Starting phenix.real_space_refine
on Mon Jul 28 20:12:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qno_4598/07_2025/6qno_4598_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qno_4598/07_2025/6qno_4598.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.38
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6qno_4598/07_2025/6qno_4598.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qno_4598/07_2025/6qno_4598.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qno_4598/07_2025/6qno_4598_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qno_4598/07_2025/6qno_4598_neut.cif"
  }
  resolution = 4.38
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      78      5.16       5
     C    6647      2.51       5
     N    1718      2.21       5
     O    1986      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10429
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1711
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1711
          Classifications: {'peptide': 212}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 209}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2392
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 312, 2392
          Classifications: {'peptide': 312}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 306}
    Chain: "G"
      Number of atoms: 293
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 293
          Classifications: {'peptide': 36}
          Link IDs: {'PTRANS': 3, 'TRANS': 32}
    Chain: "L"
      Number of atoms: 1679
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1679
          Classifications: {'peptide': 217}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 205}
    Chain: "H"
      Number of atoms: 1660
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 221, 1654
          Classifications: {'peptide': 221}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 206}
      Conformer: "B"
        Number of residues, atoms: 221, 1654
          Classifications: {'peptide': 221}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 206}
          bond proxies already assigned to first conformer: 1692
    Chain: "R"
      Number of atoms: 2646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2646
          Classifications: {'peptide': 334}
          Link IDs: {'PTRANS': 19, 'TRANS': 314}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "R"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 20
          Unusual residues: {'RET': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'RET:plan-5': 1}
          Unresolved non-hydrogen planarities: 1
  Residues with excluded nonbonded symmetry interactions: 5
    residue:
      pdb=" N   SER L  42 " occ=0.94
      ... (4 atoms not shown)
      pdb=" OG  SER L  42 " occ=0.94
    residue:
      pdb=" N   SER H 176 " occ=0.54
      ... (7 atoms not shown)
      pdb=" OG BSER H 176 " occ=0.34
    residue:
      pdb=" N   GLN R  64 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NE2 GLN R  64 " occ=0.50
    residue:
      pdb=" N   TRP R 161 " occ=0.50
      ... (12 atoms not shown)
      pdb=" CH2 TRP R 161 " occ=0.50
    residue:
      pdb=" N   PHE R 313 " occ=0.50
      ... (9 atoms not shown)
      pdb=" CZ  PHE R 313 " occ=0.50
  Time building chain proxies: 7.25, per 1000 atoms: 0.70
  Number of scatterers: 10429
  At special positions: 0
  Unit cell: (90.47, 117.86, 156.04, 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      78     16.00
     O    1986      8.00
     N    1718      7.00
     C    6647      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  43 " - pdb=" SG  CYS L 113 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 159 " - pdb=" SG  CYS L 219 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  41 " - pdb=" SG  CYS H 115 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 167 " - pdb=" SG  CYS H 222 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R   2 " - pdb=" SG  CYS R 282 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 110 " - pdb=" SG  CYS R 187 " 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=1, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
    NAG-ASN
      " NAG C   1 " - " ASN R  15 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.94
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2474

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 17 sheets defined
      28.7% alpha, 22.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 25
      removed outlier: 3.734A  pdb=" N   ASN A  22 " --> pdb=" O   MET A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 215
      removed outlier: 4.038A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 254
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.510A  pdb=" N   PHE A 274 " --> pdb=" O   LYS A 270 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 296 through 308
    Processing helix  chain 'A' and resid 331 through 349
    Processing helix  chain 'B' and resid 30 through 34
    Processing helix  chain 'G' and resid 32 through 45
      removed outlier: 3.793A  pdb=" N   CYS G  36 " --> pdb=" O   LEU G  32 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'G' and resid 58 through 62
      removed outlier: 3.539A  pdb=" N   ASN G  62 " --> pdb=" O   GLU G  59 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 146 through 153
      removed outlier: 3.535A  pdb=" N   GLY L 153 " --> pdb=" O   GLN L 149 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 208 through 213
    Processing helix  chain 'H' and resid 72 through 75
      removed outlier: 4.437A  pdb=" N   GLY H  75 " --> pdb=" O   SER H  72 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 72 through 75'
    Processing helix  chain 'H' and resid 106 through 110
    Processing helix  chain 'H' and resid 213 through 218
      removed outlier: 3.864A  pdb=" N   SER H 217 " --> pdb=" O   SER H 213 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 33 through 65
      removed outlier: 3.543A  pdb=" N   PHE R  37 " --> pdb=" O   GLU R  33 " (cutoff:3.500A)
      Proline residue:  R  53  - end of helix
      removed outlier: 3.598A  pdb=" N   HIS R  65 " --> pdb=" O   VAL R  61 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 69
      removed outlier: 4.143A  pdb=" N   ARG R  69 " --> pdb=" O   LYS R  66 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 66 through 69'
    Processing helix  chain 'R' and resid 73 through 101
      removed outlier: 3.541A  pdb=" N   LEU R  77 " --> pdb=" O   ASN R  73 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   PHE R  91 " --> pdb=" O   VAL R  87 " (cutoff:3.500A)
      removed outlier: 4.914A  pdb=" N   THR R  92 " --> pdb=" O   PHE R  88 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   THR R  93 " --> pdb=" O   GLY R  89 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   THR R  94 " --> pdb=" O   GLY R  90 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 105 through 141
      removed outlier: 3.508A  pdb=" N   GLY R 109 " --> pdb=" O   PHE R 105 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 149 through 169
      removed outlier: 3.814A  pdb=" N   ALA R 153 " --> pdb=" O   GLY R 149 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   CYS R 167 " --> pdb=" O   MET R 163 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 170 through 173
    Processing helix  chain 'R' and resid 199 through 212
      removed outlier: 3.832A  pdb=" N   PHE R 203 " --> pdb=" O   ASN R 199 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 212 through 237
      removed outlier: 3.509A  pdb=" N   GLN R 237 " --> pdb=" O   ALA R 233 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 240 through 278
      removed outlier: 3.620A  pdb=" N   GLN R 244 " --> pdb=" O   SER R 240 " (cutoff:3.500A)
      Proline residue:  R 267  - end of helix
    Processing helix  chain 'R' and resid 284 through 306
      removed outlier: 3.923A  pdb=" N   ILE R 290 " --> pdb=" O   ILE R 286 " (cutoff:3.500A)
      Proline residue:  R 291  - end of helix
      Proline residue:  R 303  - end of helix
      removed outlier: 3.579A  pdb=" N   TYR R 306 " --> pdb=" O   ASN R 302 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 307 through 309
      No H-bonds generated for 'chain 'R' and resid 307 through 309'
    Processing helix  chain 'R' and resid 310 through 319
      removed outlier: 5.528A  pdb=" N   CYS R 316 " --> pdb=" O   GLN R 312 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   MET R 317 " --> pdb=" O   PHE R 313 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   VAL R 318 " --> pdb=" O   ARG R 314 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 38
      removed outlier: 6.513A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   PHE A 267 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.622A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.979A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105
      removed outlier: 4.085A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.952A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.871A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.817A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.714A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277
      removed outlier: 7.062A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 5.108A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 7.149A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 5.728A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 24 through 25
    Processing sheet with id=AB1, first strand: chain 'L' and resid 78 through 79
      removed outlier: 3.521A  pdb=" N   ASN L  78 " --> pdb=" O   TYR L  74 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLN L  70 " --> pdb=" O   LEU L  62 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   TRP L  60 " --> pdb=" O   LEU L  72 " (cutoff:3.500A)
      removed outlier: 4.749A  pdb=" N   TYR L  74 " --> pdb=" O   LEU L  58 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   LEU L  58 " --> pdb=" O   TYR L  74 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 139 through 143
    Processing sheet with id=AB3, first strand: chain 'L' and resid 178 through 179
    Processing sheet with id=AB4, first strand: chain 'H' and resid 22 through 26
      removed outlier: 5.604A  pdb=" N   GLY H  35 " --> pdb=" O   SER H 104 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   LEU H  98 " --> pdb=" O   CYS H  41 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 29 through 31
      removed outlier: 6.074A  pdb=" N   ARG H  57 " --> pdb=" O   TRP H  66 " (cutoff:3.500A)
      removed outlier: 5.529A  pdb=" N   TRP H  66 " --> pdb=" O   ARG H  57 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 147 through 151
      removed outlier: 6.457A  pdb=" N   TYR H 202 " --> pdb=" O   GLY H 171 " (cutoff:3.500A)
      removed outlier: 5.986A  pdb=" N   LEU H 201 " --> pdb=" O   LEU H 197 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   LEU H 197 " --> pdb=" O   LEU H 201 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   THR H 203 " --> pdb=" O   ALA H 195 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   ALA H 195 " --> pdb=" O   THR H 203 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'H' and resid 178 through 181
    Processing sheet with id=AB8, first strand: chain 'R' and resid 178 through 181
      removed outlier: 4.261A  pdb=" N   SER R 186 " --> pdb=" O   GLU R 181 " (cutoff:3.500A)

    438 hydrogen bonds defined for protein.
    1214 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: 3.12

  Time building geometry restraints manager: 3.15 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: 3215
        1.34 -     1.46: 2756
        1.46 -     1.59: 4591
        1.59 -     1.71: 5
        1.71 -     1.83: 113
  Bond restraints: 10680
  Sorted by residual:
  bond pdb=" C6  RET R 401 "
       pdb=" C7  RET R 401 "
    ideal  model  delta    sigma   weight residual
    1.459  1.657 -0.198 2.00e-02 2.50e+03 9.80e+01
  bond pdb=" C8  RET R 401 "
       pdb=" C9  RET R 401 "
    ideal  model  delta    sigma   weight residual
    1.450  1.593 -0.143 2.00e-02 2.50e+03 5.09e+01
  bond pdb=" C10 RET R 401 "
       pdb=" C11 RET R 401 "
    ideal  model  delta    sigma   weight residual
    1.433  1.548 -0.115 2.00e-02 2.50e+03 3.28e+01
  bond pdb=" C14 RET R 401 "
       pdb=" C15 RET R 401 "
    ideal  model  delta    sigma   weight residual
    1.448  1.536 -0.088 2.00e-02 2.50e+03 1.95e+01
  bond pdb=" C12 RET R 401 "
       pdb=" C13 RET R 401 "
    ideal  model  delta    sigma   weight residual
    1.446  1.534 -0.088 2.00e-02 2.50e+03 1.94e+01
  ... (remaining 10675 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.42: 13645
        2.42 -     4.84: 719
        4.84 -     7.27: 106
        7.27 -     9.69: 23
        9.69 -    12.11: 5
  Bond angle restraints: 14498
  Sorted by residual:
  angle pdb=" N   PRO R 170 "
        pdb=" CA  PRO R 170 "
        pdb=" C   PRO R 170 "
      ideal   model   delta    sigma   weight residual
     110.70  117.34   -6.64 1.22e+00 6.72e-01 2.96e+01
  angle pdb=" C   GLN A 204 "
        pdb=" N   ARG A 205 "
        pdb=" CA  ARG A 205 "
      ideal   model   delta    sigma   weight residual
     121.54  130.63   -9.09 1.91e+00 2.74e-01 2.26e+01
  angle pdb=" C   LYS R 311 "
        pdb=" N   GLN R 312 "
        pdb=" CA  GLN R 312 "
      ideal   model   delta    sigma   weight residual
     120.38  126.94   -6.56 1.46e+00 4.69e-01 2.02e+01
  angle pdb=" CA  GLU A  43 "
        pdb=" CB  GLU A  43 "
        pdb=" CG  GLU A  43 "
      ideal   model   delta    sigma   weight residual
     114.10  122.49   -8.39 2.00e+00 2.50e-01 1.76e+01
  angle pdb=" CA  TYR R 301 "
        pdb=" CB  TYR R 301 "
        pdb=" CG  TYR R 301 "
      ideal   model   delta    sigma   weight residual
     113.90  121.38   -7.48 1.80e+00 3.09e-01 1.73e+01
  ... (remaining 14493 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.88: 5828
       15.88 -    31.76: 406
       31.76 -    47.64: 73
       47.64 -    63.52: 12
       63.52 -    79.39: 8
  Dihedral angle restraints: 6327
    sinusoidal: 2470
      harmonic: 3857
  Sorted by residual:
  dihedral pdb=" CA  PHE H 173 "
           pdb=" C   PHE H 173 "
           pdb=" N   PRO H 174 "
           pdb=" CA  PRO H 174 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  125.94   54.06     0      5.00e+00 4.00e-02 1.17e+02
  dihedral pdb=" CA  TRP R 175 "
           pdb=" C   TRP R 175 "
           pdb=" N   SER R 176 "
           pdb=" CA  SER R 176 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -127.18  -52.82     0      5.00e+00 4.00e-02 1.12e+02
  dihedral pdb=" CA  PRO R 327 "
           pdb=" C   PRO R 327 "
           pdb=" N   LEU R 328 "
           pdb=" CA  LEU R 328 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  130.79   49.21     0      5.00e+00 4.00e-02 9.69e+01
  ... (remaining 6324 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 1206
       0.071 -    0.142: 357
       0.142 -    0.212: 53
       0.212 -    0.283: 4
       0.283 -    0.354: 4
  Chirality restraints: 1624
  Sorted by residual:
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN R  15 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.05   -0.35 2.00e-01 2.50e+01 3.13e+00
  chirality pdb=" CB  ILE H 119 "
            pdb=" CA  ILE H 119 "
            pdb=" CG1 ILE H 119 "
            pdb=" CG2 ILE H 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.30    0.34 2.00e-01 2.50e+01 2.91e+00
  chirality pdb=" CG  LEU H 237 "
            pdb=" CB  LEU H 237 "
            pdb=" CD1 LEU H 237 "
            pdb=" CD2 LEU H 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.29   -0.30 2.00e-01 2.50e+01 2.31e+00
  ... (remaining 1621 not shown)

  Planarity restraints: 1842
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 297 "    0.041 2.00e-02 2.50e+03   2.60e-02 1.69e+01
        pdb=" CG  TRP B 297 "   -0.066 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 297 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 297 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 297 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 297 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 297 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 297 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 297 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 297 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H 130 "    0.008 2.00e-02 2.50e+03   1.97e-02 9.67e+00
        pdb=" CG  TRP H 130 "   -0.044 2.00e-02 2.50e+03
        pdb=" CD1 TRP H 130 "    0.040 2.00e-02 2.50e+03
        pdb=" CD2 TRP H 130 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP H 130 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE2 TRP H 130 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP H 130 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H 130 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H 130 "    0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP H 130 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 163 "   -0.015 2.00e-02 2.50e+03   2.95e-02 8.69e+00
        pdb=" C   ASP B 163 "    0.051 2.00e-02 2.50e+03
        pdb=" O   ASP B 163 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   THR B 164 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1839 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1916
        2.76 -     3.30: 10033
        3.30 -     3.83: 17865
        3.83 -     4.37: 19716
        4.37 -     4.90: 32970
  Nonbonded interactions: 82500
  Sorted by model distance:
  nonbonded pdb=" O   PHE R 273 "
            pdb=" OG1 THR R 277 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" O   ALA B  56 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OG1 THR B 173 "
            pdb=" OE1 GLN B 175 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" OG  SER L  90 "
            pdb=" O   THR L  97 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" O   VAL R 157 "
            pdb=" OG1 THR R 160 "
     model   vdw
     2.251 3.040
  ... (remaining 82495 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.34 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     27.450
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
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      :  0.010   0.198  10689  Z= 0.474
  Angle     :  1.252  12.112  14516  Z= 0.684
  Chirality :  0.066   0.354   1624
  Planarity :  0.008   0.069   1841
  Dihedral  : 11.761  79.395   3835
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.63 %
    Favored  : 88.37 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  :  3.83 %
    Favored  : 94.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.16 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.96 (0.19), residues: 1318
  helix: -2.37 (0.21), residues: 341
  sheet: -1.91 (0.26), residues: 322
  loop : -3.18 (0.21), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.066   0.006   TRP B 297 
 HIS   0.027   0.005   HIS H  54 
 PHE   0.042   0.005   PHE A 215 
 TYR   0.041   0.004   TYR R 257 
 ARG   0.010   0.002   ARG H  57 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00876 (    1)
  link_NAG-ASN         : angle       5.43787 (    3)
  link_BETA1-4         : bond        0.00613 (    1)
  link_BETA1-4         : angle       3.69685 (    3)
  hydrogen bonds       : bond        0.11947 (  438)
  hydrogen bonds       : angle       8.05162 ( 1214)
  SS BOND              : bond        0.00957 (    6)
  SS BOND              : angle       1.98476 (   12)
  covalent geometry    : bond        0.01016 (10680)
  covalent geometry    : angle       1.24755 (14498)
  Misc. bond           : bond        0.00152 (    1)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 208
  time to evaluate  : 1.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.8725 (m-40) cc_final: 0.7306 (t0)
REVERT: A  304 GLN cc_start: 0.7462 (tt0) cc_final: 0.7188 (tm-30)
REVERT: B   76 ASP cc_start: 0.8235 (p0) cc_final: 0.7855 (t0)
REVERT: B  187 VAL cc_start: 0.7742 (t) cc_final: 0.7526 (t)
REVERT: B  313 ASN cc_start: 0.8473 (t0) cc_final: 0.8100 (t0)
REVERT: G   36 CYS cc_start: 0.8316 (m) cc_final: 0.7326 (m)
REVERT: G   39 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8751 (mt-10)
REVERT: L   34 THR cc_start: 0.8661 (m) cc_final: 0.8190 (p)
REVERT: L   37 GLU cc_start: 0.8563 (mt-10) cc_final: 0.7986 (mt-10)
REVERT: H  172 TYR cc_start: 0.7838 (p90) cc_final: 0.7177 (p90)
REVERT: R   39 MET cc_start: 0.7449 (mmp) cc_final: 0.7203 (mmm)
REVERT: R   69 ARG cc_start: 0.8210 (mtm-85) cc_final: 0.7608 (ptp-170)
REVERT: R  207 MET cc_start: 0.9121 (mmm) cc_final: 0.8705 (tpp)
REVERT: R  253 MET cc_start: 0.9315 (mmm) cc_final: 0.8899 (mmm)
REVERT: R  308 MET cc_start: 0.8799 (mtp) cc_final: 0.8479 (mtp)
  outliers start: 16
  outliers final: 6
  residues processed: 222
  average time/residue: 0.2766
  time to fit residues: 81.9572
Evaluate side-chains
  119 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 113
  time to evaluate  : 1.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 110 optimal weight:    0.8980
   chunk 99 optimal weight:    0.6980
   chunk 55 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 66 optimal weight:    7.9990
   chunk 53 optimal weight:    0.4980
   chunk 102 optimal weight:    7.9990
   chunk 39 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 76 optimal weight:    0.8980
   chunk 118 optimal weight:    2.9990
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
A 204 GLN
B  62 HIS
B  91 HIS
B 176 GLN
B 295 ASN
** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 163 ASN
L 235 ASN
H 101 GLN
H 191 HIS
R  73 ASN
R 100 HIS
** R 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 302 ASN
R 312 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.079750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.062946 restraints weight = 115684.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.064852 restraints weight = 58819.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.065339 restraints weight = 41626.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3391
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3391 r_free = 0.3391    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3385 r_free = 0.3385    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3385
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.2342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  10689  Z= 0.156
  Angle     :  0.767   8.397  14516  Z= 0.406
  Chirality :  0.046   0.232   1624
  Planarity :  0.006   0.075   1841
  Dihedral  :  7.855  68.567   1488
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  3.91 %
    Favored  : 95.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.85 %
    Twisted General : 0.16 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.82 (0.21), residues: 1318
  helix: -0.74 (0.26), residues: 329
  sheet: -1.54 (0.27), residues: 321
  loop : -2.68 (0.22), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B  82 
 HIS   0.007   0.002   HIS R  65 
 PHE   0.016   0.002   PHE A 215 
 TYR   0.030   0.002   TYR R 301 
 ARG   0.006   0.001   ARG B 134 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00467 (    1)
  link_NAG-ASN         : angle       4.42020 (    3)
  link_BETA1-4         : bond        0.00117 (    1)
  link_BETA1-4         : angle       2.68387 (    3)
  hydrogen bonds       : bond        0.04965 (  438)
  hydrogen bonds       : angle       6.42991 ( 1214)
  SS BOND              : bond        0.00676 (    6)
  SS BOND              : angle       1.24953 (   12)
  covalent geometry    : bond        0.00335 (10680)
  covalent geometry    : angle       0.76291 (14498)
  Misc. bond           : bond        0.00002 (    1)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 186
  time to evaluate  : 1.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.8800 (m-40) cc_final: 0.7649 (t0)
REVERT: A   24 ARG cc_start: 0.8479 (ppt170) cc_final: 0.8225 (ttp80)
REVERT: A  304 GLN cc_start: 0.7427 (tt0) cc_final: 0.7117 (tm-30)
REVERT: A  305 CYS cc_start: 0.7922 (m) cc_final: 0.7504 (t)
REVERT: B   58 ILE cc_start: 0.8944 (mt) cc_final: 0.8289 (pt)
REVERT: B   76 ASP cc_start: 0.8368 (p0) cc_final: 0.8081 (t0)
REVERT: B   91 HIS cc_start: 0.7168 (m90) cc_final: 0.6801 (m170)
REVERT: B  111 TYR cc_start: 0.8196 (m-10) cc_final: 0.7565 (m-10)
REVERT: B  160 SER cc_start: 0.8715 (p) cc_final: 0.8200 (p)
REVERT: B  187 VAL cc_start: 0.7476 (t) cc_final: 0.7201 (t)
REVERT: B  217 MET cc_start: 0.7156 (mpp) cc_final: 0.6877 (mpp)
REVERT: B  313 ASN cc_start: 0.8530 (t0) cc_final: 0.8187 (t0)
REVERT: G   36 CYS cc_start: 0.8343 (m) cc_final: 0.6785 (m)
REVERT: G   39 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8767 (mt-10)
REVERT: L   34 THR cc_start: 0.8804 (m) cc_final: 0.8349 (p)
REVERT: L   37 GLU cc_start: 0.8601 (mt-10) cc_final: 0.7919 (mt-10)
REVERT: L  172 LYS cc_start: 0.8737 (mtmt) cc_final: 0.8287 (mtmm)
REVERT: L  190 ASP cc_start: 0.8248 (p0) cc_final: 0.8004 (p0)
REVERT: H   22 GLN cc_start: 0.7762 (mp10) cc_final: 0.7483 (mp10)
REVERT: H  129 PHE cc_start: 0.8657 (t80) cc_final: 0.8345 (t80)
REVERT: H  172 TYR cc_start: 0.8027 (p90) cc_final: 0.7334 (p90)
REVERT: R   69 ARG cc_start: 0.8091 (mtm-85) cc_final: 0.7262 (mpt-90)
REVERT: R  183 MET cc_start: 0.8782 (mtm) cc_final: 0.8420 (mmm)
REVERT: R  207 MET cc_start: 0.8929 (mmm) cc_final: 0.8563 (tpp)
REVERT: R  253 MET cc_start: 0.9435 (mmm) cc_final: 0.9000 (mmt)
REVERT: R  302 ASN cc_start: 0.8810 (m110) cc_final: 0.8203 (m110)
REVERT: R  305 ILE cc_start: 0.9324 (pt) cc_final: 0.9000 (tt)
  outliers start: 3
  outliers final: 0
  residues processed: 188
  average time/residue: 0.2632
  time to fit residues: 67.4369
Evaluate side-chains
  127 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 1.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 61 optimal weight:    4.9990
   chunk 127 optimal weight:    0.0270
   chunk 25 optimal weight:    2.9990
   chunk 66 optimal weight:   10.0000
   chunk 72 optimal weight:    5.9990
   chunk 96 optimal weight:   10.0000
   chunk 130 optimal weight:    9.9990
   chunk 111 optimal weight:    0.9990
   chunk 59 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   overall best weight:    2.4046

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

Flipped N/Q/H residues before XYZ refinement:
B 119 ASN
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 115 GLN
L 116 HIS
L 149 GLN
** R 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.078143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.062229 restraints weight = 94134.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.063323 restraints weight = 46039.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.063982 restraints weight = 32600.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3363
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3363 r_free = 0.3363    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3363 r_free = 0.3363    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3363
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.2982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079  10689  Z= 0.193
  Angle     :  0.745   9.129  14516  Z= 0.395
  Chirality :  0.046   0.218   1624
  Planarity :  0.005   0.048   1841
  Dihedral  :  7.383  67.730   1488
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 15.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.73 %
    Favored  : 90.27 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  3.48 %
    Favored  : 96.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.85 %
    Twisted General : 0.16 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.54 (0.22), residues: 1318
  helix: -0.66 (0.26), residues: 347
  sheet: -1.20 (0.28), residues: 306
  loop : -2.53 (0.23), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 297 
 HIS   0.009   0.002   HIS B  54 
 PHE   0.037   0.002   PHE R  85 
 TYR   0.018   0.002   TYR A 287 
 ARG   0.007   0.001   ARG B 134 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00606 (    1)
  link_NAG-ASN         : angle       4.09287 (    3)
  link_BETA1-4         : bond        0.00689 (    1)
  link_BETA1-4         : angle       2.04125 (    3)
  hydrogen bonds       : bond        0.04867 (  438)
  hydrogen bonds       : angle       6.17824 ( 1214)
  SS BOND              : bond        0.00728 (    6)
  SS BOND              : angle       1.40696 (   12)
  covalent geometry    : bond        0.00415 (10680)
  covalent geometry    : angle       0.74165 (14498)
  Misc. bond           : bond        0.00166 (    1)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 164
  time to evaluate  : 1.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ARG cc_start: 0.8618 (ppt170) cc_final: 0.8212 (ttp80)
REVERT: A   53 MET cc_start: 0.5052 (ttp) cc_final: 0.4837 (ttp)
REVERT: A  188 HIS cc_start: 0.8329 (m-70) cc_final: 0.8118 (m-70)
REVERT: A  305 CYS cc_start: 0.7729 (m) cc_final: 0.7272 (t)
REVERT: B   58 ILE cc_start: 0.8994 (mt) cc_final: 0.8526 (pt)
REVERT: B   91 HIS cc_start: 0.7012 (m90) cc_final: 0.6782 (m170)
REVERT: B  111 TYR cc_start: 0.8083 (m-10) cc_final: 0.7634 (m-10)
REVERT: B  262 MET cc_start: 0.7972 (mmm) cc_final: 0.7652 (mmm)
REVERT: B  313 ASN cc_start: 0.8628 (t0) cc_final: 0.8412 (t0)
REVERT: B  325 MET cc_start: 0.7747 (tmm) cc_final: 0.6922 (tmm)
REVERT: G   36 CYS cc_start: 0.8111 (m) cc_final: 0.7358 (m)
REVERT: L   34 THR cc_start: 0.8961 (m) cc_final: 0.8496 (p)
REVERT: L   37 GLU cc_start: 0.8541 (mt-10) cc_final: 0.7810 (mt-10)
REVERT: L  114 MET cc_start: 0.7446 (ttm) cc_final: 0.6927 (ttm)
REVERT: L  190 ASP cc_start: 0.8181 (p0) cc_final: 0.7979 (p0)
REVERT: H  172 TYR cc_start: 0.7923 (p90) cc_final: 0.7183 (p90)
REVERT: R   69 ARG cc_start: 0.8068 (mtm-85) cc_final: 0.7451 (mtt90)
REVERT: R  183 MET cc_start: 0.8819 (mtm) cc_final: 0.8457 (mmm)
REVERT: R  253 MET cc_start: 0.9388 (mmm) cc_final: 0.8895 (mmt)
REVERT: R  305 ILE cc_start: 0.9341 (pt) cc_final: 0.9061 (tt)
  outliers start: 3
  outliers final: 1
  residues processed: 166
  average time/residue: 0.2417
  time to fit residues: 55.7156
Evaluate side-chains
  122 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 121
  time to evaluate  : 1.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 15 optimal weight:    9.9990
   chunk 82 optimal weight:    7.9990
   chunk 112 optimal weight:    0.9980
   chunk 93 optimal weight:    4.9990
   chunk 42 optimal weight:    5.9990
   chunk 79 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 78 optimal weight:    0.7980
   chunk 120 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   chunk 101 optimal weight:    4.9990
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 311 HIS
L 115 GLN
H 191 HIS
** R 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.080600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.063742 restraints weight = 125591.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.066658 restraints weight = 59459.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.066583 restraints weight = 37766.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3432
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3432 r_free = 0.3432    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3432 r_free = 0.3432    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3432
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.3521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  10689  Z= 0.136
  Angle     :  0.689   8.690  14516  Z= 0.359
  Chirality :  0.045   0.228   1624
  Planarity :  0.005   0.057   1841
  Dihedral  :  6.872  69.988   1488
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  2.61 %
    Favored  : 97.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.85 %
    Twisted General : 0.16 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.18 (0.22), residues: 1318
  helix: -0.19 (0.27), residues: 338
  sheet: -1.17 (0.29), residues: 292
  loop : -2.26 (0.23), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP R 126 
 HIS   0.006   0.001   HIS R 211 
 PHE   0.025   0.002   PHE A 215 
 TYR   0.016   0.002   TYR A 287 
 ARG   0.006   0.000   ARG A 242 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00315 (    1)
  link_NAG-ASN         : angle       3.86981 (    3)
  link_BETA1-4         : bond        0.00359 (    1)
  link_BETA1-4         : angle       1.81351 (    3)
  hydrogen bonds       : bond        0.04182 (  438)
  hydrogen bonds       : angle       5.88410 ( 1214)
  SS BOND              : bond        0.00522 (    6)
  SS BOND              : angle       1.13920 (   12)
  covalent geometry    : bond        0.00292 (10680)
  covalent geometry    : angle       0.68623 (14498)
  Misc. bond           : bond        0.00311 (    1)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 170
  time to evaluate  : 1.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.8801 (m-40) cc_final: 0.7373 (t0)
REVERT: A   24 ARG cc_start: 0.8488 (ppt170) cc_final: 0.8101 (ttp80)
REVERT: A   53 MET cc_start: 0.5180 (ttp) cc_final: 0.4920 (ttp)
REVERT: A  242 ARG cc_start: 0.5712 (mtt-85) cc_final: 0.4663 (mmp80)
REVERT: A  345 LYS cc_start: 0.8253 (ptmm) cc_final: 0.8018 (pttp)
REVERT: B   58 ILE cc_start: 0.8875 (mt) cc_final: 0.8378 (pt)
REVERT: B   91 HIS cc_start: 0.6985 (m90) cc_final: 0.6714 (m170)
REVERT: B  111 TYR cc_start: 0.8096 (m-10) cc_final: 0.7550 (m-10)
REVERT: B  253 PHE cc_start: 0.6745 (m-80) cc_final: 0.6439 (m-80)
REVERT: B  313 ASN cc_start: 0.8495 (t0) cc_final: 0.8178 (t0)
REVERT: B  325 MET cc_start: 0.8268 (tmm) cc_final: 0.7338 (tmm)
REVERT: G   31 MET cc_start: 0.7322 (ppp) cc_final: 0.6898 (tpp)
REVERT: G   36 CYS cc_start: 0.8114 (m) cc_final: 0.7413 (m)
REVERT: L  115 GLN cc_start: 0.7122 (OUTLIER) cc_final: 0.6730 (pp30)
REVERT: L  190 ASP cc_start: 0.8143 (p0) cc_final: 0.7902 (p0)
REVERT: H  129 PHE cc_start: 0.8824 (t80) cc_final: 0.8546 (t80)
REVERT: H  172 TYR cc_start: 0.7778 (p90) cc_final: 0.7067 (p90)
REVERT: H  198 GLN cc_start: 0.8936 (tp40) cc_final: 0.8531 (tp40)
REVERT: R   69 ARG cc_start: 0.8133 (mtm-85) cc_final: 0.7387 (mtt90)
REVERT: R  183 MET cc_start: 0.8782 (mtm) cc_final: 0.8514 (mmm)
REVERT: R  189 ILE cc_start: 0.8702 (pt) cc_final: 0.8395 (mp)
REVERT: R  207 MET cc_start: 0.8646 (tpp) cc_final: 0.8388 (tpp)
REVERT: R  253 MET cc_start: 0.9291 (mmm) cc_final: 0.8853 (mmt)
REVERT: R  305 ILE cc_start: 0.9281 (pt) cc_final: 0.8998 (tt)
  outliers start: 1
  outliers final: 0
  residues processed: 171
  average time/residue: 0.2584
  time to fit residues: 60.8527
Evaluate side-chains
  125 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 124
  time to evaluate  : 1.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 107 optimal weight:    4.9990
   chunk 112 optimal weight:    4.9990
   chunk 130 optimal weight:    3.9990
   chunk 71 optimal weight:    5.9990
   chunk 116 optimal weight:    9.9990
   chunk 111 optimal weight:    0.7980
   chunk 46 optimal weight:    4.9990
   chunk 74 optimal weight:    6.9990
   chunk 8 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.079153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.062997 restraints weight = 110663.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.064572 restraints weight = 54059.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.065258 restraints weight = 39102.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3395
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3395 r_free = 0.3395    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3396 r_free = 0.3396    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3396
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.3731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  10689  Z= 0.173
  Angle     :  0.691   9.807  14516  Z= 0.361
  Chirality :  0.045   0.207   1624
  Planarity :  0.005   0.049   1841
  Dihedral  :  6.851  69.076   1488
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 15.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.65 %
    Favored  : 90.35 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  2.09 %
    Favored  : 97.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.85 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.12 (0.22), residues: 1318
  helix: -0.09 (0.27), residues: 338
  sheet: -1.14 (0.28), residues: 309
  loop : -2.28 (0.23), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP R 175 
 HIS   0.007   0.002   HIS R  65 
 PHE   0.029   0.002   PHE L 123 
 TYR   0.014   0.002   TYR A 287 
 ARG   0.005   0.001   ARG L  44 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00322 (    1)
  link_NAG-ASN         : angle       3.82539 (    3)
  link_BETA1-4         : bond        0.00422 (    1)
  link_BETA1-4         : angle       2.03057 (    3)
  hydrogen bonds       : bond        0.04278 (  438)
  hydrogen bonds       : angle       5.84653 ( 1214)
  SS BOND              : bond        0.00599 (    6)
  SS BOND              : angle       1.74271 (   12)
  covalent geometry    : bond        0.00378 (10680)
  covalent geometry    : angle       0.68677 (14498)
  Misc. bond           : bond        0.00214 (    1)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 1.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.8821 (m-40) cc_final: 0.7359 (t0)
REVERT: A   24 ARG cc_start: 0.8687 (ppt170) cc_final: 0.8307 (ttp80)
REVERT: A   53 MET cc_start: 0.5315 (ttp) cc_final: 0.5034 (ttp)
REVERT: A  198 MET cc_start: 0.8227 (mtp) cc_final: 0.7958 (mtm)
REVERT: A  304 GLN cc_start: 0.6770 (tm-30) cc_final: 0.6519 (tm-30)
REVERT: A  345 LYS cc_start: 0.8247 (ptmm) cc_final: 0.8003 (pttp)
REVERT: B  111 TYR cc_start: 0.8200 (m-10) cc_final: 0.7558 (m-10)
REVERT: B  313 ASN cc_start: 0.8617 (t0) cc_final: 0.8180 (t0)
REVERT: B  325 MET cc_start: 0.8227 (tmm) cc_final: 0.7350 (tmm)
REVERT: G   31 MET cc_start: 0.7337 (ppp) cc_final: 0.7108 (tmm)
REVERT: G   35 LYS cc_start: 0.8250 (tptt) cc_final: 0.7932 (ptmt)
REVERT: G   41 ARG cc_start: 0.8792 (mtt90) cc_final: 0.8044 (mtt90)
REVERT: L   37 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8450 (pt0)
REVERT: L  190 ASP cc_start: 0.8181 (p0) cc_final: 0.7964 (p0)
REVERT: H  172 TYR cc_start: 0.7945 (p90) cc_final: 0.7191 (p90)
REVERT: R   69 ARG cc_start: 0.8121 (mtm-85) cc_final: 0.7373 (mtt90)
REVERT: R  183 MET cc_start: 0.8887 (mtm) cc_final: 0.8587 (mmm)
REVERT: R  189 ILE cc_start: 0.8708 (pt) cc_final: 0.8358 (mp)
REVERT: R  207 MET cc_start: 0.8941 (tpp) cc_final: 0.8669 (tpp)
REVERT: R  253 MET cc_start: 0.9353 (mmm) cc_final: 0.8906 (mmt)
REVERT: R  296 LYS cc_start: 0.8656 (mmpt) cc_final: 0.8388 (mtmm)
REVERT: R  305 ILE cc_start: 0.9347 (pt) cc_final: 0.9033 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.2567
  time to fit residues: 55.2495
Evaluate side-chains
  115 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 1.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 120 optimal weight:    3.9990
   chunk 56 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 83 optimal weight:    6.9990
   chunk 94 optimal weight:    9.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 191 HIS
** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.079269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.064071 restraints weight = 76119.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.065199 restraints weight = 42664.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.065724 restraints weight = 33749.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3418
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3418 r_free = 0.3418    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3418 r_free = 0.3418    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3418
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.3950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  10689  Z= 0.162
  Angle     :  0.680  10.206  14516  Z= 0.358
  Chirality :  0.045   0.241   1624
  Planarity :  0.005   0.054   1841
  Dihedral  :  6.673  68.942   1488
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 13.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.74 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  1.22 %
    Favored  : 98.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.85 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.04 (0.22), residues: 1318
  helix: -0.01 (0.27), residues: 336
  sheet: -1.11 (0.28), residues: 323
  loop : -2.23 (0.23), residues: 659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP R 175 
 HIS   0.006   0.002   HIS R  65 
 PHE   0.036   0.002   PHE R 159 
 TYR   0.013   0.002   TYR R 178 
 ARG   0.005   0.001   ARG A 205 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00345 (    1)
  link_NAG-ASN         : angle       3.70205 (    3)
  link_BETA1-4         : bond        0.00311 (    1)
  link_BETA1-4         : angle       1.85060 (    3)
  hydrogen bonds       : bond        0.04231 (  438)
  hydrogen bonds       : angle       5.78476 ( 1214)
  SS BOND              : bond        0.00578 (    6)
  SS BOND              : angle       1.56632 (   12)
  covalent geometry    : bond        0.00355 (10680)
  covalent geometry    : angle       0.67640 (14498)
  Misc. bond           : bond        0.00047 (    1)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 1.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.8789 (m-40) cc_final: 0.7343 (t0)
REVERT: A   24 ARG cc_start: 0.8738 (ppt170) cc_final: 0.8320 (ttp80)
REVERT: A  188 HIS cc_start: 0.8483 (m-70) cc_final: 0.8110 (m-70)
REVERT: A  242 ARG cc_start: 0.5942 (mtt-85) cc_final: 0.4741 (mmp-170)
REVERT: A  304 GLN cc_start: 0.6887 (tm-30) cc_final: 0.6539 (tm-30)
REVERT: A  345 LYS cc_start: 0.8280 (ptmm) cc_final: 0.8024 (pttp)
REVERT: B  111 TYR cc_start: 0.8118 (m-10) cc_final: 0.7464 (m-10)
REVERT: B  313 ASN cc_start: 0.8657 (t0) cc_final: 0.8275 (t0)
REVERT: B  325 MET cc_start: 0.8300 (tmm) cc_final: 0.7321 (tmm)
REVERT: G   31 MET cc_start: 0.7431 (ppp) cc_final: 0.7151 (tmm)
REVERT: G   35 LYS cc_start: 0.8210 (tptt) cc_final: 0.7829 (ptmt)
REVERT: L  123 PHE cc_start: 0.6884 (m-80) cc_final: 0.6652 (m-80)
REVERT: L  190 ASP cc_start: 0.8281 (p0) cc_final: 0.8031 (p0)
REVERT: H  172 TYR cc_start: 0.7820 (p90) cc_final: 0.7101 (p90)
REVERT: R   69 ARG cc_start: 0.8107 (mtm-85) cc_final: 0.7452 (mtt90)
REVERT: R  155 MET cc_start: 0.9335 (ppp) cc_final: 0.9106 (ppp)
REVERT: R  183 MET cc_start: 0.8755 (mtm) cc_final: 0.8507 (mmm)
REVERT: R  189 ILE cc_start: 0.8788 (pt) cc_final: 0.8456 (mp)
REVERT: R  253 MET cc_start: 0.9319 (mmm) cc_final: 0.8863 (mmt)
REVERT: R  305 ILE cc_start: 0.9357 (pt) cc_final: 0.9044 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.2541
  time to fit residues: 53.7275
Evaluate side-chains
  116 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 1.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 64 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 107 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 129 optimal weight:    0.9980
   chunk 125 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 128 optimal weight:    1.9990
   chunk 75 optimal weight:    7.9990
   chunk 9 optimal weight:    8.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
B 239 ASN
** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.078277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.063533 restraints weight = 68420.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.063526 restraints weight = 44420.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.064187 restraints weight = 33906.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3372
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3372 r_free = 0.3372    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3372 r_free = 0.3372    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3372
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.4097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076  10689  Z= 0.193
  Angle     :  0.708   8.458  14516  Z= 0.371
  Chirality :  0.045   0.236   1624
  Planarity :  0.005   0.050   1841
  Dihedral  :  6.759  67.269   1488
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 15.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.42 %
    Favored  : 90.58 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  2.00 %
    Favored  : 97.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.85 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.02 (0.22), residues: 1318
  helix: -0.10 (0.27), residues: 339
  sheet: -1.01 (0.28), residues: 321
  loop : -2.22 (0.23), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B  82 
 HIS   0.008   0.001   HIS R  65 
 PHE   0.030   0.002   PHE R 159 
 TYR   0.015   0.002   TYR R 301 
 ARG   0.006   0.001   ARG B 134 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00379 (    1)
  link_NAG-ASN         : angle       3.65731 (    3)
  link_BETA1-4         : bond        0.00367 (    1)
  link_BETA1-4         : angle       1.97632 (    3)
  hydrogen bonds       : bond        0.04350 (  438)
  hydrogen bonds       : angle       5.87227 ( 1214)
  SS BOND              : bond        0.00553 (    6)
  SS BOND              : angle       1.34613 (   12)
  covalent geometry    : bond        0.00421 (10680)
  covalent geometry    : angle       0.70519 (14498)
  Misc. bond           : bond        0.00103 (    1)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 1.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ARG cc_start: 0.8755 (ppt170) cc_final: 0.8201 (ttp80)
REVERT: A  188 HIS cc_start: 0.8428 (m-70) cc_final: 0.7980 (m-70)
REVERT: A  242 ARG cc_start: 0.6063 (mtt-85) cc_final: 0.4831 (mmp-170)
REVERT: A  345 LYS cc_start: 0.8272 (ptmm) cc_final: 0.7981 (pttp)
REVERT: B   91 HIS cc_start: 0.7131 (m170) cc_final: 0.6751 (m-70)
REVERT: B  111 TYR cc_start: 0.7785 (m-10) cc_final: 0.7438 (m-10)
REVERT: B  313 ASN cc_start: 0.8663 (t0) cc_final: 0.8349 (t0)
REVERT: B  325 MET cc_start: 0.8077 (tmm) cc_final: 0.7266 (tmm)
REVERT: H  172 TYR cc_start: 0.7784 (p90) cc_final: 0.7120 (p90)
REVERT: R   69 ARG cc_start: 0.8129 (mtm-85) cc_final: 0.7498 (mtt90)
REVERT: R  155 MET cc_start: 0.9314 (ppp) cc_final: 0.9073 (ppp)
REVERT: R  207 MET cc_start: 0.8469 (tpt) cc_final: 0.8081 (tpp)
REVERT: R  211 HIS cc_start: 0.8209 (m-70) cc_final: 0.7995 (m90)
REVERT: R  253 MET cc_start: 0.9254 (mmm) cc_final: 0.8755 (mmt)
REVERT: R  305 ILE cc_start: 0.9349 (pt) cc_final: 0.9068 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.2505
  time to fit residues: 48.0270
Evaluate side-chains
  110 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 49 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 6 optimal weight:    6.9990
   chunk 24 optimal weight:    3.9990
   chunk 52 optimal weight:    0.7980
   chunk 124 optimal weight:    0.9990
   chunk 18 optimal weight:    9.9990
   chunk 9 optimal weight:    6.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** R 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.080735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.065237 restraints weight = 91574.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.067691 restraints weight = 54089.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.067340 restraints weight = 41888.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3454
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3454 r_free = 0.3454    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3454 r_free = 0.3454    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3454
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.4376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10689  Z= 0.128
  Angle     :  0.691  14.735  14516  Z= 0.353
  Chirality :  0.045   0.366   1624
  Planarity :  0.005   0.058   1841
  Dihedral  :  6.486  71.400   1488
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  0.78 %
    Favored  : 98.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.85 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.77 (0.23), residues: 1318
  helix:  0.26 (0.28), residues: 335
  sheet: -1.02 (0.29), residues: 312
  loop : -2.03 (0.23), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP R 175 
 HIS   0.006   0.001   HIS R  65 
 PHE   0.025   0.001   PHE R 159 
 TYR   0.013   0.001   TYR R 178 
 ARG   0.005   0.000   ARG B 134 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00360 (    1)
  link_NAG-ASN         : angle       3.45696 (    3)
  link_BETA1-4         : bond        0.00057 (    1)
  link_BETA1-4         : angle       1.65844 (    3)
  hydrogen bonds       : bond        0.04025 (  438)
  hydrogen bonds       : angle       5.73836 ( 1214)
  SS BOND              : bond        0.00385 (    6)
  SS BOND              : angle       1.12448 (   12)
  covalent geometry    : bond        0.00275 (10680)
  covalent geometry    : angle       0.68810 (14498)
  Misc. bond           : bond        0.00700 (    1)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 1.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ARG cc_start: 0.8748 (ppt170) cc_final: 0.8190 (ttp80)
REVERT: A  188 HIS cc_start: 0.8453 (m-70) cc_final: 0.7972 (m-70)
REVERT: A  242 ARG cc_start: 0.6014 (mtt-85) cc_final: 0.4843 (mmp-170)
REVERT: A  345 LYS cc_start: 0.8204 (ptmm) cc_final: 0.7900 (pttp)
REVERT: B  111 TYR cc_start: 0.7970 (m-10) cc_final: 0.7393 (m-10)
REVERT: B  313 ASN cc_start: 0.8435 (t0) cc_final: 0.8096 (t0)
REVERT: B  325 MET cc_start: 0.8133 (tmm) cc_final: 0.7310 (tmm)
REVERT: G   35 LYS cc_start: 0.7275 (ptmt) cc_final: 0.6828 (ptmt)
REVERT: H  172 TYR cc_start: 0.7808 (p90) cc_final: 0.7153 (p90)
REVERT: H  196 LEU cc_start: 0.8559 (tp) cc_final: 0.8330 (tt)
REVERT: H  198 GLN cc_start: 0.8914 (tp40) cc_final: 0.8502 (tp40)
REVERT: R   69 ARG cc_start: 0.8113 (mtm-85) cc_final: 0.7209 (mpt-90)
REVERT: R  155 MET cc_start: 0.9352 (ppp) cc_final: 0.9104 (ppp)
REVERT: R  253 MET cc_start: 0.9254 (mmm) cc_final: 0.8787 (mmt)
REVERT: R  294 PHE cc_start: 0.8796 (m-80) cc_final: 0.8494 (m-80)
REVERT: R  305 ILE cc_start: 0.9333 (pt) cc_final: 0.9036 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.2718
  time to fit residues: 59.0952
Evaluate side-chains
  117 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 1.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 14 optimal weight:    0.0470
   chunk 33 optimal weight:    4.9990
   chunk 120 optimal weight:    0.9980
   chunk 15 optimal weight:    9.9990
   chunk 75 optimal weight:    0.2980
   chunk 7 optimal weight:    5.9990
   chunk 105 optimal weight:    5.9990
   chunk 69 optimal weight:    0.6980
   chunk 94 optimal weight:    8.9990
   chunk 8 optimal weight:    0.0980
   chunk 102 optimal weight:    5.9990
   overall best weight:    0.4278

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

Flipped N/Q/H residues before XYZ refinement:
B  91 HIS
L  26 GLN
** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.080962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.064461 restraints weight = 93786.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.065530 restraints weight = 44118.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.066015 restraints weight = 33402.496|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3436
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3436 r_free = 0.3436    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3436 r_free = 0.3436    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3436
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.4588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  10689  Z= 0.118
  Angle     :  0.672   9.458  14516  Z= 0.347
  Chirality :  0.044   0.188   1624
  Planarity :  0.005   0.053   1841
  Dihedral  :  6.439  74.604   1488
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  0.52 %
    Favored  : 99.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.85 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (0.22), residues: 1318
  helix:  0.33 (0.27), residues: 334
  sheet: -0.83 (0.29), residues: 308
  loop : -2.02 (0.23), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP R 175 
 HIS   0.005   0.001   HIS R  65 
 PHE   0.030   0.001   PHE R 159 
 TYR   0.015   0.001   TYR B  59 
 ARG   0.010   0.001   ARG A  32 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00272 (    1)
  link_NAG-ASN         : angle       3.36560 (    3)
  link_BETA1-4         : bond        0.00387 (    1)
  link_BETA1-4         : angle       1.73864 (    3)
  hydrogen bonds       : bond        0.03825 (  438)
  hydrogen bonds       : angle       5.59753 ( 1214)
  SS BOND              : bond        0.00438 (    6)
  SS BOND              : angle       1.06345 (   12)
  covalent geometry    : bond        0.00248 (10680)
  covalent geometry    : angle       0.66956 (14498)
  Misc. bond           : bond        0.00022 (    1)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 1.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.8723 (m-40) cc_final: 0.7368 (t0)
REVERT: A   24 ARG cc_start: 0.8719 (ppt170) cc_final: 0.8178 (ttp80)
REVERT: A  188 HIS cc_start: 0.8522 (m-70) cc_final: 0.8011 (m-70)
REVERT: A  345 LYS cc_start: 0.8108 (ptmm) cc_final: 0.7781 (pttp)
REVERT: B  253 PHE cc_start: 0.6994 (m-80) cc_final: 0.6639 (m-80)
REVERT: B  262 MET cc_start: 0.6985 (mmm) cc_final: 0.6731 (mmm)
REVERT: B  313 ASN cc_start: 0.8375 (t0) cc_final: 0.8010 (t0)
REVERT: B  325 MET cc_start: 0.8082 (tmm) cc_final: 0.7319 (tmm)
REVERT: L  190 ASP cc_start: 0.8283 (p0) cc_final: 0.8020 (p0)
REVERT: H  172 TYR cc_start: 0.7804 (p90) cc_final: 0.7044 (p90)
REVERT: H  196 LEU cc_start: 0.8702 (tp) cc_final: 0.8418 (tt)
REVERT: H  198 GLN cc_start: 0.9014 (tp40) cc_final: 0.8620 (tp40)
REVERT: R   69 ARG cc_start: 0.8026 (mtm-85) cc_final: 0.7073 (mpt-90)
REVERT: R  155 MET cc_start: 0.9385 (ppp) cc_final: 0.9149 (ppp)
REVERT: R  253 MET cc_start: 0.9394 (mmm) cc_final: 0.8817 (mmt)
REVERT: R  294 PHE cc_start: 0.9012 (m-80) cc_final: 0.8630 (m-80)
REVERT: R  305 ILE cc_start: 0.9419 (pt) cc_final: 0.9145 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.2573
  time to fit residues: 55.4310
Evaluate side-chains
  120 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 97 optimal weight:    0.3980
   chunk 58 optimal weight:    0.6980
   chunk 71 optimal weight:    4.9990
   chunk 81 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   chunk 87 optimal weight:    1.9990
   chunk 122 optimal weight:    0.2980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
B  91 HIS
L  26 GLN
** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.081940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.066334 restraints weight = 78338.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.067510 restraints weight = 42739.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.068201 restraints weight = 32662.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3475
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3475 r_free = 0.3475    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3475 r_free = 0.3475    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3475
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.4757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10689  Z= 0.117
  Angle     :  0.650   8.633  14516  Z= 0.338
  Chirality :  0.044   0.197   1624
  Planarity :  0.004   0.052   1841
  Dihedral  :  6.183  76.974   1488
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  0.43 %
    Favored  : 99.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.85 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.23), residues: 1318
  helix:  0.47 (0.27), residues: 337
  sheet: -0.82 (0.28), residues: 323
  loop : -1.92 (0.24), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP R 175 
 HIS   0.005   0.001   HIS R  65 
 PHE   0.029   0.001   PHE R 159 
 TYR   0.011   0.001   TYR R 178 
 ARG   0.009   0.000   ARG A  32 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00299 (    1)
  link_NAG-ASN         : angle       3.17324 (    3)
  link_BETA1-4         : bond        0.00113 (    1)
  link_BETA1-4         : angle       1.56879 (    3)
  hydrogen bonds       : bond        0.03687 (  438)
  hydrogen bonds       : angle       5.46474 ( 1214)
  SS BOND              : bond        0.00559 (    6)
  SS BOND              : angle       0.93036 (   12)
  covalent geometry    : bond        0.00253 (10680)
  covalent geometry    : angle       0.64742 (14498)
  Misc. bond           : bond        0.00157 (    1)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 1.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.8713 (m-40) cc_final: 0.7385 (t0)
REVERT: A   24 ARG cc_start: 0.8732 (ppt170) cc_final: 0.8299 (ttp80)
REVERT: A  188 HIS cc_start: 0.8369 (m-70) cc_final: 0.7954 (m-70)
REVERT: A  304 GLN cc_start: 0.6182 (tm-30) cc_final: 0.5935 (tm-30)
REVERT: A  345 LYS cc_start: 0.8172 (ptmm) cc_final: 0.7841 (pttp)
REVERT: B  111 TYR cc_start: 0.7964 (m-10) cc_final: 0.7470 (m-10)
REVERT: B  313 ASN cc_start: 0.8237 (t0) cc_final: 0.7909 (t0)
REVERT: B  325 MET cc_start: 0.8042 (tmm) cc_final: 0.6485 (tmm)
REVERT: L  190 ASP cc_start: 0.8135 (p0) cc_final: 0.7887 (p0)
REVERT: H  112 MET cc_start: 0.7647 (tpt) cc_final: 0.7329 (tpt)
REVERT: H  172 TYR cc_start: 0.7548 (p90) cc_final: 0.6997 (p90)
REVERT: H  196 LEU cc_start: 0.8500 (tp) cc_final: 0.8225 (tt)
REVERT: H  198 GLN cc_start: 0.8975 (tp40) cc_final: 0.8565 (tp40)
REVERT: R   69 ARG cc_start: 0.8131 (mtm-85) cc_final: 0.7390 (mtt90)
REVERT: R  155 MET cc_start: 0.9364 (ppp) cc_final: 0.9097 (ppp)
REVERT: R  253 MET cc_start: 0.9170 (mmm) cc_final: 0.8588 (mmt)
REVERT: R  305 ILE cc_start: 0.9361 (pt) cc_final: 0.9000 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.2844
  time to fit residues: 63.5744
Evaluate side-chains
  119 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 1.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 21 optimal weight:    0.4980
   chunk 111 optimal weight:    7.9990
   chunk 85 optimal weight:    5.9990
   chunk 71 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 79 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 22 optimal weight:    8.9990
   chunk 63 optimal weight:    0.4980
   overall best weight:    1.5782

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

Flipped N/Q/H residues before XYZ refinement:
B  91 HIS
L  26 GLN
L 115 GLN
** R 195 HIS ** 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 = 0.3813 r_free = 0.3813 target = 0.080078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.062490 restraints weight = 119317.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.065029 restraints weight = 54904.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.065616 restraints weight = 35029.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3437
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3437 r_free = 0.3437    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3437 r_free = 0.3437    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3437
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.4804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10689  Z= 0.146
  Angle     :  0.676   8.879  14516  Z= 0.351
  Chirality :  0.045   0.267   1624
  Planarity :  0.005   0.054   1841
  Dihedral  :  6.211  77.165   1488
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.83 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  0.26 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.85 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.23), residues: 1318
  helix:  0.46 (0.27), residues: 337
  sheet: -0.72 (0.29), residues: 311
  loop : -1.90 (0.24), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP R 175 
 HIS   0.006   0.001   HIS R  65 
 PHE   0.026   0.002   PHE R 159 
 TYR   0.012   0.001   TYR A 296 
 ARG   0.010   0.001   ARG A  32 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00228 (    1)
  link_NAG-ASN         : angle       3.18890 (    3)
  link_BETA1-4         : bond        0.00129 (    1)
  link_BETA1-4         : angle       1.78858 (    3)
  hydrogen bonds       : bond        0.03900 (  438)
  hydrogen bonds       : angle       5.52366 ( 1214)
  SS BOND              : bond        0.00781 (    6)
  SS BOND              : angle       1.01575 (   12)
  covalent geometry    : bond        0.00319 (10680)
  covalent geometry    : angle       0.67397 (14498)
  Misc. bond           : bond        0.00246 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4865.94 seconds
wall clock time: 87 minutes 22.72 seconds (5242.72 seconds total)