A 277 " --> pdb=" O   HIS A  49 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLN A 271 " --> pdb=" O   PHE A  55 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   ASP A 287 " --> pdb=" O   LYS A 278 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 63 through 67
      removed outlier: 4.369A  pdb=" N   LYS A 187 " --> pdb=" O   ILE A 210 " (cutoff:3.500A)
      removed outlier: 5.910A  pdb=" N   SER A 205 " --> pdb=" O   PRO A 225 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 83 through 85
      removed outlier: 3.838A  pdb=" N   PHE A 168 " --> pdb=" O   VAL A 130 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 151 through 163
      removed outlier: 6.522A  pdb=" N   SER A 151 " --> pdb=" O   TYR A 144 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   TYR A 144 " --> pdb=" O   SER A 151 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   MET A 153 " --> pdb=" O   GLY A 142 " (cutoff:3.500A)
      removed outlier: 7.183A  pdb=" N   GLY A 142 " --> pdb=" O   MET A 153 " (cutoff:3.500A)
      removed outlier: 9.300A  pdb=" N   SER A 155 " --> pdb=" O   PHE A 140 " (cutoff:3.500A)
      removed outlier: 11.347A  pdb=" N   PHE A 140 " --> pdb=" O   SER A 155 " (cutoff:3.500A)
      removed outlier: 9.837A  pdb=" N   PHE A 157 " --> pdb=" O   ASP A 138 " (cutoff:3.500A)
      removed outlier: 11.223A  pdb=" N   ASP A 138 " --> pdb=" O   PHE A 157 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   VAL A 159 " --> pdb=" O   CYS A 136 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   GLN A 134 " --> pdb=" O   SER A 161 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 311 through 313
      removed outlier: 3.569A  pdb=" N   GLY A 311 " --> pdb=" O   THR A 599 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 324 through 328
      removed outlier: 3.761A  pdb=" N   VAL A 539 " --> pdb=" O   GLY A 550 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   THR A 588 " --> pdb=" O   VAL A 551 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   THR A 553 " --> pdb=" O   ASP A 586 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ASP A 586 " --> pdb=" O   THR A 553 " (cutoff:3.500A)
      removed outlier: 5.192A  pdb=" N   ASP A 574 " --> pdb=" O   ILE A 587 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   GLY A 566 " --> pdb=" O   ASP A 574 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.912A  pdb=" N   ILE A 358 " --> pdb=" O   VAL A 395 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
      removed outlier: 4.907A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 4.906A  pdb=" N   GLU A 516 " --> pdb=" O   ASN A 394 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ALA A 435 " --> pdb=" O   THR A 376 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AC1, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AC2, first strand: chain 'A' and resid 664 through 667
      removed outlier: 6.263A  pdb=" N   ILE A 670 " --> pdb=" O   ILE A 666 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'M' and resid 4 through 7
    Processing sheet with id=AC4, first strand: chain 'M' and resid 10 through 13
      removed outlier: 6.247A  pdb=" N   LEU M  11 " --> pdb=" O   GLU M 111 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   TRP M  41 " --> pdb=" O   LEU M  53 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'M' and resid 30 through 31
      removed outlier: 3.773A  pdb=" N   LYS M  36 " --> pdb=" O   TYR M  31 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'M' and resid 120 through 124
      removed outlier: 3.879A  pdb=" N   SER M 120 " --> pdb=" O   ASN M 143 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ASN M 143 " --> pdb=" O   SER M 120 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'M' and resid 159 through 160
      removed outlier: 3.637A  pdb=" N   TYR M 198 " --> pdb=" O   PHE M 215 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 49 through 55
      removed outlier: 3.512A  pdb=" N   HIS B  49 " --> pdb=" O   LEU B 277 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU B 277 " --> pdb=" O   HIS B  49 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLN B 271 " --> pdb=" O   PHE B  55 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   ASP B 287 " --> pdb=" O   LYS B 278 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'B' and resid 63 through 67
      removed outlier: 4.368A  pdb=" N   LYS B 187 " --> pdb=" O   ILE B 210 " (cutoff:3.500A)
      removed outlier: 5.910A  pdb=" N   SER B 205 " --> pdb=" O   PRO B 225 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'B' and resid 83 through 85
      removed outlier: 3.838A  pdb=" N   PHE B 168 " --> pdb=" O   VAL B 130 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'B' and resid 151 through 163
      removed outlier: 6.522A  pdb=" N   SER B 151 " --> pdb=" O   TYR B 144 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   TYR B 144 " --> pdb=" O   SER B 151 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   MET B 153 " --> pdb=" O   GLY B 142 " (cutoff:3.500A)
      removed outlier: 7.183A  pdb=" N   GLY B 142 " --> pdb=" O   MET B 153 " (cutoff:3.500A)
      removed outlier: 9.300A  pdb=" N   SER B 155 " --> pdb=" O   PHE B 140 " (cutoff:3.500A)
      removed outlier: 11.347A  pdb=" N   PHE B 140 " --> pdb=" O   SER B 155 " (cutoff:3.500A)
      removed outlier: 9.838A  pdb=" N   PHE B 157 " --> pdb=" O   ASP B 138 " (cutoff:3.500A)
      removed outlier: 11.224A  pdb=" N   ASP B 138 " --> pdb=" O   PHE B 157 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   VAL B 159 " --> pdb=" O   CYS B 136 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   GLN B 134 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'B' and resid 311 through 313
      removed outlier: 3.569A  pdb=" N   GLY B 311 " --> pdb=" O   THR B 599 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'B' and resid 324 through 328
      removed outlier: 3.761A  pdb=" N   VAL B 539 " --> pdb=" O   GLY B 550 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   THR B 588 " --> pdb=" O   VAL B 551 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   THR B 553 " --> pdb=" O   ASP B 586 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ASP B 586 " --> pdb=" O   THR B 553 " (cutoff:3.500A)
      removed outlier: 5.192A  pdb=" N   ASP B 574 " --> pdb=" O   ILE B 587 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   GLY B 566 " --> pdb=" O   ASP B 574 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.912A  pdb=" N   ILE B 358 " --> pdb=" O   VAL B 395 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   VAL B 395 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 4.907A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 4.907A  pdb=" N   GLU B 516 " --> pdb=" O   ASN B 394 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ALA B 435 " --> pdb=" O   THR B 376 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AD7, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AD8, first strand: chain 'B' and resid 664 through 667
      removed outlier: 6.264A  pdb=" N   ILE B 670 " --> pdb=" O   ILE B 666 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'I' and resid 3 through 6
    Processing sheet with id=AE1, first strand: chain 'I' and resid 10 through 11
      removed outlier: 3.749A  pdb=" N   GLU I  10 " --> pdb=" O   THR I 114 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   THR I 116 " --> pdb=" O   GLU I  10 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLY I  49 " --> pdb=" O   TRP I  36 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ARG I  38 " --> pdb=" O   TRP I  47 " (cutoff:3.500A)
      removed outlier: 5.556A  pdb=" N   TRP I  47 " --> pdb=" O   ARG I  38 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'I' and resid 10 through 11
      removed outlier: 3.749A  pdb=" N   GLU I  10 " --> pdb=" O   THR I 114 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   THR I 116 " --> pdb=" O   GLU I  10 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   VAL I 108 " --> pdb=" O   GLY I  98 " (cutoff:3.500A)
    Processing sheet with id=AE3, first strand: chain 'I' and resid 124 through 128
      removed outlier: 4.343A  pdb=" N   GLY I 143 " --> pdb=" O   LEU I 128 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   CYS I 144 " --> pdb=" O   SER I 184 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   SER I 184 " --> pdb=" O   CYS I 144 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ASP I 148 " --> pdb=" O   TYR I 180 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   TYR I 180 " --> pdb=" O   ASP I 148 " (cutoff:3.500A)
    Processing sheet with id=AE4, first strand: chain 'I' and resid 155 through 158
      removed outlier: 4.747A  pdb=" N   TYR I 198 " --> pdb=" O   VAL I 215 " (cutoff:3.500A)

    528 hydrogen bonds defined for protein.
    1344 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: 6.95

  Time building geometry restraints manager: 5.10 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 4594
        1.33 -     1.46: 3725
        1.46 -     1.58: 8629
        1.58 -     1.70: 0
        1.70 -     1.82: 80
  Bond restraints: 17028
  Sorted by residual:
  bond pdb=" N   VAL B 595 "
       pdb=" CA  VAL B 595 "
    ideal  model  delta    sigma   weight residual
    1.456  1.497 -0.040 1.14e-02 7.69e+03 1.25e+01
  bond pdb=" N   VAL A 595 "
       pdb=" CA  VAL A 595 "
    ideal  model  delta    sigma   weight residual
    1.456  1.497 -0.040 1.14e-02 7.69e+03 1.24e+01
  bond pdb=" N   VAL A 534 "
       pdb=" CA  VAL A 534 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.039 1.15e-02 7.56e+03 1.13e+01
  bond pdb=" N   VAL B 534 "
       pdb=" CA  VAL B 534 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.038 1.15e-02 7.56e+03 1.11e+01
  bond pdb=" N   VAL B 551 "
       pdb=" CA  VAL B 551 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.22e-02 6.72e+03 1.07e+01
  ... (remaining 17023 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.74: 21616
        1.74 -     3.49: 1281
        3.49 -     5.23: 231
        5.23 -     6.98: 30
        6.98 -     8.72: 14
  Bond angle restraints: 23172
  Sorted by residual:
  angle pdb=" N   PRO A 217 "
        pdb=" CA  PRO A 217 "
        pdb=" C   PRO A 217 "
      ideal   model   delta    sigma   weight residual
     111.22  116.86   -5.64 1.40e+00 5.10e-01 1.62e+01
  angle pdb=" N   PRO B 217 "
        pdb=" CA  PRO B 217 "
        pdb=" C   PRO B 217 "
      ideal   model   delta    sigma   weight residual
     111.22  116.86   -5.64 1.40e+00 5.10e-01 1.62e+01
  angle pdb=" N   ASN B 536 "
        pdb=" CA  ASN B 536 "
        pdb=" C   ASN B 536 "
      ideal   model   delta    sigma   weight residual
     111.74  117.02   -5.28 1.35e+00 5.49e-01 1.53e+01
  angle pdb=" N   ASN A 536 "
        pdb=" CA  ASN A 536 "
        pdb=" C   ASN A 536 "
      ideal   model   delta    sigma   weight residual
     111.74  117.02   -5.28 1.35e+00 5.49e-01 1.53e+01
  angle pdb=" CA  GLY B 268 "
        pdb=" C   GLY B 268 "
        pdb=" O   GLY B 268 "
      ideal   model   delta    sigma   weight residual
     121.76  117.78    3.98 1.03e+00 9.43e-01 1.49e+01
  ... (remaining 23167 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 9249
       17.87 -    35.75: 635
       35.75 -    53.62: 146
       53.62 -    71.49: 30
       71.49 -    89.37: 8
  Dihedral angle restraints: 10068
    sinusoidal: 3908
      harmonic: 6160
  Sorted by residual:
  dihedral pdb=" C   ASP A 578 "
           pdb=" N   ASP A 578 "
           pdb=" CA  ASP A 578 "
           pdb=" CB  ASP A 578 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.80   11.20     0      2.50e+00 1.60e-01 2.01e+01
  dihedral pdb=" C   ASP B 578 "
           pdb=" N   ASP B 578 "
           pdb=" CA  ASP B 578 "
           pdb=" CB  ASP B 578 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.73   11.13     0      2.50e+00 1.60e-01 1.98e+01
  dihedral pdb=" C   ASN B 280 "
           pdb=" N   ASN B 280 "
           pdb=" CA  ASN B 280 "
           pdb=" CB  ASN B 280 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.43   10.83     0      2.50e+00 1.60e-01 1.87e+01
  ... (remaining 10065 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 2015
       0.069 -    0.137: 474
       0.137 -    0.206: 61
       0.206 -    0.275: 20
       0.275 -    0.343: 6
  Chirality restraints: 2576
  Sorted by residual:
  chirality pdb=" CA  ASN B 536 "
            pdb=" N   ASN B 536 "
            pdb=" C   ASN B 536 "
            pdb=" CB  ASN B 536 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.95e+00
  chirality pdb=" CA  ASN A 536 "
            pdb=" N   ASN A 536 "
            pdb=" C   ASN A 536 "
            pdb=" CB  ASN A 536 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.94e+00
  chirality pdb=" CA  ASP A 578 "
            pdb=" N   ASP A 578 "
            pdb=" C   ASP A 578 "
            pdb=" CB  ASP A 578 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.80e+00
  ... (remaining 2573 not shown)

  Planarity restraints: 2976
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 548 "   -0.018 2.00e-02 2.50e+03   3.54e-02 1.25e+01
        pdb=" C   GLY B 548 "    0.061 2.00e-02 2.50e+03
        pdb=" O   GLY B 548 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   THR B 549 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 548 "    0.018 2.00e-02 2.50e+03   3.51e-02 1.23e+01
        pdb=" C   GLY A 548 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   GLY A 548 "    0.023 2.00e-02 2.50e+03
        pdb=" N   THR A 549 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 571 "   -0.013 2.00e-02 2.50e+03   2.61e-02 6.81e+00
        pdb=" C   ASP A 571 "    0.045 2.00e-02 2.50e+03
        pdb=" O   ASP A 571 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   THR A 572 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 2973 not shown)

  Histogram of nonbonded interaction distances:
        1.19 -     1.93: 6
        1.93 -     2.67: 303
        2.67 -     3.42: 20450
        3.42 -     4.16: 36938
        4.16 -     4.90: 65913
  Nonbonded interactions: 123610
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG B 273 "
            pdb=" OD2 ASP B 290 "
     model   vdw
     1.188 3.120
  nonbonded pdb=" NH2 ARG A 273 "
            pdb=" OD2 ASP A 290 "
     model   vdw
     1.189 3.120
  nonbonded pdb=" NH2 ARG A 273 "
            pdb=" CG  ASP A 290 "
     model   vdw
     1.373 3.350
  nonbonded pdb=" NH2 ARG B 273 "
            pdb=" CG  ASP B 290 "
     model   vdw
     1.373 3.350
  nonbonded pdb=" NH2 ARG A 273 "
            pdb=" OD1 ASP A 290 "
     model   vdw
     1.766 3.120
  ... (remaining 123605 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: 0.09
Found NCS groups:
ncs_group {
  reference = chain 'D'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'I'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'M'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             3.850
  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:             0.020
  Extract box with map and model:          0.620
  Check model and map are aligned:         0.110
  Set scattering table:                    0.150
  Process input model:                     46.260
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.080
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   54.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6684
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      :  0.006   0.041  17032  Z= 0.370
  Angle     :  0.932   8.725  23184  Z= 0.569
  Chirality :  0.062   0.343   2576
  Planarity :  0.005   0.051   2974
  Dihedral  : 13.403  89.368   6136
  Min Nonbonded Distance : 1.188

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  6.94 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  5.66 %
    Favored  : 93.70 %
  Cbeta Deviations :  0.20 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    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: -2.00 (0.17), residues: 2104
  helix: -2.03 (0.51), residues: 88
  sheet:  0.09 (0.20), residues: 698
  loop : -2.23 (0.15), residues: 1318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP H  83 
 HIS   0.010   0.001   HIS L 195 
 PHE   0.017   0.002   PHE H  29 
 TYR   0.019   0.002   TYR B 351 
 ARG   0.006   0.001   ARG B 328 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00032 (    2)
  link_NAG-ASN         : angle       2.40095 (    6)
  link_BETA1-4         : bond        0.00292 (    2)
  link_BETA1-4         : angle       1.30212 (    6)
  hydrogen bonds       : bond        0.14456 (  520)
  hydrogen bonds       : angle       8.38848 ( 1344)
  covalent geometry    : bond        0.00606 (17028)
  covalent geometry    : angle       0.93115 (23172)

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 200
  time to evaluate  : 2.006 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 MET cc_start: -0.2022 (ttm) cc_final: -0.4005 (mtp)
REVERT: B  177 MET cc_start: -0.1960 (ttm) cc_final: -0.3964 (mtp)
  outliers start: 12
  outliers final: 2
  residues processed: 208
  average time/residue: 0.3503
  time to fit residues: 104.1393
Evaluate side-chains
  92 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 90
  time to evaluate  : 1.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain B residue  525 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 177 optimal weight:    2.9990
   chunk 159 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 54 optimal weight:   30.0000
   chunk 107 optimal weight:    1.9990
   chunk 85 optimal weight:    0.0670
   chunk 164 optimal weight:    0.8980
   chunk 63 optimal weight:    5.9990
   chunk 100 optimal weight:    0.9990
   chunk 122 optimal weight:    3.9990
   chunk 190 optimal weight:    4.9990
   overall best weight:    1.1924

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

Flipped N/Q/H residues before XYZ refinement:
H   1 GLN
H  39 GLN
H  77 ASN
L   6 GLN
L  35 ASN
L  44 GLN
L  95 GLN
L 106 GLN
L 164 ASN
A  66 HIS
A 115 GLN
A 146 HIS
A 164 ASN
A 218 GLN
A 239 GLN
A 245 HIS
A 271 GLN
A 321 GLN
A 540 ASN
A 542 ASN
A 563 GLN
A 613 GLN
A 641 ASN
A 658 ASN
A 675 GLN
M   6 GLN
M  35 ASN
M  44 GLN
M  95 GLN
M 106 GLN
B  66 HIS
B 115 GLN
B 146 HIS
B 164 ASN
B 218 GLN
B 239 GLN
B 245 HIS
B 271 GLN
B 321 GLN
B 370 ASN
B 493 GLN
B 540 ASN
B 542 ASN
B 613 GLN
B 641 ASN
B 658 ASN
B 675 GLN
I  77 ASN
** I 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 48

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.106033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.076423 restraints weight = 55297.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.073829 restraints weight = 42405.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.074389 restraints weight = 48138.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.2375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  17032  Z= 0.177
  Angle     :  0.692   7.192  23184  Z= 0.362
  Chirality :  0.047   0.145   2576
  Planarity :  0.005   0.039   2974
  Dihedral  :  5.565  44.414   2380
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.23 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 10.02 %
    Favored  : 88.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    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: -1.63 (0.17), residues: 2104
  helix: -2.12 (0.57), residues: 74
  sheet:  0.43 (0.19), residues: 716
  loop : -2.03 (0.15), residues: 1314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP I  83 
 HIS   0.004   0.001   HIS M 195 
 PHE   0.024   0.002   PHE A  55 
 TYR   0.030   0.002   TYR B 612 
 ARG   0.005   0.001   ARG L  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00228 (    2)
  link_NAG-ASN         : angle       1.76686 (    6)
  link_BETA1-4         : bond        0.00366 (    2)
  link_BETA1-4         : angle       1.03217 (    6)
  hydrogen bonds       : bond        0.04399 (  520)
  hydrogen bonds       : angle       7.00305 ( 1344)
  covalent geometry    : bond        0.00414 (17028)
  covalent geometry    : angle       0.69119 (23172)

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 105
  time to evaluate  : 1.819 
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: H  149 TYR cc_start: 0.8809 (p90) cc_final: 0.8585 (p90)
REVERT: A  153 MET cc_start: 0.7427 (ppp) cc_final: 0.7225 (ppp)
REVERT: A  177 MET cc_start: -0.3028 (ttm) cc_final: -0.3479 (mtp)
REVERT: B  153 MET cc_start: 0.7517 (ppp) cc_final: 0.7292 (ppp)
REVERT: B  177 MET cc_start: -0.3263 (ttm) cc_final: -0.4207 (mtp)
REVERT: I    2 MET cc_start: 0.7798 (ppp) cc_final: 0.6979 (ppp)
  outliers start: 29
  outliers final: 18
  residues processed: 127
  average time/residue: 0.2721
  time to fit residues: 54.7406
Evaluate side-chains
  99 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 2.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  655 HIS
Chi-restraints excluded: chain M residue  195 HIS
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  649 CYS
Chi-restraints excluded: chain B residue  650 LEU
Chi-restraints excluded: chain B residue  655 HIS
Chi-restraints excluded: chain I residue  104 THR
Chi-restraints excluded: chain I residue  179 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 43 optimal weight:    5.9990
   chunk 80 optimal weight:    0.9980
   chunk 180 optimal weight:    6.9990
   chunk 183 optimal weight:    4.9990
   chunk 123 optimal weight:    6.9990
   chunk 78 optimal weight:    2.9990
   chunk 52 optimal weight:   20.0000
   chunk 143 optimal weight:   10.0000
   chunk 41 optimal weight:    0.0970
   chunk 100 optimal weight:    0.5980
   overall best weight:    1.5382

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

Flipped N/Q/H residues before XYZ refinement:
** H   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  95 GLN
** L 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 216 ASN
A 370 ASN
A 474 GLN
A 493 GLN
A 563 GLN
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  95 GLN
** M 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 164 ASN
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 216 ASN
B 474 GLN
** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 196 GLN
** I 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.102860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.073792 restraints weight = 55927.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.071873 restraints weight = 48148.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.072114 restraints weight = 61980.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.3278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  17032  Z= 0.199
  Angle     :  0.651   8.988  23184  Z= 0.341
  Chirality :  0.046   0.156   2576
  Planarity :  0.004   0.044   2974
  Dihedral  :  5.458  46.952   2378
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 12.61 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    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: -1.45 (0.17), residues: 2104
  helix: -2.28 (0.57), residues: 76
  sheet:  0.50 (0.19), residues: 730
  loop : -1.87 (0.16), residues: 1298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 633 
 HIS   0.009   0.001   HIS M 195 
 PHE   0.013   0.002   PHE I 170 
 TYR   0.013   0.002   TYR A 612 
 ARG   0.004   0.000   ARG B 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00104 (    2)
  link_NAG-ASN         : angle       1.47637 (    6)
  link_BETA1-4         : bond        0.00479 (    2)
  link_BETA1-4         : angle       1.23606 (    6)
  hydrogen bonds       : bond        0.04257 (  520)
  hydrogen bonds       : angle       6.60436 ( 1344)
  covalent geometry    : bond        0.00469 (17028)
  covalent geometry    : angle       0.65083 (23172)

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 84
  time to evaluate  : 1.797 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   51 ILE cc_start: 0.8765 (tp) cc_final: 0.8491 (tt)
REVERT: H  149 TYR cc_start: 0.8583 (p90) cc_final: 0.8285 (p90)
REVERT: A  153 MET cc_start: 0.7672 (ppp) cc_final: 0.6317 (pmm)
REVERT: A  177 MET cc_start: -0.3236 (ttm) cc_final: -0.4296 (mpp)
REVERT: A  353 TRP cc_start: 0.8826 (OUTLIER) cc_final: 0.7773 (p-90)
REVERT: B  128 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8828 (tp)
REVERT: B  153 MET cc_start: 0.7642 (ppp) cc_final: 0.6197 (pmm)
REVERT: B  177 MET cc_start: -0.3269 (ttm) cc_final: -0.3486 (mmm)
REVERT: B  353 TRP cc_start: 0.8828 (OUTLIER) cc_final: 0.7757 (p-90)
  outliers start: 39
  outliers final: 27
  residues processed: 113
  average time/residue: 0.2388
  time to fit residues: 44.7471
Evaluate side-chains
  106 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 76
  time to evaluate  : 1.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain L residue  191 ASP
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  353 TRP
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  655 HIS
Chi-restraints excluded: chain M residue  191 ASP
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  353 TRP
Chi-restraints excluded: chain B residue  361 CYS
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  552 LEU
Chi-restraints excluded: chain B residue  650 LEU
Chi-restraints excluded: chain B residue  655 HIS
Chi-restraints excluded: chain I residue  173 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 132 optimal weight:    6.9990
   chunk 120 optimal weight:    0.8980
   chunk 110 optimal weight:    0.0000
   chunk 161 optimal weight:    0.5980
   chunk 75 optimal weight:    3.9990
   chunk 92 optimal weight:    0.0170
   chunk 4 optimal weight:    0.9990
   chunk 102 optimal weight:    6.9990
   chunk 203 optimal weight:    1.9990
   chunk 60 optimal weight:    0.2980
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.3622

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

Flipped N/Q/H residues before XYZ refinement:
L  95 GLN
** L 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 153 GLN
** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 422 ASN
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  95 GLN
** M 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 422 ASN
** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.102069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.068109 restraints weight = 54339.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.067448 restraints weight = 33385.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.067598 restraints weight = 26690.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.3481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  17032  Z= 0.102
  Angle     :  0.555   7.024  23184  Z= 0.288
  Chirality :  0.044   0.150   2576
  Planarity :  0.004   0.053   2974
  Dihedral  :  5.052  49.300   2378
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 14.33 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    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: -1.24 (0.18), residues: 2104
  helix: -2.32 (0.53), residues: 88
  sheet:  0.64 (0.19), residues: 754
  loop : -1.74 (0.16), residues: 1262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP I  83 
 HIS   0.003   0.000   HIS A  66 
 PHE   0.021   0.001   PHE B 135 
 TYR   0.024   0.001   TYR I 180 
 ARG   0.003   0.000   ARG L  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00239 (    2)
  link_NAG-ASN         : angle       1.14430 (    6)
  link_BETA1-4         : bond        0.00296 (    2)
  link_BETA1-4         : angle       0.78810 (    6)
  hydrogen bonds       : bond        0.03429 (  520)
  hydrogen bonds       : angle       6.10527 ( 1344)
  covalent geometry    : bond        0.00228 (17028)
  covalent geometry    : angle       0.55468 (23172)

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 94
  time to evaluate  : 1.977 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   51 ILE cc_start: 0.8757 (tp) cc_final: 0.8489 (tt)
REVERT: A  128 ILE cc_start: 0.9451 (OUTLIER) cc_final: 0.9117 (tp)
REVERT: A  153 MET cc_start: 0.8022 (ppp) cc_final: 0.6794 (pmm)
REVERT: B  128 ILE cc_start: 0.9462 (OUTLIER) cc_final: 0.9085 (tp)
REVERT: B  153 MET cc_start: 0.7978 (ppp) cc_final: 0.6659 (pmm)
REVERT: B  168 PHE cc_start: 0.8096 (t80) cc_final: 0.7875 (t80)
  outliers start: 32
  outliers final: 16
  residues processed: 121
  average time/residue: 0.2565
  time to fit residues: 50.8854
Evaluate side-chains
  96 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 1.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  361 CYS
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  650 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 147 optimal weight:    0.0070
   chunk 1 optimal weight:    0.0670
   chunk 117 optimal weight:    0.7980
   chunk 174 optimal weight:    4.9990
   chunk 181 optimal weight:    0.0970
   chunk 188 optimal weight:    3.9990
   chunk 101 optimal weight:    8.9990
   chunk 135 optimal weight:    4.9990
   chunk 209 optimal weight:    5.9990
   chunk 88 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   overall best weight:    0.9936

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

Flipped N/Q/H residues before XYZ refinement:
** H   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 130 GLN
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.100443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.065968 restraints weight = 54993.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.065894 restraints weight = 32644.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.065787 restraints weight = 25808.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.3801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  17032  Z= 0.146
  Angle     :  0.564   6.307  23184  Z= 0.296
  Chirality :  0.044   0.157   2576
  Planarity :  0.004   0.040   2974
  Dihedral  :  5.013  54.506   2378
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 14.92 %
    Favored  : 83.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    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: -1.21 (0.18), residues: 2104
  helix: -2.23 (0.57), residues: 76
  sheet:  0.62 (0.19), residues: 766
  loop : -1.73 (0.16), residues: 1262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP I  83 
 HIS   0.003   0.001   HIS A  66 
 PHE   0.010   0.001   PHE A 175 
 TYR   0.019   0.001   TYR I 180 
 ARG   0.003   0.000   ARG L  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00089 (    2)
  link_NAG-ASN         : angle       1.28282 (    6)
  link_BETA1-4         : bond        0.00023 (    2)
  link_BETA1-4         : angle       0.95780 (    6)
  hydrogen bonds       : bond        0.03682 (  520)
  hydrogen bonds       : angle       6.01450 ( 1344)
  covalent geometry    : bond        0.00347 (17028)
  covalent geometry    : angle       0.56376 (23172)

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 83
  time to evaluate  : 2.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   22 CYS cc_start: 0.9303 (OUTLIER) cc_final: 0.9068 (t)
REVERT: H   51 ILE cc_start: 0.8859 (tp) cc_final: 0.8597 (tt)
REVERT: L   31 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.7311 (t80)
REVERT: A  128 ILE cc_start: 0.9516 (OUTLIER) cc_final: 0.9148 (tp)
REVERT: A  153 MET cc_start: 0.8110 (ppp) cc_final: 0.6989 (pmm)
REVERT: M   31 TYR cc_start: 0.8688 (OUTLIER) cc_final: 0.6983 (t80)
REVERT: B  128 ILE cc_start: 0.9516 (OUTLIER) cc_final: 0.9043 (tp)
REVERT: B  153 MET cc_start: 0.8094 (ppp) cc_final: 0.6875 (pmm)
REVERT: B  229 LEU cc_start: 0.9490 (mt) cc_final: 0.9208 (mp)
REVERT: I  185 VAL cc_start: 0.9064 (OUTLIER) cc_final: 0.8819 (m)
  outliers start: 38
  outliers final: 22
  residues processed: 117
  average time/residue: 0.2909
  time to fit residues: 55.6617
Evaluate side-chains
  102 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 74
  time to evaluate  : 2.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue  125 VAL
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   31 TYR
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain M residue    2 ILE
Chi-restraints excluded: chain M residue   31 TYR
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  361 CYS
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain I residue  185 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 88 optimal weight:    0.7980
   chunk 141 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 79 optimal weight:    0.9980
   chunk 142 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 23 optimal weight:    4.9990
   chunk 143 optimal weight:    8.9990
   chunk 173 optimal weight:    2.9990
   chunk 52 optimal weight:   20.0000
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
L 130 GLN
** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.101497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.071747 restraints weight = 56162.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.068951 restraints weight = 44060.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.069565 restraints weight = 58166.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.4073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  17032  Z= 0.128
  Angle     :  0.537   6.688  23184  Z= 0.281
  Chirality :  0.044   0.154   2576
  Planarity :  0.004   0.041   2974
  Dihedral  :  4.798  48.925   2378
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 14.87 %
    Favored  : 82.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    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: -1.15 (0.18), residues: 2104
  helix: -2.15 (0.56), residues: 76
  sheet:  0.59 (0.19), residues: 784
  loop : -1.67 (0.16), residues: 1244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H  83 
 HIS   0.002   0.001   HIS B  66 
 PHE   0.009   0.001   PHE B  79 
 TYR   0.015   0.001   TYR I 180 
 ARG   0.002   0.000   ARG L  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00185 (    2)
  link_NAG-ASN         : angle       1.20455 (    6)
  link_BETA1-4         : bond        0.00299 (    2)
  link_BETA1-4         : angle       0.93779 (    6)
  hydrogen bonds       : bond        0.03425 (  520)
  hydrogen bonds       : angle       5.82022 ( 1344)
  covalent geometry    : bond        0.00300 (17028)
  covalent geometry    : angle       0.53661 (23172)

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 77
  time to evaluate  : 1.787 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   22 CYS cc_start: 0.9278 (OUTLIER) cc_final: 0.9046 (t)
REVERT: H   51 ILE cc_start: 0.8856 (tp) cc_final: 0.8531 (tt)
REVERT: L   31 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.7078 (t80)
REVERT: A  128 ILE cc_start: 0.9458 (OUTLIER) cc_final: 0.9097 (tp)
REVERT: A  153 MET cc_start: 0.7989 (ppp) cc_final: 0.6856 (pmm)
REVERT: A  229 LEU cc_start: 0.9423 (mt) cc_final: 0.9145 (mp)
REVERT: A  353 TRP cc_start: 0.8899 (OUTLIER) cc_final: 0.7808 (p-90)
REVERT: M   31 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.7022 (t80)
REVERT: B  128 ILE cc_start: 0.9460 (OUTLIER) cc_final: 0.8997 (tp)
REVERT: B  153 MET cc_start: 0.8057 (ppp) cc_final: 0.6896 (pmm)
REVERT: B  229 LEU cc_start: 0.9354 (mt) cc_final: 0.9091 (mp)
REVERT: B  353 TRP cc_start: 0.8874 (OUTLIER) cc_final: 0.7800 (p-90)
REVERT: I  185 VAL cc_start: 0.9148 (OUTLIER) cc_final: 0.8886 (m)
  outliers start: 41
  outliers final: 24
  residues processed: 114
  average time/residue: 0.2317
  time to fit residues: 43.8740
Evaluate side-chains
  104 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 72
  time to evaluate  : 1.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain L residue   31 TYR
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  353 TRP
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  655 HIS
Chi-restraints excluded: chain M residue   31 TYR
Chi-restraints excluded: chain M residue  191 ASP
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  192 PHE
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  353 TRP
Chi-restraints excluded: chain B residue  361 CYS
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain I residue  125 VAL
Chi-restraints excluded: chain I residue  173 VAL
Chi-restraints excluded: chain I residue  185 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 46 optimal weight:    8.9990
   chunk 186 optimal weight:    8.9990
   chunk 169 optimal weight:    2.9990
   chunk 70 optimal weight:    6.9990
   chunk 68 optimal weight:    8.9990
   chunk 87 optimal weight:    2.9990
   chunk 47 optimal weight:   10.0000
   chunk 149 optimal weight:    6.9990
   chunk 20 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 89 optimal weight:    0.5980
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
L 161 GLN
** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 321 GLN
A 422 ASN
** M 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 321 GLN
B 422 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.099086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.070869 restraints weight = 55982.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.068636 restraints weight = 49058.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.069129 restraints weight = 63343.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.4426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063  17032  Z= 0.211
  Angle     :  0.604   7.703  23184  Z= 0.317
  Chirality :  0.046   0.146   2576
  Planarity :  0.004   0.041   2974
  Dihedral  :  4.882  38.160   2378
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 14.22 %
    Favored  : 83.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    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: -1.30 (0.17), residues: 2104
  helix: -2.22 (0.55), residues: 76
  sheet:  0.62 (0.19), residues: 742
  loop : -1.79 (0.16), residues: 1286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP I  83 
 HIS   0.003   0.001   HIS M 195 
 PHE   0.015   0.002   PHE I 170 
 TYR   0.016   0.002   TYR I 180 
 ARG   0.003   0.000   ARG A 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00055 (    2)
  link_NAG-ASN         : angle       1.38149 (    6)
  link_BETA1-4         : bond        0.00090 (    2)
  link_BETA1-4         : angle       1.10614 (    6)
  hydrogen bonds       : bond        0.04009 (  520)
  hydrogen bonds       : angle       5.99122 ( 1344)
  covalent geometry    : bond        0.00502 (17028)
  covalent geometry    : angle       0.60323 (23172)

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 73
  time to evaluate  : 2.032 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   22 CYS cc_start: 0.9344 (OUTLIER) cc_final: 0.9097 (t)
REVERT: H   51 ILE cc_start: 0.8909 (tp) cc_final: 0.8646 (tt)
REVERT: L   31 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.7018 (t80)
REVERT: A  128 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8860 (tp)
REVERT: A  153 MET cc_start: 0.7643 (ppp) cc_final: 0.6465 (pmm)
REVERT: A  353 TRP cc_start: 0.8923 (OUTLIER) cc_final: 0.8036 (p-90)
REVERT: M   31 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.6988 (t80)
REVERT: B  128 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8778 (tp)
REVERT: B  153 MET cc_start: 0.7651 (ppp) cc_final: 0.6610 (pmm)
REVERT: B  177 MET cc_start: -0.1612 (mmm) cc_final: -0.2526 (mpp)
REVERT: B  353 TRP cc_start: 0.8900 (OUTLIER) cc_final: 0.8018 (p-90)
REVERT: I  185 VAL cc_start: 0.9181 (OUTLIER) cc_final: 0.8929 (m)
  outliers start: 48
  outliers final: 30
  residues processed: 115
  average time/residue: 0.2482
  time to fit residues: 46.9187
Evaluate side-chains
  105 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 67
  time to evaluate  : 1.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue  125 VAL
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain L residue   31 TYR
Chi-restraints excluded: chain L residue   89 VAL
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  353 TRP
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  655 HIS
Chi-restraints excluded: chain M residue    2 ILE
Chi-restraints excluded: chain M residue   31 TYR
Chi-restraints excluded: chain M residue   89 VAL
Chi-restraints excluded: chain M residue  191 ASP
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  192 PHE
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  353 TRP
Chi-restraints excluded: chain B residue  361 CYS
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain B residue  655 HIS
Chi-restraints excluded: chain I residue  125 VAL
Chi-restraints excluded: chain I residue  173 VAL
Chi-restraints excluded: chain I residue  185 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 105 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0870
   chunk 170 optimal weight:    3.9990
   chunk 172 optimal weight:    2.9990
   chunk 178 optimal weight:    6.9990
   chunk 47 optimal weight:    4.9990
   chunk 169 optimal weight:    2.9990
   chunk 110 optimal weight:    0.7980
   chunk 91 optimal weight:    0.8980
   chunk 114 optimal weight:    0.9990
   overall best weight:    1.1562

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

Flipped N/Q/H residues before XYZ refinement:
** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 422 ASN
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 422 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.099827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.071190 restraints weight = 55604.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.068748 restraints weight = 46400.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.069225 restraints weight = 65366.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.4575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  17032  Z= 0.148
  Angle     :  0.546   6.585  23184  Z= 0.287
  Chirality :  0.045   0.185   2576
  Planarity :  0.004   0.038   2974
  Dihedral  :  4.685  36.899   2378
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 15.03 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    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: -1.24 (0.17), residues: 2104
  helix: -2.50 (0.45), residues: 100
  sheet:  0.65 (0.19), residues: 742
  loop : -1.70 (0.16), residues: 1262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP H  83 
 HIS   0.004   0.001   HIS M 195 
 PHE   0.016   0.001   PHE A 106 
 TYR   0.012   0.001   TYR L  55 
 ARG   0.002   0.000   ARG H  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00209 (    2)
  link_NAG-ASN         : angle       1.18608 (    6)
  link_BETA1-4         : bond        0.00236 (    2)
  link_BETA1-4         : angle       0.96154 (    6)
  hydrogen bonds       : bond        0.03550 (  520)
  hydrogen bonds       : angle       5.75402 ( 1344)
  covalent geometry    : bond        0.00348 (17028)
  covalent geometry    : angle       0.54539 (23172)

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 67
  time to evaluate  : 2.018 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   22 CYS cc_start: 0.9283 (OUTLIER) cc_final: 0.9053 (t)
REVERT: H   51 ILE cc_start: 0.8892 (tp) cc_final: 0.8583 (tt)
REVERT: L   31 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.7086 (t80)
REVERT: A  128 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.8902 (tp)
REVERT: A  153 MET cc_start: 0.7935 (ppp) cc_final: 0.6806 (pmm)
REVERT: A  177 MET cc_start: -0.1675 (mmm) cc_final: -0.2364 (mpp)
REVERT: A  353 TRP cc_start: 0.8906 (OUTLIER) cc_final: 0.7894 (p-90)
REVERT: M   31 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.7043 (t80)
REVERT: B  128 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.8909 (tp)
REVERT: B  153 MET cc_start: 0.7888 (ppp) cc_final: 0.6886 (pmm)
REVERT: B  353 TRP cc_start: 0.8885 (OUTLIER) cc_final: 0.7902 (p-90)
  outliers start: 41
  outliers final: 30
  residues processed: 104
  average time/residue: 0.2583
  time to fit residues: 44.3570
Evaluate side-chains
  103 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 66
  time to evaluate  : 2.040 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue  125 VAL
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  183 SER
Chi-restraints excluded: chain L residue   31 TYR
Chi-restraints excluded: chain L residue   89 VAL
Chi-restraints excluded: chain L residue  191 ASP
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  353 TRP
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain M residue   31 TYR
Chi-restraints excluded: chain M residue   89 VAL
Chi-restraints excluded: chain M residue  191 ASP
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  192 PHE
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  353 TRP
Chi-restraints excluded: chain B residue  361 CYS
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain I residue  125 VAL
Chi-restraints excluded: chain I residue  173 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 137 optimal weight:   30.0000
   chunk 75 optimal weight:    3.9990
   chunk 176 optimal weight:    4.9990
   chunk 165 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 124 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 173 optimal weight:    0.9990
   chunk 141 optimal weight:    0.9990
   chunk 100 optimal weight:    4.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.099930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.071609 restraints weight = 55974.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.069102 restraints weight = 48576.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.069764 restraints weight = 63672.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.4709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  17032  Z= 0.130
  Angle     :  0.533   8.310  23184  Z= 0.280
  Chirality :  0.044   0.170   2576
  Planarity :  0.004   0.040   2974
  Dihedral  :  4.546  36.193   2378
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 15.52 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    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: -1.17 (0.18), residues: 2104
  helix: -2.48 (0.45), residues: 100
  sheet:  0.77 (0.19), residues: 734
  loop : -1.68 (0.16), residues: 1270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H  83 
 HIS   0.002   0.001   HIS B  66 
 PHE   0.010   0.001   PHE B  79 
 TYR   0.013   0.001   TYR L  55 
 ARG   0.003   0.000   ARG H  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00186 (    2)
  link_NAG-ASN         : angle       1.24664 (    6)
  link_BETA1-4         : bond        0.00138 (    2)
  link_BETA1-4         : angle       0.93858 (    6)
  hydrogen bonds       : bond        0.03347 (  520)
  hydrogen bonds       : angle       5.59259 ( 1344)
  covalent geometry    : bond        0.00306 (17028)
  covalent geometry    : angle       0.53243 (23172)

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 69
  time to evaluate  : 1.994 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   22 CYS cc_start: 0.9277 (OUTLIER) cc_final: 0.9066 (t)
REVERT: H   51 ILE cc_start: 0.8871 (tp) cc_final: 0.8550 (tt)
REVERT: L   31 TYR cc_start: 0.8705 (OUTLIER) cc_final: 0.7052 (t80)
REVERT: A  128 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.8799 (tp)
REVERT: A  153 MET cc_start: 0.7761 (ppp) cc_final: 0.6631 (pmm)
REVERT: A  177 MET cc_start: -0.1748 (mmm) cc_final: -0.2415 (mpp)
REVERT: A  192 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7829 (m-80)
REVERT: A  353 TRP cc_start: 0.8909 (OUTLIER) cc_final: 0.7892 (p-90)
REVERT: M   31 TYR cc_start: 0.8648 (OUTLIER) cc_final: 0.6921 (t80)
REVERT: B  128 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.8844 (tp)
REVERT: B  153 MET cc_start: 0.7843 (ppp) cc_final: 0.6692 (pmm)
REVERT: B  177 MET cc_start: -0.2016 (mmm) cc_final: -0.2978 (mpp)
REVERT: B  353 TRP cc_start: 0.8904 (OUTLIER) cc_final: 0.7889 (p-90)
REVERT: I    2 MET cc_start: 0.8770 (ppp) cc_final: 0.7452 (ppp)
  outliers start: 41
  outliers final: 28
  residues processed: 106
  average time/residue: 0.2635
  time to fit residues: 45.3011
Evaluate side-chains
  102 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 66
  time to evaluate  : 1.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue  125 VAL
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  183 SER
Chi-restraints excluded: chain L residue   31 TYR
Chi-restraints excluded: chain L residue   89 VAL
Chi-restraints excluded: chain L residue  191 ASP
Chi-restraints excluded: chain L residue  216 ASN
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  353 TRP
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain M residue   31 TYR
Chi-restraints excluded: chain M residue   89 VAL
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  192 PHE
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  353 TRP
Chi-restraints excluded: chain B residue  361 CYS
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain I residue  125 VAL
Chi-restraints excluded: chain I residue  173 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 180 optimal weight:    2.9990
   chunk 67 optimal weight:    0.8980
   chunk 181 optimal weight:    0.9980
   chunk 120 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0770
   chunk 65 optimal weight:   20.0000
   chunk 113 optimal weight:    2.9990
   chunk 155 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0370
   chunk 188 optimal weight:    3.9990
   overall best weight:    0.5816

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

Flipped N/Q/H residues before XYZ refinement:
** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 321 GLN
** B 564 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 = 0.3975 r_free = 0.3975 target = 0.100528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.072148 restraints weight = 55698.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.070445 restraints weight = 48008.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.070828 restraints weight = 62096.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.4763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  17032  Z= 0.103
  Angle     :  0.514   7.808  23184  Z= 0.269
  Chirality :  0.044   0.156   2576
  Planarity :  0.004   0.038   2974
  Dihedral  :  4.388  34.506   2378
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 16.00 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    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: -1.08 (0.18), residues: 2104
  helix: -2.44 (0.45), residues: 100
  sheet:  0.78 (0.19), residues: 738
  loop : -1.60 (0.16), residues: 1266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A 258 
 HIS   0.002   0.000   HIS B  66 
 PHE   0.012   0.001   PHE A 106 
 TYR   0.013   0.001   TYR L  55 
 ARG   0.002   0.000   ARG L  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00212 (    2)
  link_NAG-ASN         : angle       1.20046 (    6)
  link_BETA1-4         : bond        0.00225 (    2)
  link_BETA1-4         : angle       0.90759 (    6)
  hydrogen bonds       : bond        0.03103 (  520)
  hydrogen bonds       : angle       5.40299 ( 1344)
  covalent geometry    : bond        0.00239 (17028)
  covalent geometry    : angle       0.51377 (23172)

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 68
  time to evaluate  : 1.769 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    2 MET cc_start: 0.8464 (ppp) cc_final: 0.7317 (ppp)
REVERT: H   22 CYS cc_start: 0.9258 (OUTLIER) cc_final: 0.9023 (t)
REVERT: H   51 ILE cc_start: 0.8827 (tp) cc_final: 0.8521 (tt)
REVERT: L   31 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.7130 (t80)
REVERT: A  128 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.8802 (tp)
REVERT: A  153 MET cc_start: 0.7758 (ppp) cc_final: 0.6714 (pmm)
REVERT: A  177 MET cc_start: -0.2012 (mmm) cc_final: -0.2844 (mpp)
REVERT: A  192 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7814 (m-80)
REVERT: M   31 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.6865 (t80)
REVERT: B  128 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.8842 (tp)
REVERT: B  153 MET cc_start: 0.7877 (ppp) cc_final: 0.6801 (pmm)
REVERT: B  177 MET cc_start: -0.2241 (mmm) cc_final: -0.3159 (mpp)
REVERT: B  258 TRP cc_start: 0.2905 (p-90) cc_final: 0.2666 (p-90)
REVERT: I    2 MET cc_start: 0.8651 (ppp) cc_final: 0.7410 (ppp)
  outliers start: 32
  outliers final: 24
  residues processed: 98
  average time/residue: 0.2720
  time to fit residues: 42.6143
Evaluate side-chains
  93 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 63
  time to evaluate  : 2.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue  125 VAL
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  183 SER
Chi-restraints excluded: chain L residue   31 TYR
Chi-restraints excluded: chain L residue   89 VAL
Chi-restraints excluded: chain L residue  216 ASN
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain M residue   31 TYR
Chi-restraints excluded: chain M residue   89 VAL
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  192 PHE
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  361 CYS
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain I residue  125 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 91 optimal weight:    0.0870
   chunk 26 optimal weight:    0.6980
   chunk 128 optimal weight:    0.9990
   chunk 171 optimal weight:    2.9990
   chunk 144 optimal weight:    0.0670
   chunk 46 optimal weight:    7.9990
   chunk 173 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 113 optimal weight:    2.9990
   chunk 145 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.7700

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

Flipped N/Q/H residues before XYZ refinement:
L 153 GLN
** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 564 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 = 0.3969 r_free = 0.3969 target = 0.100202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.071281 restraints weight = 56003.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.068907 restraints weight = 47015.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.069711 restraints weight = 55944.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.4860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  17032  Z= 0.117
  Angle     :  0.521   7.582  23184  Z= 0.273
  Chirality :  0.044   0.155   2576
  Planarity :  0.004   0.039   2974
  Dihedral  :  4.372  34.340   2378
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 15.84 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    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: -1.06 (0.18), residues: 2104
  helix: -2.45 (0.45), residues: 100
  sheet:  0.80 (0.19), residues: 738
  loop : -1.58 (0.16), residues: 1266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 258 
 HIS   0.002   0.000   HIS B  66 
 PHE   0.010   0.001   PHE A  79 
 TYR   0.013   0.001   TYR L  55 
 ARG   0.002   0.000   ARG L  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00174 (    2)
  link_NAG-ASN         : angle       1.25364 (    6)
  link_BETA1-4         : bond        0.00245 (    2)
  link_BETA1-4         : angle       1.01949 (    6)
  hydrogen bonds       : bond        0.03245 (  520)
  hydrogen bonds       : angle       5.36643 ( 1344)
  covalent geometry    : bond        0.00273 (17028)
  covalent geometry    : angle       0.52052 (23172)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5685.00 seconds
wall clock time: 102 minutes 21.04 seconds (6141.04 seconds total)