Starting phenix.real_space_refine
on Sun Aug 24 08:02:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hws_35063/08_2025/8hws_35063.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hws_35063/08_2025/8hws_35063.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hws_35063/08_2025/8hws_35063.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hws_35063/08_2025/8hws_35063.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hws_35063/08_2025/8hws_35063.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hws_35063/08_2025/8hws_35063.cif"
  }
  resolution = 2.36
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 8168 atoms to isotropic.
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      46      5.16       5
     C    7244      2.51       5
     N    1930      2.21       5
     O    2291      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11511
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1563
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1563
          Classifications: {'peptide': 196}
          Link IDs: {'PTRANS': 12, 'TRANS': 183}
    Chain: "H"
      Number of atoms: 1617
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1617
          Classifications: {'peptide': 219}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 206}
    Chain: "L"
      Number of atoms: 1632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1632
          Classifications: {'peptide': 213}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202}
    Chain: "D"
      Number of atoms: 1662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1662
          Classifications: {'peptide': 222}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 210}
    Chain: "E"
      Number of atoms: 1634
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1634
          Classifications: {'peptide': 214}
          Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201}
    Chain: "I"
      Number of atoms: 1732
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 230, 1729
          Classifications: {'peptide': 230}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 217}
      Conformer: "B"
        Number of residues, atoms: 230, 1729
          Classifications: {'peptide': 230}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 217}
          bond proxies already assigned to first conformer: 1768
    Chain: "J"
      Number of atoms: 1633
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 214, 1630
          Classifications: {'peptide': 214}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202}
      Conformer: "B"
        Number of residues, atoms: 214, 1630
          Classifications: {'peptide': 214}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202}
          bond proxies already assigned to first conformer: 1659
    Chain: "B"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 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: 3.54, per 1000 atoms: 0.31
  Number of scatterers: 11511
  At special positions: 0
  Unit cell: (87.55, 113.9, 167.45, 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      46     16.00
     O    2291      8.00
     N    1930      7.00
     C    7244      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=19, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 144 " - pdb=" SG  CYS H 200 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 134 " - pdb=" SG  CYS L 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  95 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 147 " - pdb=" SG  CYS D 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 223 " - pdb=" SG  CYS E 215 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  23 " - pdb=" SG  CYS E  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 135 " - pdb=" SG  CYS E 195 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  22 " - pdb=" SG  CYS I  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I 154 " - pdb=" SG  CYS I 210 " distance=2.04
    Simple disulfide: pdb=" SG  CYS I 230 " - pdb=" SG  CYS J 214 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J  23 " - pdb=" SG  CYS J  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS J 134 " - pdb=" SG ACYS J 194 " distance=2.04
    Simple disulfide: pdb=" SG  CYS J 134 " - pdb=" SG BCYS J 194 " 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 B   1 " - " NAG B   2 "
    BETA1-6
      " NAG B   1 " - " FUC B   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG B   1 " - " ASN A 343 "
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 701.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2768

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 36 sheets defined
      9.7% alpha, 47.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 349 through 353
      removed outlier: 3.766A  pdb=" N   TRP A 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 371
      removed outlier: 3.831A  pdb=" N   PHE A 371 " --> pdb=" O   VAL A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 390
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.344A  pdb=" N   SER A 408 " --> pdb=" O   ASN A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.785A  pdb=" N   ASN H  32 " --> pdb=" O   VAL H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 86 through 90
      removed outlier: 3.927A  pdb=" N   THR H  90 " --> pdb=" O   ALA H  87 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 131 through 133
      No H-bonds generated for 'chain 'H' and resid 131 through 133'
    Processing helix  chain 'H' and resid 160 through 162
      No H-bonds generated for 'chain 'H' and resid 160 through 162'
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 4.270A  pdb=" N   PHE L  83 " --> pdb=" O   PRO L  80 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 121 through 127
      removed outlier: 3.546A  pdb=" N   SER L 127 " --> pdb=" O   GLU L 123 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 183 through 187
    Processing helix  chain 'D' and resid 28 through 32
      removed outlier: 3.514A  pdb=" N   SER D  31 " --> pdb=" O   THR D  28 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   TYR D  32 " --> pdb=" O   PHE D  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 28 through 32'
    Processing helix  chain 'D' and resid 86 through 90
      removed outlier: 3.950A  pdb=" N   THR D  90 " --> pdb=" O   ALA D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 163 through 165
      No H-bonds generated for 'chain 'D' and resid 163 through 165'
    Processing helix  chain 'D' and resid 194 through 196
      No H-bonds generated for 'chain 'D' and resid 194 through 196'
    Processing helix  chain 'D' and resid 208 through 211
    Processing helix  chain 'E' and resid 79 through 83
      removed outlier: 3.833A  pdb=" N   PHE E  83 " --> pdb=" O   PRO E  80 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 122 through 128
    Processing helix  chain 'E' and resid 184 through 189
    Processing helix  chain 'I' and resid 28 through 32
      removed outlier: 3.520A  pdb=" N   TYR I  32 " --> pdb=" O   PHE I  29 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 87 through 91
    Processing helix  chain 'I' and resid 170 through 172
      No H-bonds generated for 'chain 'I' and resid 170 through 172'
    Processing helix  chain 'J' and resid 30 through 32
      No H-bonds generated for 'chain 'J' and resid 30 through 32'
    Processing helix  chain 'J' and resid 80 through 84
      removed outlier: 3.912A  pdb=" N   PHE J  84 " --> pdb=" O   PRO J  81 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 121 through 126
    Processing helix  chain 'J' and resid 183 through 188
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.947A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12
      removed outlier: 4.039A  pdb=" N   TYR H  33 " --> pdb=" O   ASP H  98 " (cutoff:3.500A)
      removed outlier: 6.034A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.166A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 7.262A  pdb=" N   ALA H  40 " --> pdb=" O   LEU H  45 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   LEU H  45 " --> pdb=" O   ALA H  40 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12
      removed outlier: 4.252A  pdb=" N   VAL H 106 " --> pdb=" O   ARG H  97 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 124 through 128
      removed outlier: 6.060A  pdb=" N   TYR H 180 " --> pdb=" O   ASP H 148 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 135 through 136
      removed outlier: 6.060A  pdb=" N   TYR H 180 " --> pdb=" O   ASP H 148 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   SER H 181 " --> pdb=" O   VAL H 173 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 155 through 158
      removed outlier: 4.199A  pdb=" N   TYR H 198 " --> pdb=" O   VAL H 215 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 6
      removed outlier: 4.116A  pdb=" N   GLU L  70 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13
      removed outlier: 7.014A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13
      removed outlier: 7.014A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 114 through 118
      removed outlier: 6.015A  pdb=" N   TYR L 173 " --> pdb=" O   ASN L 138 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   THR L 178 " --> pdb=" O   GLN L 160 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   GLN L 160 " --> pdb=" O   THR L 178 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 153 through 154
    Processing sheet with id=AB6, first strand: chain 'D' and resid 3 through 7
    Processing sheet with id=AB7, first strand: chain 'D' and resid 11 through 12
      removed outlier: 4.308A  pdb=" N   ASP D  33 " --> pdb=" O   GLY D  98 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   MET D  34 " --> pdb=" O   THR D  50 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   THR D  50 " --> pdb=" O   MET D  34 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 11 through 12
      removed outlier: 6.969A  pdb=" N   CYS D  95 " --> pdb=" O   TRP D 110 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   TRP D 110 " --> pdb=" O   CYS D  95 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   ARG D  97 " --> pdb=" O   ASP D 108 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 127 through 131
      removed outlier: 6.129A  pdb=" N   TYR D 183 " --> pdb=" O   ASP D 151 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 138 through 139
      removed outlier: 6.129A  pdb=" N   TYR D 183 " --> pdb=" O   ASP D 151 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'D' and resid 158 through 161
    Processing sheet with id=AC3, first strand: chain 'E' and resid 4 through 7
      removed outlier: 3.677A  pdb=" N   ASP E  70 " --> pdb=" O   SER E  67 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'E' and resid 10 through 13
      removed outlier: 6.887A  pdb=" N   LEU E  11 " --> pdb=" O   ASP E 106 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   LEU E  33 " --> pdb=" O   TYR E  49 " (cutoff:3.500A)
      removed outlier: 4.893A  pdb=" N   TYR E  49 " --> pdb=" O   LEU E  33 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   TRP E  35 " --> pdb=" O   LEU E  47 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'E' and resid 10 through 13
      removed outlier: 6.887A  pdb=" N   LEU E  11 " --> pdb=" O   ASP E 106 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   THR E  98 " --> pdb=" O   GLN E  90 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'E' and resid 115 through 119
      removed outlier: 5.783A  pdb=" N   TYR E 174 " --> pdb=" O   ASN E 139 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'E' and resid 145 through 151
    Processing sheet with id=AC8, first strand: chain 'I' and resid 3 through 6
    Processing sheet with id=AC9, first strand: chain 'I' and resid 10 through 12
      removed outlier: 6.327A  pdb=" N   GLU I  10 " --> pdb=" O   THR I 124 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   GLY I  33 " --> pdb=" O   ASP I  99 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   GLY I  49 " --> pdb=" O   TRP I  36 " (cutoff:3.500A)
      removed outlier: 6.033A  pdb=" N   ARG I  38 " --> pdb=" O   TRP I  47 " (cutoff:3.500A)
      removed outlier: 5.321A  pdb=" N   TRP I  47 " --> pdb=" O   ARG I  38 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'I' and resid 10 through 12
      removed outlier: 6.327A  pdb=" N   GLU I  10 " --> pdb=" O   THR I 124 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   CYS I  96 " --> pdb=" O   TRP I 117 " (cutoff:3.500A)
      removed outlier: 4.797A  pdb=" N   TRP I 117 " --> pdb=" O   CYS I  96 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'I' and resid 134 through 138
      removed outlier: 6.019A  pdb=" N   TYR I 190 " --> pdb=" O   ASP I 158 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'I' and resid 134 through 138
      removed outlier: 6.019A  pdb=" N   TYR I 190 " --> pdb=" O   ASP I 158 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'I' and resid 165 through 168
      removed outlier: 4.185A  pdb=" N   TYR I 208 " --> pdb=" O   VAL I 225 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'J' and resid 4 through 7
    Processing sheet with id=AD6, first strand: chain 'J' and resid 10 through 12
      removed outlier: 6.864A  pdb=" N   LEU J  34 " --> pdb=" O   TYR J  50 " (cutoff:3.500A)
      removed outlier: 4.671A  pdb=" N   TYR J  50 " --> pdb=" O   LEU J  34 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   TRP J  36 " --> pdb=" O   LEU J  48 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'J' and resid 10 through 12
    Processing sheet with id=AD8, first strand: chain 'J' and resid 114 through 118
      removed outlier: 6.347A  pdb=" N   TYR J 173 " --> pdb=" O   ASN J 138 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'J' and resid 154 through 155
      removed outlier: 4.677A  pdb=" N   TRP J 148 " --> pdb=" O   GLN J 155 " (cutoff:3.500A)

    511 hydrogen bonds defined for protein.
    1271 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: 2.13

  Time building geometry restraints manager: 1.31 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: 3687
        1.34 -     1.47: 3032
        1.47 -     1.59: 5009
        1.59 -     1.71: 0
        1.71 -     1.83: 55
  Bond restraints: 11783
  Sorted by residual:
  bond pdb=" N   GLY I 113 "
       pdb=" CA  GLY I 113 "
    ideal  model  delta    sigma   weight residual
    1.453  1.442  0.011 8.60e-03 1.35e+04 1.65e+00
  bond pdb=" C1  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.431 -0.025 2.00e-02 2.50e+03 1.62e+00
  bond pdb=" C5  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.22e+00
  bond pdb=" C5  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.434 -0.021 2.00e-02 2.50e+03 1.06e+00
  bond pdb=" CB  PRO J 141 "
       pdb=" CG  PRO J 141 "
    ideal  model  delta    sigma   weight residual
    1.506  1.468  0.038 3.90e-02 6.57e+02 9.55e-01
  ... (remaining 11778 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 15813
        2.12 -     4.24: 189
        4.24 -     6.36: 27
        6.36 -     8.48: 1
        8.48 -    10.60: 2
  Bond angle restraints: 16032
  Sorted by residual:
  angle pdb=" CA  LEU I 192 "
        pdb=" CB  LEU I 192 "
        pdb=" CG  LEU I 192 "
      ideal   model   delta    sigma   weight residual
     116.30  126.90  -10.60 3.50e+00 8.16e-02 9.16e+00
  angle pdb=" CA  TYR D 152 "
        pdb=" CB  TYR D 152 "
        pdb=" CG  TYR D 152 "
      ideal   model   delta    sigma   weight residual
     113.90  118.74   -4.84 1.80e+00 3.09e-01 7.22e+00
  angle pdb=" CA  LEU D 115 "
        pdb=" CB  LEU D 115 "
        pdb=" CG  LEU D 115 "
      ideal   model   delta    sigma   weight residual
     116.30  125.50   -9.20 3.50e+00 8.16e-02 6.91e+00
  angle pdb=" CA  LYS J 145 "
        pdb=" CB  LYS J 145 "
        pdb=" CG  LYS J 145 "
      ideal   model   delta    sigma   weight residual
     114.10  119.16   -5.06 2.00e+00 2.50e-01 6.40e+00
  angle pdb=" C   VAL D  48 "
        pdb=" N   SER D  49 "
        pdb=" CA  SER D  49 "
      ideal   model   delta    sigma   weight residual
     121.85  117.39    4.46 1.77e+00 3.19e-01 6.36e+00
  ... (remaining 16027 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.07: 6195
       17.07 -    34.14: 620
       34.14 -    51.20: 193
       51.20 -    68.27: 50
       68.27 -    85.34: 17
  Dihedral angle restraints: 7075
    sinusoidal: 2724
      harmonic: 4351
  Sorted by residual:
  dihedral pdb=" CB  CYS I 154 "
           pdb=" SG  CYS I 154 "
           pdb=" SG  CYS I 210 "
           pdb=" CB  CYS I 210 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  139.68  -46.68     1      1.00e+01 1.00e-02 3.01e+01
  dihedral pdb=" CB  CYS I 230 "
           pdb=" SG  CYS I 230 "
           pdb=" SG  CYS J 214 "
           pdb=" CB  CYS J 214 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -125.91   39.91     1      1.00e+01 1.00e-02 2.24e+01
  dihedral pdb=" CB  CYS D  22 "
           pdb=" SG  CYS D  22 "
           pdb=" SG  CYS D  95 "
           pdb=" CB  CYS D  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   55.96   37.04     1      1.00e+01 1.00e-02 1.94e+01
  ... (remaining 7072 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1068
       0.030 -    0.059: 470
       0.059 -    0.089: 133
       0.089 -    0.118: 112
       0.118 -    0.147: 20
  Chirality restraints: 1803
  Sorted by residual:
  chirality pdb=" CA  VAL H  37 "
            pdb=" N   VAL H  37 "
            pdb=" C   VAL H  37 "
            pdb=" CB  VAL H  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.44e-01
  chirality pdb=" CB  THR A 430 "
            pdb=" CA  THR A 430 "
            pdb=" OG1 THR A 430 "
            pdb=" CG2 THR A 430 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.41    0.15 2.00e-01 2.50e+01 5.27e-01
  chirality pdb=" C1  NAG B   1 "
            pdb=" ND2 ASN A 343 "
            pdb=" C2  NAG B   1 "
            pdb=" O5  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.26   -0.14 2.00e-01 2.50e+01 5.06e-01
  ... (remaining 1800 not shown)

  Planarity restraints: 2056
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY E 100 "    0.029 5.00e-02 4.00e+02   4.45e-02 3.18e+00
        pdb=" N   PRO E 101 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO E 101 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO E 101 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER J   7 "   -0.027 5.00e-02 4.00e+02   4.15e-02 2.76e+00
        pdb=" N   PRO J   8 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO J   8 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO J   8 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU I 162 "   -0.027 5.00e-02 4.00e+02   4.13e-02 2.73e+00
        pdb=" N   PRO I 163 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO I 163 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO I 163 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 2053 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 495
        2.72 -     3.26: 10143
        3.26 -     3.81: 17777
        3.81 -     4.35: 22144
        4.35 -     4.90: 39420
  Nonbonded interactions: 89979
  Sorted by model distance:
  nonbonded pdb=" OG  SER L  30 "
            pdb=" N   SER L  31 "
     model   vdw
     2.174 3.120
  nonbonded pdb=" OH  TYR H  52 "
            pdb=" OD1 ASP L  94 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" O   GLN L 124 "
            pdb=" OG  SER L 127 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OG  SER J  64 "
            pdb=" OG1 THR J  75 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" O   SER A 438 "
            pdb=" OG  SER A 438 "
     model   vdw
     2.252 3.040
  ... (remaining 89974 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 'D' and (resid 2 through 11 or resid 13 through 26 or resid 30 through 31 \ 
 or resid 34 or resid 36 through 39 or resid 42 through 49 or resid 51 or resid  \ 
55 or resid 57 or resid 59 or resid 61 through 71 or resid 75 through 76 or resi \ 
d 78 through 82 or resid 84 through 87 or resid 89 through 97 or resid 99 or res \ 
id 102 or resid 104 or resid 108 or resid 110 through 114 or resid 117 through 2 \ 
22))
  selection = (chain 'H' and (resid 2 through 11 or resid 13 through 26 or resid 30 through 31 \ 
 or resid 34 or resid 36 through 39 or resid 42 through 49 or resid 51 or resid  \ 
55 or resid 57 or resid 59 or resid 61 through 71 or resid 75 through 76 or resi \ 
d 78 through 82 or resid 84 through 87 or resid 89 through 98 or resid 100 or re \ 
sid 102 or resid 105 or resid 107 through 111 or resid 114 through 219))
}
ncs_group {
  reference = (chain 'E' and (resid 2 or resid 5 through 9 or resid 11 through 13 or resid 15  \ 
through 27 or resid 29 or resid 31 or resid 33 or resid 35 through 44 or resid 4 \ 
6 through 52 or resid 54 through 69 or resid 71 through 84 or resid 86 through 9 \ 
0 or resid 94 or resid 97 through 100 or resid 102 through 104 or resid 107 thro \ 
ugh 214))
  selection = (chain 'L' and (resid 2 or resid 5 through 9 or resid 11 through 13 or resid 15  \ 
through 27 or resid 29 or resid 31 or resid 33 or resid 35 through 44 or resid 4 \ 
6 through 52 or resid 54 through 69 or resid 71 through 84 or resid 86 through 9 \ 
0 or resid 93 or resid 96 through 99 or resid 101 through 103 or resid 106 throu \ 
gh 213))
}

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=0.01 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.450
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11805  Z= 0.153
  Angle     :  0.573  10.595  16079  Z= 0.290
  Chirality :  0.043   0.147   1803
  Planarity :  0.005   0.045   2055
  Dihedral  : 15.867  85.340   4250
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 20.81 %
    Favored  : 75.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.22), residues: 1496
  helix: -1.86 (0.55), residues: 75
  sheet:  1.33 (0.20), residues: 674
  loop : -0.31 (0.23), residues: 747

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG I  85 
 TYR   0.017   0.001   TYR A 473 
 PHE   0.017   0.001   PHE A 371 
 TRP   0.012   0.001   TRP I  50 
 HIS   0.002   0.001   HIS J  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (11783)
  covalent geometry    : angle       0.57093 (16032)
  SS BOND              : bond        0.00524 (   19)
  SS BOND              : angle       0.90966 (   38)
  hydrogen bonds       : bond        0.13253 (  456)
  hydrogen bonds       : angle       6.53916 ( 1271)
  link_BETA1-4         : bond        0.00317 (    1)
  link_BETA1-4         : angle       1.61273 (    3)
  link_BETA1-6         : bond        0.00262 (    1)
  link_BETA1-6         : angle       1.65403 (    3)
  link_NAG-ASN         : bond        0.00290 (    1)
  link_NAG-ASN         : angle       1.08228 (    3)

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

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

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 181
  time to evaluate  : 0.463 
Fit side-chains
  outliers start: 42
  outliers final: 38
  residues processed: 221
  average time/residue: 0.4209
  time to fit residues: 103.6282
Evaluate side-chains
  225 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 187
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  359 SER
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue   70 SER
Chi-restraints excluded: chain H residue   73 ASN
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain H residue  154 VAL
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain H residue  181 SER
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue  107 LYS
Chi-restraints excluded: chain L residue  197 THR
Chi-restraints excluded: chain D residue   18 LEU
Chi-restraints excluded: chain D residue   33 ASP
Chi-restraints excluded: chain D residue   56 ASP
Chi-restraints excluded: chain D residue   70 SER
Chi-restraints excluded: chain D residue   76 ASN
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  214 VAL
Chi-restraints excluded: chain D residue  223 CYS
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   77 SER
Chi-restraints excluded: chain E residue   94 SER
Chi-restraints excluded: chain E residue  133 VAL
Chi-restraints excluded: chain I residue   18 VAL
Chi-restraints excluded: chain I residue  124 THR
Chi-restraints excluded: chain I residue  152 LEU
Chi-restraints excluded: chain I residue  196 VAL
Chi-restraints excluded: chain I residue  197 THR
Chi-restraints excluded: chain I residue  211 ASN
Chi-restraints excluded: chain J residue  197 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    0.4980
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    0.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
H 175 GLN
D 204 ASN
E   6 GLN
** J   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.177450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.141963 restraints weight = 15740.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.3849 rms_B_bonded: 2.52
r_work: 0.3748 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3602 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3600
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3600 r_free = 0.3600    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3600 r_free = 0.3600    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3600
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.0517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  11805  Z= 0.152
  Angle     :  0.568  11.045  16079  Z= 0.290
  Chirality :  0.043   0.145   1803
  Planarity :  0.005   0.043   2055
  Dihedral  :  6.341  57.888   1748
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 18.87 %
    Favored  : 77.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.22), residues: 1496
  helix: -1.79 (0.58), residues: 69
  sheet:  1.34 (0.20), residues: 686
  loop : -0.27 (0.23), residues: 741

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG I  85 
 TYR   0.023   0.001   TYR D 152 
 PHE   0.016   0.001   PHE E  99 
 TRP   0.010   0.001   TRP I  50 
 HIS   0.003   0.001   HIS J  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (11783)
  covalent geometry    : angle       0.56585 (16032)
  SS BOND              : bond        0.00557 (   19)
  SS BOND              : angle       0.96215 (   38)
  hydrogen bonds       : bond        0.03627 (  456)
  hydrogen bonds       : angle       5.65573 ( 1271)
  link_BETA1-4         : bond        0.00226 (    1)
  link_BETA1-4         : angle       1.24396 (    3)
  link_BETA1-6         : bond        0.00432 (    1)
  link_BETA1-6         : angle       1.37334 (    3)
  link_NAG-ASN         : bond        0.00169 (    1)
  link_NAG-ASN         : angle       1.14720 (    3)

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

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

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 202
  time to evaluate  : 0.420 
Fit side-chains
  outliers start: 49
  outliers final: 31
  residues processed: 233
  average time/residue: 0.3509
  time to fit residues: 91.0230
Evaluate side-chains
  223 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 192
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  354 ASN
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   73 ASN
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain H residue  154 VAL
Chi-restraints excluded: chain H residue  167 VAL
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue  107 LYS
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain L residue  175 LEU
Chi-restraints excluded: chain L residue  197 THR
Chi-restraints excluded: chain D residue   18 LEU
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue  158 THR
Chi-restraints excluded: chain D residue  204 ASN
Chi-restraints excluded: chain D residue  223 CYS
Chi-restraints excluded: chain E residue   33 LEU
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain I residue  110 LEU
Chi-restraints excluded: chain I residue  124 THR
Chi-restraints excluded: chain I residue  152 LEU
Chi-restraints excluded: chain I residue  192 LEU
Chi-restraints excluded: chain I residue  197 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 145 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 127 optimal weight:    0.7980
   chunk 89 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 22 optimal weight:    0.3980
   chunk 47 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 7 optimal weight:    0.7980
   chunk 111 optimal weight:    0.2980
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
H  73 ASN
H 175 GLN
L  37 GLN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 204 ASN
E   6 GLN
** J   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.177879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.142085 restraints weight = 18332.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3845 rms_B_bonded: 2.74
r_work: 0.3736 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3583 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3586
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3586 r_free = 0.3586    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3586 r_free = 0.3586    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3586
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.0699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11805  Z= 0.133
  Angle     :  0.555  11.154  16079  Z= 0.281
  Chirality :  0.043   0.177   1803
  Planarity :  0.005   0.042   2055
  Dihedral  :  5.500  56.544   1719
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 19.72 %
    Favored  : 77.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.22), residues: 1496
  helix: -1.80 (0.58), residues: 69
  sheet:  1.36 (0.20), residues: 687
  loop : -0.23 (0.23), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG I  85 
 TYR   0.024   0.001   TYR D 152 
 PHE   0.020   0.001   PHE A 371 
 TRP   0.010   0.001   TRP I  50 
 HIS   0.002   0.000   HIS J  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (11783)
  covalent geometry    : angle       0.55293 (16032)
  SS BOND              : bond        0.00531 (   19)
  SS BOND              : angle       0.93859 (   38)
  hydrogen bonds       : bond        0.03408 (  456)
  hydrogen bonds       : angle       5.50880 ( 1271)
  link_BETA1-4         : bond        0.00288 (    1)
  link_BETA1-4         : angle       1.21707 (    3)
  link_BETA1-6         : bond        0.00356 (    1)
  link_BETA1-6         : angle       1.30231 (    3)
  link_NAG-ASN         : bond        0.00183 (    1)
  link_NAG-ASN         : angle       1.16030 (    3)

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

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

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 191
  time to evaluate  : 0.259 
Fit side-chains
  outliers start: 41
  outliers final: 27
  residues processed: 213
  average time/residue: 0.3644
  time to fit residues: 86.4642
Evaluate side-chains
  211 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 184
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  354 ASN
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   73 ASN
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain L residue   65 SER
Chi-restraints excluded: chain L residue  107 LYS
Chi-restraints excluded: chain L residue  175 LEU
Chi-restraints excluded: chain L residue  197 THR
Chi-restraints excluded: chain D residue   18 LEU
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue   70 SER
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain D residue  223 CYS
Chi-restraints excluded: chain E residue   18 ARG
Chi-restraints excluded: chain E residue   33 LEU
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   67 SER
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain I residue  124 THR
Chi-restraints excluded: chain I residue  192 LEU
Chi-restraints excluded: chain I residue  212 VAL
Chi-restraints excluded: chain J residue   27 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 12 optimal weight:    0.4980
   chunk 45 optimal weight:    0.0770
   chunk 129 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 98 optimal weight:    6.9990
   chunk 146 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 22 optimal weight:    0.0270
   chunk 136 optimal weight:    0.4980
   chunk 77 optimal weight:    0.0870
   overall best weight:    0.2374

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN
** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  37 GLN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 204 ASN
D 207 HIS
E   6 GLN
** J   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.179921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.143757 restraints weight = 18861.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3876 rms_B_bonded: 2.84
r_work: 0.3769 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3630 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3628
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3628 r_free = 0.3628    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3628 r_free = 0.3628    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3628
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.0954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  11805  Z= 0.090
  Angle     :  0.518  10.424  16079  Z= 0.259
  Chirality :  0.042   0.254   1803
  Planarity :  0.004   0.042   2055
  Dihedral  :  4.943  48.267   1713
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 20.03 %
    Favored  : 77.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.75 (0.22), residues: 1496
  helix: -1.74 (0.57), residues: 69
  sheet:  1.44 (0.20), residues: 676
  loop : -0.12 (0.23), residues: 751

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG I  85 
 TYR   0.025   0.001   TYR D 152 
 PHE   0.015   0.001   PHE A 371 
 TRP   0.009   0.001   TRP I  50 
 HIS   0.002   0.000   HIS J  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 (11783)
  covalent geometry    : angle       0.51679 (16032)
  SS BOND              : bond        0.00382 (   19)
  SS BOND              : angle       0.63466 (   38)
  hydrogen bonds       : bond        0.02816 (  456)
  hydrogen bonds       : angle       5.25415 ( 1271)
  link_BETA1-4         : bond        0.00328 (    1)
  link_BETA1-4         : angle       1.30558 (    3)
  link_BETA1-6         : bond        0.00289 (    1)
  link_BETA1-6         : angle       1.23384 (    3)
  link_NAG-ASN         : bond        0.00142 (    1)
  link_NAG-ASN         : angle       1.01936 (    3)

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

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

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 194
  time to evaluate  : 0.387 
Fit side-chains
REVERT: I  125 VAL cc_start: 0.7707 (m) cc_final: 0.7331 (p)
  outliers start: 36
  outliers final: 25
  residues processed: 211
  average time/residue: 0.3801
  time to fit residues: 89.2196
Evaluate side-chains
  217 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 192
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   73 ASN
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain L residue  107 LYS
Chi-restraints excluded: chain L residue  175 LEU
Chi-restraints excluded: chain L residue  197 THR
Chi-restraints excluded: chain D residue   18 LEU
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue   70 SER
Chi-restraints excluded: chain D residue  158 THR
Chi-restraints excluded: chain D residue  204 ASN
Chi-restraints excluded: chain D residue  223 CYS
Chi-restraints excluded: chain E residue   18 ARG
Chi-restraints excluded: chain E residue   33 LEU
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   67 SER
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain I residue  196 VAL
Chi-restraints excluded: chain J residue   27 GLN
Chi-restraints excluded: chain J residue   70 THR
Chi-restraints excluded: chain J residue  109 THR
Chi-restraints excluded: chain J residue  117 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9990
   chunk 70 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 107 optimal weight:    1.9990
   chunk 100 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 68 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
H  76 ASN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 199 GLN
D 204 ASN
E   6 GLN
** J   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  90 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.176394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.140457 restraints weight = 18681.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3844 rms_B_bonded: 2.79
r_work: 0.3735 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3599 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3598
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3598 r_free = 0.3598    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3598 r_free = 0.3598    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3598
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.0929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11805  Z= 0.177
  Angle     :  0.578  11.005  16079  Z= 0.289
  Chirality :  0.043   0.156   1803
  Planarity :  0.004   0.042   2055
  Dihedral  :  4.980  47.477   1708
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 19.95 %
    Favored  : 76.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.22), residues: 1496
  helix: -1.67 (0.59), residues: 69
  sheet:  1.39 (0.20), residues: 689
  loop : -0.19 (0.23), residues: 738

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG I  85 
 TYR   0.015   0.002   TYR E  49 
 PHE   0.015   0.001   PHE E  99 
 TRP   0.011   0.001   TRP D 110 
 HIS   0.003   0.001   HIS J  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 (11783)
  covalent geometry    : angle       0.57564 (16032)
  SS BOND              : bond        0.00583 (   19)
  SS BOND              : angle       1.04999 (   38)
  hydrogen bonds       : bond        0.03468 (  456)
  hydrogen bonds       : angle       5.30220 ( 1271)
  link_BETA1-4         : bond        0.00398 (    1)
  link_BETA1-4         : angle       1.42875 (    3)
  link_BETA1-6         : bond        0.00280 (    1)
  link_BETA1-6         : angle       1.36615 (    3)
  link_NAG-ASN         : bond        0.00228 (    1)
  link_NAG-ASN         : angle       1.14901 (    3)

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

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

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 192
  time to evaluate  : 0.451 
Fit side-chains
  outliers start: 43
  outliers final: 33
  residues processed: 216
  average time/residue: 0.4004
  time to fit residues: 96.9164
Evaluate side-chains
  224 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 191
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   69 ILE
Chi-restraints excluded: chain H residue   73 ASN
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain H residue  154 VAL
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue  175 LEU
Chi-restraints excluded: chain L residue  197 THR
Chi-restraints excluded: chain D residue   18 LEU
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue   70 SER
Chi-restraints excluded: chain D residue  158 THR
Chi-restraints excluded: chain D residue  223 CYS
Chi-restraints excluded: chain E residue   18 ARG
Chi-restraints excluded: chain E residue   33 LEU
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   67 SER
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue  133 VAL
Chi-restraints excluded: chain I residue  110 LEU
Chi-restraints excluded: chain I residue  152 LEU
Chi-restraints excluded: chain I residue  196 VAL
Chi-restraints excluded: chain J residue   27 GLN
Chi-restraints excluded: chain J residue   48 LEU
Chi-restraints excluded: chain J residue  109 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 95 optimal weight:    5.9990
   chunk 117 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 74 optimal weight:    0.0000
   chunk 56 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 122 optimal weight:    0.0030
   overall best weight:    0.5394

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

Flipped N/Q/H residues before XYZ refinement:
H  76 ASN
** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 199 GLN
D 204 ASN
E   6 GLN
** J   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  90 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.175608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.140819 restraints weight = 16178.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3859 rms_B_bonded: 2.62
r_work: 0.3763 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3638 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3635
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3635 r_free = 0.3635    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3635 r_free = 0.3635    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3635
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.1007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11805  Z= 0.126
  Angle     :  0.548  11.031  16079  Z= 0.275
  Chirality :  0.043   0.157   1803
  Planarity :  0.004   0.041   2055
  Dihedral  :  4.720  47.736   1704
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 20.26 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.22), residues: 1496
  helix: -1.64 (0.59), residues: 69
  sheet:  1.41 (0.20), residues: 670
  loop : -0.19 (0.23), residues: 757

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG I  85 
 TYR   0.027   0.001   TYR D 152 
 PHE   0.024   0.001   PHE A 371 
 TRP   0.010   0.001   TRP I  50 
 HIS   0.003   0.001   HIS J  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (11783)
  covalent geometry    : angle       0.54665 (16032)
  SS BOND              : bond        0.00490 (   19)
  SS BOND              : angle       0.86453 (   38)
  hydrogen bonds       : bond        0.03175 (  456)
  hydrogen bonds       : angle       5.24694 ( 1271)
  link_BETA1-4         : bond        0.00310 (    1)
  link_BETA1-4         : angle       1.39246 (    3)
  link_BETA1-6         : bond        0.00304 (    1)
  link_BETA1-6         : angle       1.32989 (    3)
  link_NAG-ASN         : bond        0.00240 (    1)
  link_NAG-ASN         : angle       1.14137 (    3)

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

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

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 187
  time to evaluate  : 0.444 
Fit side-chains
  outliers start: 42
  outliers final: 29
  residues processed: 210
  average time/residue: 0.3466
  time to fit residues: 81.6592
Evaluate side-chains
  219 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 190
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  459 SER
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue   73 ASN
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain H residue  154 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue  175 LEU
Chi-restraints excluded: chain L residue  197 THR
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue   82 MET
Chi-restraints excluded: chain D residue  158 THR
Chi-restraints excluded: chain D residue  204 ASN
Chi-restraints excluded: chain D residue  223 CYS
Chi-restraints excluded: chain E residue   18 ARG
Chi-restraints excluded: chain E residue   33 LEU
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   67 SER
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain I residue   81 MET
Chi-restraints excluded: chain I residue  152 LEU
Chi-restraints excluded: chain I residue  192 LEU
Chi-restraints excluded: chain I residue  196 VAL
Chi-restraints excluded: chain J residue   48 LEU
Chi-restraints excluded: chain J residue  109 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 114 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 120 optimal weight:    0.9990
   chunk 100 optimal weight:    4.9990
   chunk 52 optimal weight:   10.0000
   chunk 8 optimal weight:    1.9990
   chunk 130 optimal weight:    0.7980
   chunk 67 optimal weight:    0.8980
   chunk 45 optimal weight:    0.3980
   chunk 112 optimal weight:    1.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 199 GLN
D 204 ASN
E   6 GLN
** J   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.172957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.137268 restraints weight = 24911.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3815 rms_B_bonded: 3.22
r_work: 0.3687 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3687
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3687 r_free = 0.3687    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3687 r_free = 0.3687    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3687
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.1011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11805  Z= 0.173
  Angle     :  0.582  11.194  16079  Z= 0.290
  Chirality :  0.044   0.156   1803
  Planarity :  0.004   0.042   2055
  Dihedral  :  4.667  46.030   1702
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 20.42 %
    Favored  : 76.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.22), residues: 1496
  helix: -1.60 (0.60), residues: 69
  sheet:  1.38 (0.20), residues: 677
  loop : -0.25 (0.22), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG I  85 
 TYR   0.026   0.002   TYR D 152 
 PHE   0.023   0.002   PHE A 371 
 TRP   0.011   0.001   TRP D 110 
 HIS   0.003   0.001   HIS J  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 (11783)
  covalent geometry    : angle       0.57987 (16032)
  SS BOND              : bond        0.00576 (   19)
  SS BOND              : angle       1.01928 (   38)
  hydrogen bonds       : bond        0.03470 (  456)
  hydrogen bonds       : angle       5.30298 ( 1271)
  link_BETA1-4         : bond        0.00374 (    1)
  link_BETA1-4         : angle       1.48749 (    3)
  link_BETA1-6         : bond        0.00244 (    1)
  link_BETA1-6         : angle       1.35630 (    3)
  link_NAG-ASN         : bond        0.00251 (    1)
  link_NAG-ASN         : angle       1.22779 (    3)

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

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

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 192
  time to evaluate  : 0.456 
Fit side-chains
  outliers start: 42
  outliers final: 33
  residues processed: 215
  average time/residue: 0.3597
  time to fit residues: 87.1811
Evaluate side-chains
  225 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 192
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  459 SER
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   73 ASN
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain H residue  154 VAL
Chi-restraints excluded: chain H residue  167 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain L residue  175 LEU
Chi-restraints excluded: chain L residue  197 THR
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue  158 THR
Chi-restraints excluded: chain D residue  204 ASN
Chi-restraints excluded: chain D residue  223 CYS
Chi-restraints excluded: chain E residue   18 ARG
Chi-restraints excluded: chain E residue   33 LEU
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   67 SER
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue  133 VAL
Chi-restraints excluded: chain I residue   68 VAL
Chi-restraints excluded: chain I residue  110 LEU
Chi-restraints excluded: chain I residue  152 LEU
Chi-restraints excluded: chain I residue  192 LEU
Chi-restraints excluded: chain I residue  196 VAL
Chi-restraints excluded: chain J residue   48 LEU
Chi-restraints excluded: chain J residue  109 THR
Chi-restraints excluded: chain J residue  197 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 139 optimal weight:    1.9990
   chunk 117 optimal weight:    0.4980
   chunk 7 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 141 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 110 optimal weight:    1.9990
   chunk 107 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
H 175 GLN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 199 GLN
D 204 ASN
E   6 GLN
** J   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.171791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.135770 restraints weight = 24824.607|
|-----------------------------------------------------------------------------|
r_work (start): 0.3803 rms_B_bonded: 3.11
r_work: 0.3682 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3540 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3539
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3539 r_free = 0.3539    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3539 r_free = 0.3539    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3539
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.1056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  11805  Z= 0.222
  Angle     :  0.611  11.310  16079  Z= 0.308
  Chirality :  0.045   0.158   1803
  Planarity :  0.005   0.041   2055
  Dihedral  :  4.823  46.301   1702
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 20.42 %
    Favored  : 76.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.55 (0.22), residues: 1496
  helix: -1.61 (0.60), residues: 69
  sheet:  1.36 (0.20), residues: 678
  loop : -0.36 (0.22), residues: 749

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG I  85 
 TYR   0.025   0.002   TYR D 152 
 PHE   0.024   0.002   PHE A 371 
 TRP   0.013   0.002   TRP D 110 
 HIS   0.003   0.001   HIS J  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00530 (11783)
  covalent geometry    : angle       0.60855 (16032)
  SS BOND              : bond        0.00654 (   19)
  SS BOND              : angle       1.19224 (   38)
  hydrogen bonds       : bond        0.03806 (  456)
  hydrogen bonds       : angle       5.42452 ( 1271)
  link_BETA1-4         : bond        0.00403 (    1)
  link_BETA1-4         : angle       1.61450 (    3)
  link_BETA1-6         : bond        0.00360 (    1)
  link_BETA1-6         : angle       1.38033 (    3)
  link_NAG-ASN         : bond        0.00341 (    1)
  link_NAG-ASN         : angle       1.31442 (    3)

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

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

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 195
  time to evaluate  : 0.527 
Fit side-chains
  outliers start: 43
  outliers final: 39
  residues processed: 220
  average time/residue: 0.3640
  time to fit residues: 89.9072
Evaluate side-chains
  227 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 188
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  459 SER
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   69 ILE
Chi-restraints excluded: chain H residue   73 ASN
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain H residue  154 VAL
Chi-restraints excluded: chain H residue  167 VAL
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   65 SER
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain L residue  175 LEU
Chi-restraints excluded: chain L residue  197 THR
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue  158 THR
Chi-restraints excluded: chain D residue  204 ASN
Chi-restraints excluded: chain D residue  223 CYS
Chi-restraints excluded: chain E residue   18 ARG
Chi-restraints excluded: chain E residue   33 LEU
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   67 SER
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue  133 VAL
Chi-restraints excluded: chain I residue   18 VAL
Chi-restraints excluded: chain I residue   68 VAL
Chi-restraints excluded: chain I residue  110 LEU
Chi-restraints excluded: chain I residue  152 LEU
Chi-restraints excluded: chain I residue  192 LEU
Chi-restraints excluded: chain I residue  196 VAL
Chi-restraints excluded: chain J residue   48 LEU
Chi-restraints excluded: chain J residue  109 THR
Chi-restraints excluded: chain J residue  197 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 108 optimal weight:    0.0970
   chunk 49 optimal weight:    0.6980
   chunk 138 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 119 optimal weight:    0.8980
   chunk 126 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 103 optimal weight:    4.9990
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
H 175 GLN
** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  37 GLN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 204 ASN
E   6 GLN
** J   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.172955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.136599 restraints weight = 26360.703|
|-----------------------------------------------------------------------------|
r_work (start): 0.3815 rms_B_bonded: 3.25
r_work: 0.3687 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3689
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3689 r_free = 0.3689    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3689 r_free = 0.3689    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3689
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.1044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11805  Z= 0.146
  Angle     :  0.582  11.104  16079  Z= 0.291
  Chirality :  0.043   0.154   1803
  Planarity :  0.004   0.041   2055
  Dihedral  :  4.716  47.166   1702
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 20.50 %
    Favored  : 76.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.58 (0.22), residues: 1496
  helix: -1.62 (0.59), residues: 69
  sheet:  1.37 (0.20), residues: 674
  loop : -0.33 (0.22), residues: 753

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG I  85 
 TYR   0.027   0.001   TYR D 152 
 PHE   0.021   0.001   PHE A 371 
 TRP   0.010   0.001   TRP D 110 
 HIS   0.002   0.001   HIS J  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (11783)
  covalent geometry    : angle       0.57958 (16032)
  SS BOND              : bond        0.00549 (   19)
  SS BOND              : angle       0.99632 (   38)
  hydrogen bonds       : bond        0.03400 (  456)
  hydrogen bonds       : angle       5.35834 ( 1271)
  link_BETA1-4         : bond        0.00384 (    1)
  link_BETA1-4         : angle       1.53002 (    3)
  link_BETA1-6         : bond        0.00321 (    1)
  link_BETA1-6         : angle       1.29963 (    3)
  link_NAG-ASN         : bond        0.00308 (    1)
  link_NAG-ASN         : angle       1.21424 (    3)

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

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

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 188
  time to evaluate  : 0.463 
Fit side-chains
  outliers start: 44
  outliers final: 38
  residues processed: 212
  average time/residue: 0.3921
  time to fit residues: 93.0943
Evaluate side-chains
  230 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 192
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  459 SER
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   69 ILE
Chi-restraints excluded: chain H residue   73 ASN
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain H residue  154 VAL
Chi-restraints excluded: chain H residue  181 SER
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   65 SER
Chi-restraints excluded: chain L residue  175 LEU
Chi-restraints excluded: chain L residue  197 THR
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue  158 THR
Chi-restraints excluded: chain D residue  204 ASN
Chi-restraints excluded: chain D residue  223 CYS
Chi-restraints excluded: chain E residue   18 ARG
Chi-restraints excluded: chain E residue   33 LEU
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   67 SER
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue  133 VAL
Chi-restraints excluded: chain I residue   18 VAL
Chi-restraints excluded: chain I residue   68 VAL
Chi-restraints excluded: chain I residue  110 LEU
Chi-restraints excluded: chain I residue  152 LEU
Chi-restraints excluded: chain I residue  192 LEU
Chi-restraints excluded: chain I residue  196 VAL
Chi-restraints excluded: chain J residue   48 LEU
Chi-restraints excluded: chain J residue  109 THR
Chi-restraints excluded: chain J residue  197 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 127 optimal weight:    0.5980
   chunk 96 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   chunk 112 optimal weight:    0.5980
   chunk 91 optimal weight:    0.9980
   chunk 118 optimal weight:    6.9990
   chunk 122 optimal weight:    0.9980
   chunk 117 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
H 175 GLN
** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 199 GLN
D 204 ASN
E   6 GLN
** J   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.172049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.136622 restraints weight = 20997.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3822 rms_B_bonded: 2.89
r_work: 0.3707 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3563 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3562
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3562 r_free = 0.3562    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3562 r_free = 0.3562    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3562
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.1085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  11805  Z= 0.179
  Angle     :  0.598  11.107  16079  Z= 0.300
  Chirality :  0.044   0.155   1803
  Planarity :  0.005   0.042   2055
  Dihedral  :  4.757  47.346   1702
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 20.81 %
    Favored  : 75.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.22), residues: 1496
  helix: -1.62 (0.59), residues: 69
  sheet:  1.31 (0.20), residues: 668
  loop : -0.36 (0.22), residues: 759

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG I  85 
 TYR   0.026   0.002   TYR D 152 
 PHE   0.022   0.002   PHE A 371 
 TRP   0.011   0.001   TRP D 110 
 HIS   0.003   0.001   HIS J  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 (11783)
  covalent geometry    : angle       0.59527 (16032)
  SS BOND              : bond        0.00603 (   19)
  SS BOND              : angle       1.07335 (   38)
  hydrogen bonds       : bond        0.03557 (  456)
  hydrogen bonds       : angle       5.37348 ( 1271)
  link_BETA1-4         : bond        0.00411 (    1)
  link_BETA1-4         : angle       1.56514 (    3)
  link_BETA1-6         : bond        0.00310 (    1)
  link_BETA1-6         : angle       1.31680 (    3)
  link_NAG-ASN         : bond        0.00316 (    1)
  link_NAG-ASN         : angle       1.21423 (    3)

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

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

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 189
  time to evaluate  : 0.454 
Fit side-chains
  outliers start: 42
  outliers final: 39
  residues processed: 211
  average time/residue: 0.3504
  time to fit residues: 82.8692
Evaluate side-chains
  230 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 191
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  459 SER
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   69 ILE
Chi-restraints excluded: chain H residue   73 ASN
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain H residue  154 VAL
Chi-restraints excluded: chain H residue  181 SER
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   65 SER
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain L residue  175 LEU
Chi-restraints excluded: chain L residue  197 THR
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue  158 THR
Chi-restraints excluded: chain D residue  204 ASN
Chi-restraints excluded: chain D residue  223 CYS
Chi-restraints excluded: chain E residue   18 ARG
Chi-restraints excluded: chain E residue   33 LEU
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   67 SER
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue  133 VAL
Chi-restraints excluded: chain I residue   18 VAL
Chi-restraints excluded: chain I residue   68 VAL
Chi-restraints excluded: chain I residue  110 LEU
Chi-restraints excluded: chain I residue  152 LEU
Chi-restraints excluded: chain I residue  192 LEU
Chi-restraints excluded: chain I residue  196 VAL
Chi-restraints excluded: chain J residue   48 LEU
Chi-restraints excluded: chain J residue  109 THR
Chi-restraints excluded: chain J residue  197 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 96 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 138 optimal weight:    1.9990
   chunk 104 optimal weight:    0.3980
   chunk 26 optimal weight:    0.0980
   chunk 136 optimal weight:    0.6980
   chunk 133 optimal weight:    0.3980
   chunk 86 optimal weight:    0.9990
   chunk 80 optimal weight:    0.0470
   chunk 72 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   overall best weight:    0.3278

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

Flipped N/Q/H residues before XYZ refinement:
** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 199 GLN
D 204 ASN
E   6 GLN
** J   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.174781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.139804 restraints weight = 18364.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.3859 rms_B_bonded: 2.70
r_work: 0.3756 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3613 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3605
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3605 r_free = 0.3605    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3605 r_free = 0.3605    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3605
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.1139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  11805  Z= 0.104
  Angle     :  0.551  10.617  16079  Z= 0.276
  Chirality :  0.043   0.153   1803
  Planarity :  0.004   0.041   2055
  Dihedral  :  4.565  48.402   1702
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 21.51 %
    Favored  : 75.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.22), residues: 1496
  helix: -1.61 (0.58), residues: 69
  sheet:  1.37 (0.20), residues: 660
  loop : -0.24 (0.22), residues: 767

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG I  85 
 TYR   0.028   0.001   TYR D 152 
 PHE   0.018   0.001   PHE A 371 
 TRP   0.011   0.001   TRP I  50 
 HIS   0.002   0.000   HIS J  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 (11783)
  covalent geometry    : angle       0.54979 (16032)
  SS BOND              : bond        0.00462 (   19)
  SS BOND              : angle       0.82871 (   38)
  hydrogen bonds       : bond        0.03026 (  456)
  hydrogen bonds       : angle       5.23514 ( 1271)
  link_BETA1-4         : bond        0.00379 (    1)
  link_BETA1-4         : angle       1.50846 (    3)
  link_BETA1-6         : bond        0.00234 (    1)
  link_BETA1-6         : angle       1.22347 (    3)
  link_NAG-ASN         : bond        0.00326 (    1)
  link_NAG-ASN         : angle       1.10179 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6209.96 seconds
wall clock time: 105 minutes 56.82 seconds (6356.82 seconds total)