Starting phenix.real_space_refine
on Wed Mar  4 10:24:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7swd_25471/03_2026/7swd_25471.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7swd_25471/03_2026/7swd_25471.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7swd_25471/03_2026/7swd_25471.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7swd_25471/03_2026/7swd_25471.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7swd_25471/03_2026/7swd_25471.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7swd_25471/03_2026/7swd_25471.cif"
  }
  resolution = 3.59
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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      56      5.16       5
     C    8124      2.51       5
     N    2205      2.21       5
     O    2448      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12833
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 1153
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 151, 1153
          Classifications: {'peptide': 151}
          Link IDs: {'PTRANS': 10, 'TRANS': 140}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 758
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 758
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 4, 'TRANS': 91}
    Chain: "C"
      Number of atoms: 1153
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 151, 1153
          Classifications: {'peptide': 151}
          Link IDs: {'PTRANS': 10, 'TRANS': 140}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 758
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 758
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 4, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 1120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1120
          Classifications: {'peptide': 147}
          Link IDs: {'PTRANS': 10, 'TRANS': 136}
          Chain breaks: 2
    Chain: "F"
      Number of atoms: 758
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 758
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 4, 'TRANS': 91}
    Chain: "G"
      Number of atoms: 1734
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1734
          Classifications: {'peptide': 226}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 1734
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1734
          Classifications: {'peptide': 226}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 1760
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1760
          Classifications: {'peptide': 229}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 216}
          Chain breaks: 1
    Chain: "J"
      Number of atoms: 916
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 916
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 4, 'TRANS': 116}
    Chain: "K"
      Number of atoms: 872
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 872
          Classifications: {'peptide': 113}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 106}
    Chain: "M"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "N"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "L"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 3.04, per 1000 atoms: 0.24
  Number of scatterers: 12833
  At special positions: 0
  Unit cell: (133.1, 126.5, 104.5, 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      56     16.00
     O    2448      8.00
     N    2205      7.00
     C    8124      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=17, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 108 " - pdb=" SG  CYS A 135 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 121 " - pdb=" SG  CYS A 147 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 511 " - pdb=" SG  CYS B 556 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 108 " - pdb=" SG  CYS C 135 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 121 " - pdb=" SG  CYS C 147 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 511 " - pdb=" SG  CYS D 556 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 108 " - pdb=" SG  CYS E 135 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 121 " - pdb=" SG  CYS E 147 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 511 " - pdb=" SG  CYS F 556 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  22 " - pdb=" SG  CYS G  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 164 " - pdb=" SG  CYS G 234 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 164 " - pdb=" SG  CYS H 234 " distance=2.04
    Simple disulfide: pdb=" SG  CYS I  22 " - pdb=" SG  CYS I  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I 164 " - pdb=" SG  CYS I 234 " distance=2.04
    Simple disulfide: pdb=" SG  CYS J  22 " - pdb=" SG  CYS J  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  23 " - pdb=" SG  CYS K  94 " distance=2.04

  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 L   1 " - " NAG L   2 "
      " NAG L   2 " - " BMA L   3 "
      " NAG M   1 " - " NAG M   2 "
      " NAG M   2 " - " BMA M   3 "
      " NAG N   1 " - " NAG N   2 "
      " NAG N   2 " - " BMA N   3 "
    NAG-ASN
      " NAG L   1 " - " ASN B 563 "
      " NAG M   1 " - " ASN D 563 "
      " NAG N   1 " - " ASN F 563 "
  Time building additional restraints: 1.09
  Conformation dependent library (CDL) restraints added in 604.8 milliseconds
  

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2954

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 33 sheets defined
      12.0% alpha, 30.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 61
      No H-bonds generated for 'chain 'A' and resid 59 through 61'
    Processing helix  chain 'A' and resid 71 through 73
      No H-bonds generated for 'chain 'A' and resid 71 through 73'
    Processing helix  chain 'A' and resid 78 through 84
      removed outlier: 3.733A  pdb=" N   LYS A  84 " --> pdb=" O   PRO A  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 522 through 527
      removed outlier: 4.275A  pdb=" N   ALA B 525 " --> pdb=" O   ASP B 522 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   ILE B 527 " --> pdb=" O   GLY B 524 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 532 through 536
    Processing helix  chain 'B' and resid 551 through 576
      removed outlier: 4.956A  pdb=" N   GLN B 567 " --> pdb=" O   ASN B 563 " (cutoff:3.500A)
      removed outlier: 4.924A  pdb=" N   ALA B 568 " --> pdb=" O   GLU B 564 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 583 through 598
    Processing helix  chain 'C' and resid 59 through 61
      No H-bonds generated for 'chain 'C' and resid 59 through 61'
    Processing helix  chain 'C' and resid 71 through 74
    Processing helix  chain 'C' and resid 78 through 84
      removed outlier: 3.798A  pdb=" N   LYS C  84 " --> pdb=" O   PRO C  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 557 through 576
      removed outlier: 4.816A  pdb=" N   GLN D 567 " --> pdb=" O   ASN D 563 " (cutoff:3.500A)
      removed outlier: 4.787A  pdb=" N   ALA D 568 " --> pdb=" O   GLU D 564 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 583 through 597
      removed outlier: 3.843A  pdb=" N   ARG D 596 " --> pdb=" O   PHE D 592 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   TRP D 597 " --> pdb=" O   LEU D 593 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 59 through 61
      No H-bonds generated for 'chain 'E' and resid 59 through 61'
    Processing helix  chain 'E' and resid 78 through 83
    Processing helix  chain 'F' and resid 551 through 576
      removed outlier: 4.366A  pdb=" N   GLN F 567 " --> pdb=" O   ASN F 563 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   ALA F 568 " --> pdb=" O   GLU F 564 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 584 through 598
    Processing helix  chain 'G' and resid 88 through 92
    Processing helix  chain 'H' and resid 63 through 66
      removed outlier: 3.740A  pdb=" N   ARG H  66 " --> pdb=" O   ARG H  63 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 63 through 66'
    Processing helix  chain 'H' and resid 88 through 92
      removed outlier: 3.568A  pdb=" N   THR H  92 " --> pdb=" O   SER H  89 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 225 through 229
    Processing helix  chain 'I' and resid 63 through 66
    Processing helix  chain 'I' and resid 88 through 92
    Processing helix  chain 'J' and resid 87 through 91
    Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 38
    Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 160
      removed outlier: 5.405A  pdb=" N   ASN A  69 " --> pdb=" O   GLU A 103 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 89
    Processing sheet with id=AA4, first strand: chain 'A' and resid 165 through 167
      removed outlier: 6.646A  pdb=" N   VAL A  96 " --> pdb=" O   THR B 581 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 135 through 139
      removed outlier: 7.104A  pdb=" N   GLU A 106 " --> pdb=" O   CYS A 135 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   TYR A 137 " --> pdb=" O   GLU A 106 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 36 through 38
    Processing sheet with id=AA7, first strand: chain 'C' and resid 63 through 69
      removed outlier: 6.010A  pdb=" N   GLU C 178 " --> pdb=" O   ASN C 107 " (cutoff:3.500A)
      removed outlier: 9.158A  pdb=" N   ASN C 107 " --> pdb=" O   GLU C 178 " (cutoff:3.500A)
      removed outlier: 13.765A  pdb=" N   VAL C 180 " --> pdb=" O   ALA C 105 " (cutoff:3.500A)
      removed outlier: 12.241A  pdb=" N   ALA C 105 " --> pdb=" O   VAL C 180 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   GLU C 106 " --> pdb=" O   CYS C 135 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   GLY C 143 " --> pdb=" O   GLU C 112 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 63 through 69
      removed outlier: 6.700A  pdb=" N   VAL C  96 " --> pdb=" O   THR D 581 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 86 through 89
    Processing sheet with id=AB1, first strand: chain 'C' and resid 101 through 103
    Processing sheet with id=AB2, first strand: chain 'E' and resid 159 through 160
      removed outlier: 3.947A  pdb=" N   GLU E 103 " --> pdb=" O   GLY E  67 " (cutoff:3.500A)
      removed outlier: 5.861A  pdb=" N   ASN E  69 " --> pdb=" O   GLU E 103 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 86 through 89
      removed outlier: 3.543A  pdb=" N   PHE E 151 " --> pdb=" O   ARG E  89 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 166 through 167
      removed outlier: 7.464A  pdb=" N   VAL E  96 " --> pdb=" O   THR F 581 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 108 through 111
      removed outlier: 7.002A  pdb=" N   CYS E 108 " --> pdb=" O   HIS E 139 " (cutoff:3.500A)
      removed outlier: 7.937A  pdb=" N   VAL E 141 " --> pdb=" O   CYS E 108 " (cutoff:3.500A)
      removed outlier: 7.171A  pdb=" N   ASN E 110 " --> pdb=" O   VAL E 141 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'G' and resid 10 through 11
      removed outlier: 3.621A  pdb=" N   VAL G 117 " --> pdb=" O   GLU G  10 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   ILE G  34 " --> pdb=" O   VAL G  50 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   VAL G  50 " --> pdb=" O   ILE G  34 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   TRP G  36 " --> pdb=" O   MET G  48 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'G' and resid 18 through 23
      removed outlier: 3.723A  pdb=" N   THR G  79 " --> pdb=" O   ASP G  74 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'G' and resid 145 through 147
      removed outlier: 4.285A  pdb=" N   GLU G 158 " --> pdb=" O   VAL G 224 " (cutoff:3.500A)
      removed outlier: 5.242A  pdb=" N   ALA G 160 " --> pdb=" O   SER G 222 " (cutoff:3.500A)
      removed outlier: 5.128A  pdb=" N   SER G 222 " --> pdb=" O   ALA G 160 " (cutoff:3.500A)
      removed outlier: 7.381A  pdb=" N   ILE G 162 " --> pdb=" O   LYS G 220 " (cutoff:3.500A)
      removed outlier: 5.367A  pdb=" N   LYS G 220 " --> pdb=" O   ILE G 162 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   CYS G 164 " --> pdb=" O   THR G 218 " (cutoff:3.500A)
      removed outlier: 5.041A  pdb=" N   THR G 218 " --> pdb=" O   CYS G 164 " (cutoff:3.500A)
      removed outlier: 7.356A  pdb=" N   SER G 166 " --> pdb=" O   ASP G 216 " (cutoff:3.500A)
      removed outlier: 6.056A  pdb=" N   ASP G 216 " --> pdb=" O   SER G 166 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ASP G 216 " --> pdb=" O   SER G 213 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   SER G 209 " --> pdb=" O   LYS G 220 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'G' and resid 199 through 200
      removed outlier: 6.524A  pdb=" N   TRP G 181 " --> pdb=" O   LEU G 193 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   TYR G 195 " --> pdb=" O   VAL G 179 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   VAL G 179 " --> pdb=" O   TYR G 195 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'H' and resid 5 through 6
      removed outlier: 3.550A  pdb=" N   VAL H  80 " --> pdb=" O   CYS H  22 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 11
      removed outlier: 6.810A  pdb=" N   GLU H  10 " --> pdb=" O   VAL H 117 " (cutoff:3.500A)
      removed outlier: 7.875A  pdb=" N   TYR H  32 " --> pdb=" O   ASN H  52 " (cutoff:3.500A)
      removed outlier: 5.694A  pdb=" N   ASN H  52 " --> pdb=" O   TYR H  32 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   ILE H  34 " --> pdb=" O   VAL H  50 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   VAL H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   TRP H  36 " --> pdb=" O   MET H  48 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   THR H  58 " --> pdb=" O   ASN H  52 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'H' and resid 10 through 11
      removed outlier: 6.810A  pdb=" N   GLU H  10 " --> pdb=" O   VAL H 117 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'H' and resid 145 through 147
      removed outlier: 3.577A  pdb=" N   SER H 209 " --> pdb=" O   LYS H 220 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'H' and resid 199 through 200
      removed outlier: 6.816A  pdb=" N   TRP H 181 " --> pdb=" O   LEU H 193 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ILE H 231 " --> pdb=" O   GLN H 184 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'I' and resid 3 through 6
    Processing sheet with id=AC7, first strand: chain 'I' and resid 10 through 11
      removed outlier: 6.575A  pdb=" N   GLU I  10 " --> pdb=" O   VAL I 117 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC7
    Processing sheet with id=AC8, first strand: chain 'I' and resid 59 through 61
      removed outlier: 6.527A  pdb=" N   TRP I  36 " --> pdb=" O   MET I  48 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   VAL I  50 " --> pdb=" O   ILE I  34 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   ILE I  34 " --> pdb=" O   VAL I  50 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ARG I  99 " --> pdb=" O   VAL I 110 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   VAL I 110 " --> pdb=" O   ARG I  99 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'I' and resid 145 through 147
    Processing sheet with id=AD1, first strand: chain 'I' and resid 199 through 200
      removed outlier: 6.548A  pdb=" N   TRP I 181 " --> pdb=" O   LEU I 193 " (cutoff:3.500A)
      removed outlier: 5.064A  pdb=" N   TYR I 195 " --> pdb=" O   VAL I 179 " (cutoff:3.500A)
      removed outlier: 7.282A  pdb=" N   VAL I 179 " --> pdb=" O   TYR I 195 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'J' and resid 4 through 6
    Processing sheet with id=AD3, first strand: chain 'J' and resid 10 through 12
      removed outlier: 6.394A  pdb=" N   GLU J  10 " --> pdb=" O   THR J 121 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   GLY J  49 " --> pdb=" O   TRP J  36 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   ARG J  38 " --> pdb=" O   TRP J  47 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   TRP J  47 " --> pdb=" O   ARG J  38 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   GLY J  50 " --> pdb=" O   HIS J  59 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'K' and resid 4 through 6
    Processing sheet with id=AD5, first strand: chain 'K' and resid 12 through 13
      removed outlier: 3.760A  pdb=" N   ALA K  13 " --> pdb=" O   GLU K 111 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   PHE K  39 " --> pdb=" O   SER K  55 " (cutoff:3.500A)
      removed outlier: 4.847A  pdb=" N   SER K  55 " --> pdb=" O   PHE K  39 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   TRP K  41 " --> pdb=" O   LEU K  53 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'K' and resid 12 through 13
      removed outlier: 3.760A  pdb=" N   ALA K  13 " --> pdb=" O   GLU K 111 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   THR K 103 " --> pdb=" O   GLN K  96 " (cutoff:3.500A)

    422 hydrogen bonds defined for protein.
    1053 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.04

  Time building geometry restraints manager: 1.49 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4136
        1.34 -     1.46: 3304
        1.46 -     1.58: 5619
        1.58 -     1.71: 0
        1.71 -     1.83: 75
  Bond restraints: 13134
  Sorted by residual:
  bond pdb=" CB  PRO G  41 "
       pdb=" CG  PRO G  41 "
    ideal  model  delta    sigma   weight residual
    1.492  1.580 -0.088 5.00e-02 4.00e+02 3.12e+00
  bond pdb=" CG1 ILE K  81 "
       pdb=" CD1 ILE K  81 "
    ideal  model  delta    sigma   weight residual
    1.513  1.447  0.066 3.90e-02 6.57e+02 2.83e+00
  bond pdb=" CB  ASN I 174 "
       pdb=" CG  ASN I 174 "
    ideal  model  delta    sigma   weight residual
    1.516  1.477  0.039 2.50e-02 1.60e+03 2.41e+00
  bond pdb=" CB  TRP J 114 "
       pdb=" CG  TRP J 114 "
    ideal  model  delta    sigma   weight residual
    1.498  1.451  0.047 3.10e-02 1.04e+03 2.31e+00
  bond pdb=" CB  PRO I 159 "
       pdb=" CG  PRO I 159 "
    ideal  model  delta    sigma   weight residual
    1.492  1.567 -0.075 5.00e-02 4.00e+02 2.26e+00
  ... (remaining 13129 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 17341
        2.01 -     4.02: 430
        4.02 -     6.03: 48
        6.03 -     8.04: 14
        8.04 -    10.05: 2
  Bond angle restraints: 17835
  Sorted by residual:
  angle pdb=" CB  ARG K  18 "
        pdb=" CG  ARG K  18 "
        pdb=" CD  ARG K  18 "
      ideal   model   delta    sigma   weight residual
     111.30  121.35  -10.05 2.30e+00 1.89e-01 1.91e+01
  angle pdb=" CA  PRO G  41 "
        pdb=" N   PRO G  41 "
        pdb=" CD  PRO G  41 "
      ideal   model   delta    sigma   weight residual
     112.00  106.45    5.55 1.40e+00 5.10e-01 1.57e+01
  angle pdb=" C   ARG G  66 "
        pdb=" N   ASP G  67 "
        pdb=" CA  ASP G  67 "
      ideal   model   delta    sigma   weight residual
     121.54  129.08   -7.54 1.91e+00 2.74e-01 1.56e+01
  angle pdb=" N   ILE B 542 "
        pdb=" CA  ILE B 542 "
        pdb=" C   ILE B 542 "
      ideal   model   delta    sigma   weight residual
     111.77  108.21    3.56 1.04e+00 9.25e-01 1.17e+01
  angle pdb=" CA  LEU A  57 "
        pdb=" CB  LEU A  57 "
        pdb=" CG  LEU A  57 "
      ideal   model   delta    sigma   weight residual
     116.30  126.25   -9.95 3.50e+00 8.16e-02 8.09e+00
  ... (remaining 17830 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.41: 7274
       22.41 -    44.81: 489
       44.81 -    67.22: 36
       67.22 -    89.63: 39
       89.63 -   112.04: 16
  Dihedral angle restraints: 7854
    sinusoidal: 3190
      harmonic: 4664
  Sorted by residual:
  dihedral pdb=" CB  CYS G  22 "
           pdb=" SG  CYS G  22 "
           pdb=" SG  CYS G  97 "
           pdb=" CB  CYS G  97 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  161.39  -68.39     1      1.00e+01 1.00e-02 6.06e+01
  dihedral pdb=" CB  CYS K  23 "
           pdb=" SG  CYS K  23 "
           pdb=" SG  CYS K  94 "
           pdb=" CB  CYS K  94 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  156.93  -63.93     1      1.00e+01 1.00e-02 5.38e+01
  dihedral pdb=" CB  CYS I 164 "
           pdb=" SG  CYS I 164 "
           pdb=" SG  CYS I 234 "
           pdb=" CB  CYS I 234 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  130.18  -37.18     1      1.00e+01 1.00e-02 1.95e+01
  ... (remaining 7851 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.132: 1962
       0.132 -    0.264: 18
       0.264 -    0.396: 3
       0.396 -    0.528: 0
       0.528 -    0.660: 2
  Chirality restraints: 1985
  Sorted by residual:
  chirality pdb=" C1  NAG L   1 "
            pdb=" ND2 ASN B 563 "
            pdb=" C2  NAG L   1 "
            pdb=" O5  NAG L   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.74   -0.66 2.00e-01 2.50e+01 1.09e+01
  chirality pdb=" C1  NAG M   1 "
            pdb=" ND2 ASN D 563 "
            pdb=" C2  NAG M   1 "
            pdb=" O5  NAG M   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.80   -0.60 2.00e-01 2.50e+01 9.14e+00
  chirality pdb=" C1  NAG N   1 "
            pdb=" ND2 ASN F 563 "
            pdb=" C2  NAG N   1 "
            pdb=" O5  NAG N   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.03   -0.37 2.00e-01 2.50e+01 3.35e+00
  ... (remaining 1982 not shown)

  Planarity restraints: 2285
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA G  40 "   -0.073 5.00e-02 4.00e+02   1.09e-01 1.88e+01
        pdb=" N   PRO G  41 "    0.188 5.00e-02 4.00e+02
        pdb=" CA  PRO G  41 "   -0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO G  41 "   -0.058 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU I 158 "   -0.056 5.00e-02 4.00e+02   8.37e-02 1.12e+01
        pdb=" N   PRO I 159 "    0.145 5.00e-02 4.00e+02
        pdb=" CA  PRO I 159 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO I 159 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 115 "    0.050 5.00e-02 4.00e+02   7.57e-02 9.17e+00
        pdb=" N   PRO C 116 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO C 116 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO C 116 "    0.042 5.00e-02 4.00e+02
  ... (remaining 2282 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 281
        2.68 -     3.23: 12358
        3.23 -     3.79: 19756
        3.79 -     4.34: 26012
        4.34 -     4.90: 44123
  Nonbonded interactions: 102530
  Sorted by model distance:
  nonbonded pdb=" O6  NAG N   1 "
            pdb=" O7  NAG N   2 "
     model   vdw
     2.124 3.040
  nonbonded pdb=" OG1 THR G  70 "
            pdb=" OE2 GLU G  83 "
     model   vdw
     2.130 3.040
  nonbonded pdb=" OE2 GLU E 156 "
            pdb=" O3  NAG N   1 "
     model   vdw
     2.172 3.040
  nonbonded pdb=" OH  TYR I 195 "
            pdb=" O4  BMA M   3 "
     model   vdw
     2.174 3.040
  nonbonded pdb=" OD1 ASN G  33 "
            pdb=" ND2 ASN G  52 "
     model   vdw
     2.204 3.120
  ... (remaining 102525 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 33 through 38 or resid 42 through 187))
  selection = (chain 'C' and (resid 33 through 38 or resid 42 through 187))
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'H'
  selection = (chain 'I' and resid 2 through 250)
}
ncs_group {
  reference = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.130
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
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   0.088  13160  Z= 0.243
  Angle     :  0.781  10.052  17896  Z= 0.402
  Chirality :  0.053   0.660   1985
  Planarity :  0.006   0.109   2282
  Dihedral  : 15.797 112.036   4849
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 14.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.91 (0.21), residues: 1616
  helix:  0.17 (0.44), residues: 141
  sheet: -0.71 (0.23), residues: 540
  loop : -0.58 (0.20), residues: 935

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.027   0.002   ARG K  18 
 TYR   0.024   0.002   TYR A  99 
 PHE   0.016   0.002   PHE H 217 
 TRP   0.042   0.003   TRP I  36 
 HIS   0.016   0.002   HIS F 549 

Details of bonding type rmsd
  covalent geometry    : bond        0.00560 (13134)
  covalent geometry    : angle       0.76552 (17835)
  SS BOND              : bond        0.00514 (   17)
  SS BOND              : angle       1.66396 (   34)
  hydrogen bonds       : bond        0.15545 (  406)
  hydrogen bonds       : angle       7.60003 ( 1053)
  link_BETA1-4         : bond        0.00537 (    6)
  link_BETA1-4         : angle       1.68684 (   18)
  link_NAG-ASN         : bond        0.00482 (    3)
  link_NAG-ASN         : angle       5.88217 (    9)

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  369 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 369
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.7310 (pt0) cc_final: 0.6541 (mm-40)
REVERT: E  100 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7556 (mm-30)
REVERT: E  117 ASP cc_start: 0.7050 (m-30) cc_final: 0.6548 (p0)
REVERT: F  561 LEU cc_start: 0.8826 (tp) cc_final: 0.8548 (tt)
REVERT: G   36 TRP cc_start: 0.6665 (m-10) cc_final: 0.6362 (m100)
REVERT: G   74 ASP cc_start: 0.7132 (m-30) cc_final: 0.6893 (m-30)
REVERT: H  168 GLN cc_start: 0.8146 (tm130) cc_final: 0.7933 (tm-30)
REVERT: K   80 THR cc_start: 0.8775 (m) cc_final: 0.8551 (m)
REVERT: K   96 GLN cc_start: 0.8063 (pp30) cc_final: 0.7766 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 369
  average time/residue: 0.1097
  time to fit residues: 58.5136
Evaluate side-chains
  285 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 285
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 98 optimal weight:    0.0270
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    0.5980
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:   10.0000
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    0.0980
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    6.9990
   chunk 149 optimal weight:    0.7980
   overall best weight:    0.5040

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K  85 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.128598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.110328 restraints weight = 27351.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.113671 restraints weight = 14731.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.115937 restraints weight = 9706.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.117492 restraints weight = 7211.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.118480 restraints weight = 5800.762|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.1383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  13160  Z= 0.128
  Angle     :  0.661   9.311  17896  Z= 0.327
  Chirality :  0.046   0.242   1985
  Planarity :  0.005   0.066   2282
  Dihedral  : 10.521  90.115   1985
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 11.36 %
    Favored  : 86.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.81 (0.21), residues: 1616
  helix:  0.36 (0.44), residues: 141
  sheet: -0.56 (0.22), residues: 557
  loop : -0.59 (0.20), residues: 918

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG G 223 
 TYR   0.018   0.001   TYR I  81 
 PHE   0.028   0.002   PHE G  96 
 TRP   0.028   0.002   TRP I  36 
 HIS   0.008   0.001   HIS I  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (13134)
  covalent geometry    : angle       0.65257 (17835)
  SS BOND              : bond        0.00412 (   17)
  SS BOND              : angle       1.41678 (   34)
  hydrogen bonds       : bond        0.04140 (  406)
  hydrogen bonds       : angle       6.15733 ( 1053)
  link_BETA1-4         : bond        0.00326 (    6)
  link_BETA1-4         : angle       2.59234 (   18)
  link_NAG-ASN         : bond        0.00595 (    3)
  link_NAG-ASN         : angle       2.13003 (    9)

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  382 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 357
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.7367 (pt0) cc_final: 0.6513 (mm-40)
REVERT: A  112 GLU cc_start: 0.7560 (pt0) cc_final: 0.7274 (pt0)
REVERT: E  100 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7994 (mm-30)
REVERT: E  117 ASP cc_start: 0.7265 (m-30) cc_final: 0.6669 (p0)
REVERT: G   74 ASP cc_start: 0.6875 (m-30) cc_final: 0.6646 (m-30)
REVERT: G  249 LYS cc_start: 0.6526 (tmtt) cc_final: 0.6251 (tmmt)
REVERT: J   46 GLU cc_start: 0.7363 (pt0) cc_final: 0.6632 (pt0)
REVERT: K   42 TYR cc_start: 0.9009 (m-80) cc_final: 0.8697 (m-10)
REVERT: K   96 GLN cc_start: 0.8019 (pp30) cc_final: 0.7794 (pp30)
  outliers start: 25
  outliers final: 19
  residues processed: 364
  average time/residue: 0.1074
  time to fit residues: 56.7960
Evaluate side-chains
  311 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 292
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  592 PHE
Chi-restraints excluded: chain E residue  167 SER
Chi-restraints excluded: chain F residue  544 THR
Chi-restraints excluded: chain F residue  549 HIS
Chi-restraints excluded: chain F residue  576 THR
Chi-restraints excluded: chain G residue   51 ILE
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue  183 LEU
Chi-restraints excluded: chain G residue  227 GLU
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue  239 GLN
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   54 TYR
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   91 ASP
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue  104 TRP
Chi-restraints excluded: chain J residue  116 GLN
Chi-restraints excluded: chain K residue   20 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 157 optimal weight:    2.9990
   chunk 107 optimal weight:    6.9990
   chunk 134 optimal weight:   10.0000
   chunk 109 optimal weight:    2.9990
   chunk 66 optimal weight:    9.9990
   chunk 86 optimal weight:    3.9990
   chunk 144 optimal weight:    5.9990
   chunk 4 optimal weight:    0.0050
   chunk 104 optimal weight:    0.0020
   chunk 8 optimal weight:    9.9990
   chunk 73 optimal weight:    0.8980
   overall best weight:    1.3806

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
B 521 GLN
C 188 GLN
** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  52 ASN
H 168 GLN
** H 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 239 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.126144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.107539 restraints weight = 27598.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.110784 restraints weight = 15051.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.113031 restraints weight = 10047.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.114436 restraints weight = 7520.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.115581 restraints weight = 6171.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  13160  Z= 0.157
  Angle     :  0.639  11.023  17896  Z= 0.316
  Chirality :  0.045   0.233   1985
  Planarity :  0.005   0.058   2282
  Dihedral  :  8.930  83.078   1985
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 15.29 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.78 (0.21), residues: 1616
  helix:  0.56 (0.46), residues: 141
  sheet: -0.60 (0.22), residues: 568
  loop : -0.56 (0.20), residues: 907

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K  18 
 TYR   0.017   0.002   TYR B 543 
 PHE   0.018   0.002   PHE B 592 
 TRP   0.036   0.002   TRP B 531 
 HIS   0.009   0.001   HIS I  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (13134)
  covalent geometry    : angle       0.63028 (17835)
  SS BOND              : bond        0.00398 (   17)
  SS BOND              : angle       1.51336 (   34)
  hydrogen bonds       : bond        0.03770 (  406)
  hydrogen bonds       : angle       5.86366 ( 1053)
  link_BETA1-4         : bond        0.00402 (    6)
  link_BETA1-4         : angle       2.67112 (   18)
  link_NAG-ASN         : bond        0.00243 (    3)
  link_NAG-ASN         : angle       1.69460 (    9)

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  357 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 318
  time to evaluate  : 0.486 
Fit side-chains
   revert: symmetry clash
REVERT: B  595 GLN cc_start: 0.7578 (pt0) cc_final: 0.7174 (tp40)
REVERT: E  100 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7995 (mm-30)
REVERT: E  117 ASP cc_start: 0.7169 (m-30) cc_final: 0.6613 (p0)
REVERT: G  249 LYS cc_start: 0.6593 (tmtt) cc_final: 0.6330 (tmmt)
REVERT: I  251 GLU cc_start: 0.7962 (pm20) cc_final: 0.7351 (pm20)
REVERT: K   42 TYR cc_start: 0.9057 (m-80) cc_final: 0.8776 (m-10)
REVERT: K   89 VAL cc_start: 0.7837 (OUTLIER) cc_final: 0.7621 (p)
REVERT: K   96 GLN cc_start: 0.8117 (pp30) cc_final: 0.7804 (pp30)
  outliers start: 39
  outliers final: 35
  residues processed: 336
  average time/residue: 0.1066
  time to fit residues: 52.3651
Evaluate side-chains
  331 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 295
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 CYS
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain B residue  547 LEU
Chi-restraints excluded: chain C residue  103 GLU
Chi-restraints excluded: chain C residue  147 CYS
Chi-restraints excluded: chain C residue  188 GLN
Chi-restraints excluded: chain D residue  545 GLU
Chi-restraints excluded: chain D residue  592 PHE
Chi-restraints excluded: chain E residue  167 SER
Chi-restraints excluded: chain F residue  527 ILE
Chi-restraints excluded: chain F residue  544 THR
Chi-restraints excluded: chain F residue  549 HIS
Chi-restraints excluded: chain G residue   51 ILE
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue  183 LEU
Chi-restraints excluded: chain G residue  227 GLU
Chi-restraints excluded: chain G residue  250 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue  152 LEU
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   51 ILE
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   80 VAL
Chi-restraints excluded: chain I residue   87 LEU
Chi-restraints excluded: chain I residue   91 ASP
Chi-restraints excluded: chain I residue  142 ASP
Chi-restraints excluded: chain I residue  209 SER
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   57 VAL
Chi-restraints excluded: chain J residue  116 GLN
Chi-restraints excluded: chain K residue    5 THR
Chi-restraints excluded: chain K residue    9 ASP
Chi-restraints excluded: chain K residue   20 THR
Chi-restraints excluded: chain K residue   66 VAL
Chi-restraints excluded: chain K residue   89 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 148 optimal weight:    8.9990
   chunk 149 optimal weight:    0.0000
   chunk 143 optimal weight:    2.9990
   chunk 43 optimal weight:    8.9990
   chunk 153 optimal weight:    2.9990
   chunk 130 optimal weight:    5.9990
   chunk 125 optimal weight:    1.9990
   chunk 146 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 136 optimal weight:    0.8980
   overall best weight:    1.1788

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
C 188 GLN
** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 168 GLN
** I  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J   6 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.126169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.106772 restraints weight = 27844.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.110085 restraints weight = 15326.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.112363 restraints weight = 10317.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.113927 restraints weight = 7805.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.114917 restraints weight = 6364.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.2018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  13160  Z= 0.144
  Angle     :  0.630   7.946  17896  Z= 0.311
  Chirality :  0.045   0.243   1985
  Planarity :  0.005   0.059   2282
  Dihedral  :  7.666  76.635   1985
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 18.06 %
    Favored  : 78.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.83 (0.21), residues: 1616
  helix:  0.72 (0.47), residues: 141
  sheet: -0.64 (0.22), residues: 574
  loop : -0.62 (0.20), residues: 901

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG K  18 
 TYR   0.013   0.001   TYR H  54 
 PHE   0.018   0.002   PHE G  96 
 TRP   0.038   0.002   TRP E 104 
 HIS   0.010   0.001   HIS I  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (13134)
  covalent geometry    : angle       0.61906 (17835)
  SS BOND              : bond        0.00415 (   17)
  SS BOND              : angle       1.93965 (   34)
  hydrogen bonds       : bond        0.03606 (  406)
  hydrogen bonds       : angle       5.67992 ( 1053)
  link_BETA1-4         : bond        0.00420 (    6)
  link_BETA1-4         : angle       2.60455 (   18)
  link_NAG-ASN         : bond        0.00261 (    3)
  link_NAG-ASN         : angle       1.51275 (    9)

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  366 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 316
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
REVERT: A  140 LYS cc_start: 0.8371 (mmmm) cc_final: 0.7785 (tptp)
REVERT: B  595 GLN cc_start: 0.7592 (pt0) cc_final: 0.7002 (tp-100)
REVERT: C  117 ASP cc_start: 0.9165 (OUTLIER) cc_final: 0.8920 (t0)
REVERT: E  100 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7875 (mm-30)
REVERT: E  117 ASP cc_start: 0.7231 (m-30) cc_final: 0.6627 (p0)
REVERT: G   36 TRP cc_start: 0.8122 (m100) cc_final: 0.7773 (m100)
REVERT: G  249 LYS cc_start: 0.6536 (tmtt) cc_final: 0.6301 (tmmt)
REVERT: I  251 GLU cc_start: 0.8080 (pm20) cc_final: 0.7495 (pm20)
REVERT: K   42 TYR cc_start: 0.8985 (m-80) cc_final: 0.8320 (m-10)
REVERT: K   89 VAL cc_start: 0.7848 (OUTLIER) cc_final: 0.7636 (p)
REVERT: K   96 GLN cc_start: 0.8118 (pp30) cc_final: 0.7789 (pp30)
  outliers start: 50
  outliers final: 36
  residues processed: 345
  average time/residue: 0.1017
  time to fit residues: 51.4658
Evaluate side-chains
  326 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 288
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 SER
Chi-restraints excluded: chain A residue  108 CYS
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain B residue  547 LEU
Chi-restraints excluded: chain B residue  548 MET
Chi-restraints excluded: chain B residue  593 LEU
Chi-restraints excluded: chain C residue  103 GLU
Chi-restraints excluded: chain C residue  117 ASP
Chi-restraints excluded: chain C residue  132 PHE
Chi-restraints excluded: chain C residue  147 CYS
Chi-restraints excluded: chain D residue  592 PHE
Chi-restraints excluded: chain E residue   52 VAL
Chi-restraints excluded: chain E residue  119 SER
Chi-restraints excluded: chain E residue  167 SER
Chi-restraints excluded: chain F residue  527 ILE
Chi-restraints excluded: chain F residue  544 THR
Chi-restraints excluded: chain F residue  549 HIS
Chi-restraints excluded: chain G residue   51 ILE
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue  183 LEU
Chi-restraints excluded: chain G residue  227 GLU
Chi-restraints excluded: chain G residue  250 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue  152 LEU
Chi-restraints excluded: chain H residue  239 GLN
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   54 TYR
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   80 VAL
Chi-restraints excluded: chain I residue   87 LEU
Chi-restraints excluded: chain I residue   91 ASP
Chi-restraints excluded: chain I residue  142 ASP
Chi-restraints excluded: chain I residue  209 SER
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   57 VAL
Chi-restraints excluded: chain K residue   20 THR
Chi-restraints excluded: chain K residue   89 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 153 optimal weight:    0.3980
   chunk 106 optimal weight:    0.0970
   chunk 127 optimal weight:   10.0000
   chunk 111 optimal weight:    0.0010
   chunk 47 optimal weight:    7.9990
   chunk 10 optimal weight:    7.9990
   chunk 80 optimal weight:    9.9990
   chunk 57 optimal weight:    3.9990
   chunk 124 optimal weight:    8.9990
   chunk 145 optimal weight:   10.0000
   chunk 141 optimal weight:    7.9990
   overall best weight:    2.4988

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
** A  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 154 HIS
C 188 GLN
** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 549 HIS
G  52 ASN
H 168 GLN
** H 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 174 ASN
I 239 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.122385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.103005 restraints weight = 27972.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.106200 restraints weight = 15397.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.108427 restraints weight = 10414.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.109810 restraints weight = 7907.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.110909 restraints weight = 6559.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.2225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069  13160  Z= 0.233
  Angle     :  0.689   9.297  17896  Z= 0.343
  Chirality :  0.046   0.239   1985
  Planarity :  0.005   0.057   2282
  Dihedral  :  7.051  69.754   1985
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 19.66 %
    Favored  : 76.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.01 (0.21), residues: 1616
  helix:  0.52 (0.48), residues: 135
  sheet: -0.82 (0.21), residues: 610
  loop : -0.64 (0.21), residues: 871

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG K  18 
 TYR   0.019   0.002   TYR H  54 
 PHE   0.019   0.002   PHE H 217 
 TRP   0.021   0.002   TRP E 104 
 HIS   0.011   0.002   HIS I  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00537 (13134)
  covalent geometry    : angle       0.68091 (17835)
  SS BOND              : bond        0.00782 (   17)
  SS BOND              : angle       1.67231 (   34)
  hydrogen bonds       : bond        0.03862 (  406)
  hydrogen bonds       : angle       5.82425 ( 1053)
  link_BETA1-4         : bond        0.00385 (    6)
  link_BETA1-4         : angle       2.40666 (   18)
  link_NAG-ASN         : bond        0.00231 (    3)
  link_NAG-ASN         : angle       1.60748 (    9)

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  341 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 288
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: A  103 GLU cc_start: 0.7777 (tt0) cc_final: 0.7563 (tt0)
REVERT: A  140 LYS cc_start: 0.8386 (mmmm) cc_final: 0.7838 (tptp)
REVERT: C  117 ASP cc_start: 0.9192 (OUTLIER) cc_final: 0.8950 (t0)
REVERT: E  100 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7710 (mm-30)
REVERT: E  117 ASP cc_start: 0.7379 (m-30) cc_final: 0.6674 (p0)
REVERT: G   36 TRP cc_start: 0.8369 (m100) cc_final: 0.7590 (m100)
REVERT: G  249 LYS cc_start: 0.6635 (tmtt) cc_final: 0.6391 (tmmt)
REVERT: K   42 TYR cc_start: 0.9051 (m-80) cc_final: 0.8517 (m-10)
REVERT: K   96 GLN cc_start: 0.8294 (pp30) cc_final: 0.7864 (pp30)
  outliers start: 53
  outliers final: 44
  residues processed: 320
  average time/residue: 0.1043
  time to fit residues: 48.7963
Evaluate side-chains
  323 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 278
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue   90 SER
Chi-restraints excluded: chain A residue  147 CYS
Chi-restraints excluded: chain B residue  547 LEU
Chi-restraints excluded: chain C residue   75 VAL
Chi-restraints excluded: chain C residue  103 GLU
Chi-restraints excluded: chain C residue  117 ASP
Chi-restraints excluded: chain C residue  132 PHE
Chi-restraints excluded: chain C residue  147 CYS
Chi-restraints excluded: chain C residue  188 GLN
Chi-restraints excluded: chain E residue   52 VAL
Chi-restraints excluded: chain E residue  119 SER
Chi-restraints excluded: chain E residue  167 SER
Chi-restraints excluded: chain F residue  527 ILE
Chi-restraints excluded: chain F residue  529 LEU
Chi-restraints excluded: chain F residue  544 THR
Chi-restraints excluded: chain F residue  549 HIS
Chi-restraints excluded: chain G residue   11 VAL
Chi-restraints excluded: chain G residue   51 ILE
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue  152 LEU
Chi-restraints excluded: chain G residue  174 ASN
Chi-restraints excluded: chain G residue  183 LEU
Chi-restraints excluded: chain G residue  227 GLU
Chi-restraints excluded: chain G residue  250 VAL
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue  152 LEU
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   51 ILE
Chi-restraints excluded: chain I residue   54 TYR
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   80 VAL
Chi-restraints excluded: chain I residue   87 LEU
Chi-restraints excluded: chain I residue   91 ASP
Chi-restraints excluded: chain I residue  142 ASP
Chi-restraints excluded: chain I residue  209 SER
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   57 VAL
Chi-restraints excluded: chain K residue    5 THR
Chi-restraints excluded: chain K residue    9 ASP
Chi-restraints excluded: chain K residue   20 THR
Chi-restraints excluded: chain K residue   66 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 156 optimal weight:    6.9990
   chunk 126 optimal weight:    5.9990
   chunk 8 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   chunk 2 optimal weight:    9.9990
   chunk 91 optimal weight:   10.0000
   chunk 14 optimal weight:    0.9990
   chunk 144 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9990
   overall best weight:    1.1988

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
C 188 GLN
** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 174 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.124428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.104905 restraints weight = 27750.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.108131 restraints weight = 15428.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.110381 restraints weight = 10478.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.111888 restraints weight = 7964.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.112869 restraints weight = 6556.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.2384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  13160  Z= 0.147
  Angle     :  0.649   8.107  17896  Z= 0.321
  Chirality :  0.045   0.223   1985
  Planarity :  0.005   0.057   2282
  Dihedral  :  6.574  62.931   1985
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 20.47 %
    Favored  : 75.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.97 (0.21), residues: 1616
  helix:  0.53 (0.47), residues: 135
  sheet: -0.77 (0.22), residues: 573
  loop : -0.65 (0.20), residues: 908

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG K  18 
 TYR   0.013   0.001   TYR C 162 
 PHE   0.016   0.001   PHE G  96 
 TRP   0.020   0.001   TRP I  36 
 HIS   0.008   0.001   HIS I  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (13134)
  covalent geometry    : angle       0.64060 (17835)
  SS BOND              : bond        0.00432 (   17)
  SS BOND              : angle       1.80079 (   34)
  hydrogen bonds       : bond        0.03592 (  406)
  hydrogen bonds       : angle       5.67877 ( 1053)
  link_BETA1-4         : bond        0.00365 (    6)
  link_BETA1-4         : angle       2.31765 (   18)
  link_NAG-ASN         : bond        0.00156 (    3)
  link_NAG-ASN         : angle       1.52567 (    9)

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  345 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 295
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.8494 (pp30) cc_final: 0.6672 (mt0)
REVERT: A  103 GLU cc_start: 0.7659 (tt0) cc_final: 0.7443 (tt0)
REVERT: A  140 LYS cc_start: 0.8467 (mmmm) cc_final: 0.7840 (tptp)
REVERT: C  117 ASP cc_start: 0.9178 (OUTLIER) cc_final: 0.8969 (t0)
REVERT: E  100 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7668 (mm-30)
REVERT: E  117 ASP cc_start: 0.7421 (m-30) cc_final: 0.6696 (p0)
REVERT: G   18 VAL cc_start: 0.7953 (t) cc_final: 0.7697 (m)
REVERT: G   36 TRP cc_start: 0.8338 (m100) cc_final: 0.7670 (m100)
REVERT: G  249 LYS cc_start: 0.6638 (tmtt) cc_final: 0.6427 (tmmt)
REVERT: H    6 GLN cc_start: 0.7229 (pm20) cc_final: 0.6943 (pm20)
REVERT: K   37 ASP cc_start: 0.7161 (p0) cc_final: 0.6881 (p0)
REVERT: K   42 TYR cc_start: 0.8988 (m-80) cc_final: 0.8472 (m-10)
REVERT: K   96 GLN cc_start: 0.8189 (pp30) cc_final: 0.7793 (pp30)
  outliers start: 50
  outliers final: 36
  residues processed: 324
  average time/residue: 0.1023
  time to fit residues: 48.8622
Evaluate side-chains
  316 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 279
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 SER
Chi-restraints excluded: chain A residue  147 CYS
Chi-restraints excluded: chain B residue  506 ASN
Chi-restraints excluded: chain B residue  547 LEU
Chi-restraints excluded: chain C residue  103 GLU
Chi-restraints excluded: chain C residue  117 ASP
Chi-restraints excluded: chain C residue  132 PHE
Chi-restraints excluded: chain C residue  147 CYS
Chi-restraints excluded: chain D residue  545 GLU
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   52 VAL
Chi-restraints excluded: chain E residue  119 SER
Chi-restraints excluded: chain E residue  167 SER
Chi-restraints excluded: chain F residue  527 ILE
Chi-restraints excluded: chain F residue  544 THR
Chi-restraints excluded: chain F residue  549 HIS
Chi-restraints excluded: chain G residue   51 ILE
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue  174 ASN
Chi-restraints excluded: chain G residue  183 LEU
Chi-restraints excluded: chain G residue  227 GLU
Chi-restraints excluded: chain G residue  250 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue  152 LEU
Chi-restraints excluded: chain H residue  239 GLN
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   51 ILE
Chi-restraints excluded: chain I residue   54 TYR
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   80 VAL
Chi-restraints excluded: chain I residue   91 ASP
Chi-restraints excluded: chain I residue  142 ASP
Chi-restraints excluded: chain I residue  209 SER
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   57 VAL
Chi-restraints excluded: chain K residue   20 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 99 optimal weight:    4.9990
   chunk 80 optimal weight:    9.9990
   chunk 152 optimal weight:    5.9990
   chunk 142 optimal weight:    7.9990
   chunk 15 optimal weight:    6.9990
   chunk 143 optimal weight:    7.9990
   chunk 25 optimal weight:    0.7980
   chunk 30 optimal weight:    4.9990
   chunk 111 optimal weight:   10.0000
   overall best weight:    3.1386

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 551 GLN
C 188 GLN
** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 521 GLN
H 168 GLN
** H 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.120585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.100910 restraints weight = 28159.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.104013 restraints weight = 15740.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.106182 restraints weight = 10813.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.107555 restraints weight = 8311.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.108650 restraints weight = 6957.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.2523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.081  13160  Z= 0.277
  Angle     :  0.717   9.714  17896  Z= 0.359
  Chirality :  0.047   0.201   1985
  Planarity :  0.005   0.055   2282
  Dihedral  :  6.940  59.669   1985
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 20.90 %
    Favored  : 74.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.27 (0.21), residues: 1616
  helix:  0.28 (0.47), residues: 135
  sheet: -0.95 (0.21), residues: 603
  loop : -0.85 (0.20), residues: 878

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG K  18 
 TYR   0.021   0.002   TYR C 162 
 PHE   0.019   0.002   PHE I 217 
 TRP   0.020   0.002   TRP I  36 
 HIS   0.009   0.002   HIS I  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00640 (13134)
  covalent geometry    : angle       0.70920 (17835)
  SS BOND              : bond        0.00517 (   17)
  SS BOND              : angle       1.78589 (   34)
  hydrogen bonds       : bond        0.04051 (  406)
  hydrogen bonds       : angle       5.96947 ( 1053)
  link_BETA1-4         : bond        0.00478 (    6)
  link_BETA1-4         : angle       2.24611 (   18)
  link_NAG-ASN         : bond        0.00327 (    3)
  link_NAG-ASN         : angle       1.73293 (    9)

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  341 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 284
  time to evaluate  : 0.434 
Fit side-chains
REVERT: A   62 GLN cc_start: 0.8584 (pp30) cc_final: 0.6862 (mt0)
REVERT: B  521 GLN cc_start: 0.7407 (pt0) cc_final: 0.7138 (pt0)
REVERT: C  117 ASP cc_start: 0.9208 (OUTLIER) cc_final: 0.8995 (t0)
REVERT: E  117 ASP cc_start: 0.7481 (m-30) cc_final: 0.6729 (p0)
REVERT: G   36 TRP cc_start: 0.8460 (m100) cc_final: 0.7764 (m100)
REVERT: G  249 LYS cc_start: 0.6776 (tmtt) cc_final: 0.6495 (tmmt)
REVERT: H   32 TYR cc_start: 0.8721 (m-80) cc_final: 0.8137 (m-10)
REVERT: H   82 MET cc_start: 0.7532 (ttt) cc_final: 0.7327 (ttt)
REVERT: H   96 PHE cc_start: 0.8589 (m-80) cc_final: 0.8279 (m-10)
REVERT: I   82 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.7089 (mtm)
REVERT: K   37 ASP cc_start: 0.7389 (p0) cc_final: 0.7040 (p0)
REVERT: K   42 TYR cc_start: 0.9099 (m-80) cc_final: 0.8555 (m-10)
REVERT: K   96 GLN cc_start: 0.8363 (pp30) cc_final: 0.8097 (pp30)
  outliers start: 57
  outliers final: 48
  residues processed: 319
  average time/residue: 0.1110
  time to fit residues: 51.6560
Evaluate side-chains
  328 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 278
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   90 SER
Chi-restraints excluded: chain A residue  147 CYS
Chi-restraints excluded: chain B residue  506 ASN
Chi-restraints excluded: chain B residue  542 ILE
Chi-restraints excluded: chain B residue  547 LEU
Chi-restraints excluded: chain C residue   57 LEU
Chi-restraints excluded: chain C residue   75 VAL
Chi-restraints excluded: chain C residue  103 GLU
Chi-restraints excluded: chain C residue  117 ASP
Chi-restraints excluded: chain C residue  132 PHE
Chi-restraints excluded: chain C residue  144 THR
Chi-restraints excluded: chain C residue  167 SER
Chi-restraints excluded: chain C residue  188 GLN
Chi-restraints excluded: chain D residue  545 GLU
Chi-restraints excluded: chain D residue  573 LEU
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   52 VAL
Chi-restraints excluded: chain E residue  119 SER
Chi-restraints excluded: chain E residue  167 SER
Chi-restraints excluded: chain F residue  527 ILE
Chi-restraints excluded: chain F residue  544 THR
Chi-restraints excluded: chain F residue  549 HIS
Chi-restraints excluded: chain G residue   11 VAL
Chi-restraints excluded: chain G residue   51 ILE
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue   77 THR
Chi-restraints excluded: chain G residue  174 ASN
Chi-restraints excluded: chain G residue  183 LEU
Chi-restraints excluded: chain G residue  227 GLU
Chi-restraints excluded: chain G residue  250 VAL
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue  152 LEU
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   51 ILE
Chi-restraints excluded: chain I residue   54 TYR
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   80 VAL
Chi-restraints excluded: chain I residue   82 MET
Chi-restraints excluded: chain I residue   91 ASP
Chi-restraints excluded: chain I residue  209 SER
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   57 VAL
Chi-restraints excluded: chain K residue    5 THR
Chi-restraints excluded: chain K residue    9 ASP
Chi-restraints excluded: chain K residue   20 THR
Chi-restraints excluded: chain K residue   66 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 57 optimal weight:    5.9990
   chunk 159 optimal weight:    1.9990
   chunk 154 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9980
   chunk 150 optimal weight:    6.9990
   chunk 110 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 93 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 109 optimal weight:    3.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 174 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.124076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.105033 restraints weight = 27568.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.108245 restraints weight = 15298.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.110449 restraints weight = 10326.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.111941 restraints weight = 7830.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.112961 restraints weight = 6421.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.2643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  13160  Z= 0.142
  Angle     :  0.662   9.476  17896  Z= 0.326
  Chirality :  0.045   0.204   1985
  Planarity :  0.005   0.059   2282
  Dihedral  :  6.272  51.036   1985
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 22.72 %
    Favored  : 73.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.10 (0.21), residues: 1616
  helix:  0.43 (0.48), residues: 135
  sheet: -0.87 (0.22), residues: 569
  loop : -0.74 (0.20), residues: 912

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG J  67 
 TYR   0.014   0.001   TYR B 543 
 PHE   0.027   0.002   PHE G  96 
 TRP   0.017   0.001   TRP E 104 
 HIS   0.007   0.001   HIS I  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (13134)
  covalent geometry    : angle       0.65548 (17835)
  SS BOND              : bond        0.00392 (   17)
  SS BOND              : angle       1.57224 (   34)
  hydrogen bonds       : bond        0.03532 (  406)
  hydrogen bonds       : angle       5.61341 ( 1053)
  link_BETA1-4         : bond        0.00360 (    6)
  link_BETA1-4         : angle       2.10522 (   18)
  link_NAG-ASN         : bond        0.00217 (    3)
  link_NAG-ASN         : angle       1.60308 (    9)

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  337 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 291
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.8368 (pp30) cc_final: 0.6592 (mt0)
REVERT: B  596 ARG cc_start: 0.7987 (mtt-85) cc_final: 0.7699 (mtt-85)
REVERT: E   56 LYS cc_start: 0.7991 (mtmm) cc_final: 0.7649 (mppt)
REVERT: E   64 ARG cc_start: 0.5385 (mtt180) cc_final: 0.4876 (ttm170)
REVERT: E  100 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7708 (mm-30)
REVERT: E  117 ASP cc_start: 0.7508 (m-30) cc_final: 0.6679 (p0)
REVERT: E  156 GLU cc_start: 0.8245 (tt0) cc_final: 0.8027 (tt0)
REVERT: G   18 VAL cc_start: 0.7928 (t) cc_final: 0.7693 (m)
REVERT: G   36 TRP cc_start: 0.8367 (m100) cc_final: 0.7682 (m100)
REVERT: H   32 TYR cc_start: 0.8661 (m-80) cc_final: 0.8158 (m-10)
REVERT: H   82 MET cc_start: 0.7409 (ttt) cc_final: 0.7204 (ttt)
REVERT: H   96 PHE cc_start: 0.8577 (m-80) cc_final: 0.8219 (m-10)
REVERT: I   82 MET cc_start: 0.7240 (OUTLIER) cc_final: 0.6981 (mtm)
REVERT: K   37 ASP cc_start: 0.7298 (p0) cc_final: 0.6980 (p0)
REVERT: K   42 TYR cc_start: 0.8985 (m-80) cc_final: 0.8461 (m-10)
REVERT: K   96 GLN cc_start: 0.8225 (pp30) cc_final: 0.7845 (pp30)
  outliers start: 46
  outliers final: 39
  residues processed: 320
  average time/residue: 0.1112
  time to fit residues: 51.5076
Evaluate side-chains
  318 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 278
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 SER
Chi-restraints excluded: chain A residue  147 CYS
Chi-restraints excluded: chain B residue  506 ASN
Chi-restraints excluded: chain B residue  542 ILE
Chi-restraints excluded: chain B residue  547 LEU
Chi-restraints excluded: chain C residue   57 LEU
Chi-restraints excluded: chain C residue  103 GLU
Chi-restraints excluded: chain C residue  132 PHE
Chi-restraints excluded: chain D residue  505 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   52 VAL
Chi-restraints excluded: chain E residue  119 SER
Chi-restraints excluded: chain E residue  167 SER
Chi-restraints excluded: chain F residue  544 THR
Chi-restraints excluded: chain F residue  549 HIS
Chi-restraints excluded: chain G residue   11 VAL
Chi-restraints excluded: chain G residue   51 ILE
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue   77 THR
Chi-restraints excluded: chain G residue  174 ASN
Chi-restraints excluded: chain G residue  183 LEU
Chi-restraints excluded: chain G residue  227 GLU
Chi-restraints excluded: chain G residue  250 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue  152 LEU
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   54 TYR
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   80 VAL
Chi-restraints excluded: chain I residue   82 MET
Chi-restraints excluded: chain I residue   91 ASP
Chi-restraints excluded: chain I residue  142 ASP
Chi-restraints excluded: chain I residue  209 SER
Chi-restraints excluded: chain J residue    4 LEU
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   57 VAL
Chi-restraints excluded: chain K residue    5 THR
Chi-restraints excluded: chain K residue    9 ASP
Chi-restraints excluded: chain K residue   20 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 94 optimal weight:    7.9990
   chunk 28 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   chunk 16 optimal weight:    3.9990
   chunk 154 optimal weight:    6.9990
   chunk 79 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 153 optimal weight:    0.9980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
A  40 ASN
B 551 GLN
** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 508 GLN
D 560 GLN
** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 168 GLN
** I  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 174 ASN
J 103 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.125104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.106123 restraints weight = 27569.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.109314 restraints weight = 15292.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.111518 restraints weight = 10333.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.113017 restraints weight = 7829.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.113966 restraints weight = 6419.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.2775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069  13160  Z= 0.129
  Angle     :  0.649   9.189  17896  Z= 0.318
  Chirality :  0.044   0.202   1985
  Planarity :  0.005   0.059   2282
  Dihedral  :  5.783  51.851   1985
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 22.87 %
    Favored  : 74.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.21), residues: 1616
  helix:  0.52 (0.48), residues: 135
  sheet: -0.84 (0.22), residues: 575
  loop : -0.73 (0.20), residues: 906

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG J  67 
 TYR   0.014   0.001   TYR C 162 
 PHE   0.023   0.002   PHE G  96 
 TRP   0.025   0.001   TRP I  36 
 HIS   0.006   0.001   HIS I  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (13134)
  covalent geometry    : angle       0.64280 (17835)
  SS BOND              : bond        0.00391 (   17)
  SS BOND              : angle       1.50993 (   34)
  hydrogen bonds       : bond        0.03377 (  406)
  hydrogen bonds       : angle       5.43141 ( 1053)
  link_BETA1-4         : bond        0.00410 (    6)
  link_BETA1-4         : angle       2.06532 (   18)
  link_NAG-ASN         : bond        0.00300 (    3)
  link_NAG-ASN         : angle       1.55481 (    9)

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  330 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 290
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.8325 (pp30) cc_final: 0.6595 (mt0)
REVERT: E   56 LYS cc_start: 0.8012 (mtmm) cc_final: 0.7653 (mppt)
REVERT: E   64 ARG cc_start: 0.5314 (mtt180) cc_final: 0.4838 (ttm170)
REVERT: E  100 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7716 (mm-30)
REVERT: E  117 ASP cc_start: 0.7505 (m-30) cc_final: 0.6710 (p0)
REVERT: E  156 GLU cc_start: 0.8259 (tt0) cc_final: 0.7994 (tt0)
REVERT: G   18 VAL cc_start: 0.7804 (t) cc_final: 0.7491 (m)
REVERT: G   36 TRP cc_start: 0.8259 (m100) cc_final: 0.7622 (m100)
REVERT: H   32 TYR cc_start: 0.8631 (m-80) cc_final: 0.8135 (m-10)
REVERT: H   82 MET cc_start: 0.7373 (ttt) cc_final: 0.7160 (ttt)
REVERT: I   36 TRP cc_start: 0.8189 (m100) cc_final: 0.7749 (m100)
REVERT: I   82 MET cc_start: 0.7291 (OUTLIER) cc_final: 0.6765 (mtm)
REVERT: K   37 ASP cc_start: 0.7178 (p0) cc_final: 0.6841 (p0)
REVERT: K   96 GLN cc_start: 0.8166 (pp30) cc_final: 0.7811 (pp30)
  outliers start: 40
  outliers final: 37
  residues processed: 317
  average time/residue: 0.1019
  time to fit residues: 47.4267
Evaluate side-chains
  319 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 281
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 SER
Chi-restraints excluded: chain A residue  147 CYS
Chi-restraints excluded: chain B residue  506 ASN
Chi-restraints excluded: chain B residue  542 ILE
Chi-restraints excluded: chain B residue  547 LEU
Chi-restraints excluded: chain B residue  551 GLN
Chi-restraints excluded: chain C residue   57 LEU
Chi-restraints excluded: chain C residue  103 GLU
Chi-restraints excluded: chain C residue  132 PHE
Chi-restraints excluded: chain C residue  147 CYS
Chi-restraints excluded: chain D residue  505 VAL
Chi-restraints excluded: chain E residue   52 VAL
Chi-restraints excluded: chain E residue  119 SER
Chi-restraints excluded: chain E residue  167 SER
Chi-restraints excluded: chain E residue  174 THR
Chi-restraints excluded: chain F residue  544 THR
Chi-restraints excluded: chain F residue  549 HIS
Chi-restraints excluded: chain G residue   51 ILE
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue   77 THR
Chi-restraints excluded: chain G residue  174 ASN
Chi-restraints excluded: chain G residue  183 LEU
Chi-restraints excluded: chain G residue  227 GLU
Chi-restraints excluded: chain G residue  250 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue  152 LEU
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   54 TYR
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   82 MET
Chi-restraints excluded: chain I residue  142 ASP
Chi-restraints excluded: chain I residue  209 SER
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   51 ILE
Chi-restraints excluded: chain J residue   57 VAL
Chi-restraints excluded: chain K residue    5 THR
Chi-restraints excluded: chain K residue   20 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 24 optimal weight:    8.9990
   chunk 134 optimal weight:    8.9990
   chunk 94 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 125 optimal weight:    0.3980
   chunk 67 optimal weight:    1.9990
   chunk 148 optimal weight:    3.9990
   chunk 119 optimal weight:    7.9990
   chunk 159 optimal weight:    0.9990
   chunk 83 optimal weight:    8.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
A  40 ASN
B 551 GLN
** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 236 GLN
** I  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.124744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.105460 restraints weight = 27805.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.108693 restraints weight = 15399.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.110922 restraints weight = 10400.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.112436 restraints weight = 7884.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.113404 restraints weight = 6463.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.2834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  13160  Z= 0.140
  Angle     :  0.669   8.929  17896  Z= 0.330
  Chirality :  0.045   0.200   1985
  Planarity :  0.005   0.058   2282
  Dihedral  :  5.669  51.650   1985
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 23.31 %
    Favored  : 73.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.05 (0.21), residues: 1616
  helix:  0.53 (0.48), residues: 135
  sheet: -0.82 (0.22), residues: 575
  loop : -0.73 (0.20), residues: 906

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K  18 
 TYR   0.017   0.001   TYR H  54 
 PHE   0.029   0.002   PHE G  65 
 TRP   0.025   0.001   TRP I  36 
 HIS   0.013   0.002   HIS I  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (13134)
  covalent geometry    : angle       0.66201 (17835)
  SS BOND              : bond        0.00479 (   17)
  SS BOND              : angle       1.74273 (   34)
  hydrogen bonds       : bond        0.03393 (  406)
  hydrogen bonds       : angle       5.38497 ( 1053)
  link_BETA1-4         : bond        0.00389 (    6)
  link_BETA1-4         : angle       2.04247 (   18)
  link_NAG-ASN         : bond        0.00251 (    3)
  link_NAG-ASN         : angle       1.55594 (    9)

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

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

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3232 Ramachandran restraints generated.
    1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  331 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 291
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.8329 (pp30) cc_final: 0.6595 (mt0)
REVERT: E   56 LYS cc_start: 0.8012 (mtmm) cc_final: 0.7629 (mppt)
REVERT: E  117 ASP cc_start: 0.7510 (m-30) cc_final: 0.6711 (p0)
REVERT: E  156 GLU cc_start: 0.8241 (tt0) cc_final: 0.7966 (tt0)
REVERT: G   36 TRP cc_start: 0.8267 (m100) cc_final: 0.7592 (m100)
REVERT: G   64 ARG cc_start: 0.7717 (ttt90) cc_final: 0.7294 (tpm170)
REVERT: H    6 GLN cc_start: 0.7336 (pm20) cc_final: 0.7063 (pm20)
REVERT: H   32 TYR cc_start: 0.8632 (m-80) cc_final: 0.8140 (m-10)
REVERT: H  236 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7363 (pp30)
REVERT: I   36 TRP cc_start: 0.8130 (m100) cc_final: 0.7804 (m100)
REVERT: I   82 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6657 (mtm)
REVERT: K   37 ASP cc_start: 0.7156 (p0) cc_final: 0.6832 (p0)
REVERT: K   96 GLN cc_start: 0.8179 (pp30) cc_final: 0.7850 (pp30)
  outliers start: 40
  outliers final: 36
  residues processed: 317
  average time/residue: 0.1067
  time to fit residues: 49.8615
Evaluate side-chains
  319 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 281
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 SER
Chi-restraints excluded: chain A residue  147 CYS
Chi-restraints excluded: chain B residue  506 ASN
Chi-restraints excluded: chain B residue  542 ILE
Chi-restraints excluded: chain B residue  547 LEU
Chi-restraints excluded: chain B residue  551 GLN
Chi-restraints excluded: chain C residue   57 LEU
Chi-restraints excluded: chain C residue  103 GLU
Chi-restraints excluded: chain C residue  132 PHE
Chi-restraints excluded: chain C residue  147 CYS
Chi-restraints excluded: chain D residue  505 VAL
Chi-restraints excluded: chain E residue   52 VAL
Chi-restraints excluded: chain E residue  119 SER
Chi-restraints excluded: chain E residue  167 SER
Chi-restraints excluded: chain E residue  174 THR
Chi-restraints excluded: chain F residue  544 THR
Chi-restraints excluded: chain F residue  549 HIS
Chi-restraints excluded: chain G residue   51 ILE
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain G residue   77 THR
Chi-restraints excluded: chain G residue  174 ASN
Chi-restraints excluded: chain G residue  183 LEU
Chi-restraints excluded: chain G residue  227 GLU
Chi-restraints excluded: chain G residue  250 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue  152 LEU
Chi-restraints excluded: chain H residue  236 GLN
Chi-restraints excluded: chain H residue  239 GLN
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   54 TYR
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   82 MET
Chi-restraints excluded: chain I residue  142 ASP
Chi-restraints excluded: chain I residue  209 SER
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   57 VAL
Chi-restraints excluded: chain K residue   20 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9990
   chunk 123 optimal weight:   10.0000
   chunk 74 optimal weight:    0.1980
   chunk 47 optimal weight:    1.9990
   chunk 142 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 144 optimal weight:    2.9990
   chunk 117 optimal weight:    9.9990
   overall best weight:    1.4388

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
A  40 ASN
B 551 GLN
** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 506 ASN
** H 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.124419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.105416 restraints weight = 27690.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.108581 restraints weight = 15429.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.110764 restraints weight = 10479.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.112254 restraints weight = 7968.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.113291 restraints weight = 6547.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.2906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  13160  Z= 0.161
  Angle     :  0.670   8.425  17896  Z= 0.331
  Chirality :  0.045   0.196   1985
  Planarity :  0.005   0.061   2282
  Dihedral  :  5.613  50.826   1985
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 23.02 %
    Favored  : 73.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.10 (0.21), residues: 1616
  helix:  0.54 (0.48), residues: 135
  sheet: -0.86 (0.21), residues: 611
  loop : -0.74 (0.21), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG E  64 
 TYR   0.014   0.001   TYR K  42 
 PHE   0.028   0.002   PHE G  65 
 TRP   0.060   0.002   TRP E 104 
 HIS   0.012   0.001   HIS I  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (13134)
  covalent geometry    : angle       0.66406 (17835)
  SS BOND              : bond        0.00397 (   17)
  SS BOND              : angle       1.55198 (   34)
  hydrogen bonds       : bond        0.03419 (  406)
  hydrogen bonds       : angle       5.40763 ( 1053)
  link_BETA1-4         : bond        0.00417 (    6)
  link_BETA1-4         : angle       2.04297 (   18)
  link_NAG-ASN         : bond        0.00181 (    3)
  link_NAG-ASN         : angle       1.56919 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2214.56 seconds
wall clock time: 38 minutes 56.03 seconds (2336.03 seconds total)