Starting phenix.real_space_refine
on Fri Oct 10 14:42:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8unx_42420/10_2025/8unx_42420.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8unx_42420/10_2025/8unx_42420.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8unx_42420/10_2025/8unx_42420.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8unx_42420/10_2025/8unx_42420.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8unx_42420/10_2025/8unx_42420.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8unx_42420/10_2025/8unx_42420.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.020
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: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      43      5.16       5
     C    4297      2.51       5
     N    1155      2.21       5
     O    1190      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6688
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1783
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 244, 1771
          Classifications: {'peptide': 244}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 69}
          Link IDs: {'PTRANS': 6, 'TRANS': 237}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 262
          Unresolved non-hydrogen angles: 317
          Unresolved non-hydrogen dihedrals: 210
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 12, 'GLN:plan1': 7, 'ARG:plan': 10, 'ASN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 179
      Conformer: "B"
        Number of residues, atoms: 244, 1771
          Classifications: {'peptide': 244}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 69}
          Link IDs: {'PTRANS': 6, 'TRANS': 237}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 262
          Unresolved non-hydrogen angles: 317
          Unresolved non-hydrogen dihedrals: 210
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 12, 'GLN:plan1': 7, 'ARG:plan': 10, 'ASN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 179
          bond proxies already assigned to first conformer: 1792
    Chain: "B"
      Number of atoms: 2400
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2400
          Classifications: {'peptide': 337}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 56}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 192
          Unresolved non-hydrogen angles: 237
          Unresolved non-hydrogen dihedrals: 147
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'ASP:plan': 15, 'GLN:plan1': 5, 'ARG:plan': 9, 'GLU:plan': 5, 'ASN:plan1': 3, 'ASN%COO:plan1': 1}
          Unresolved non-hydrogen planarities: 142
    Chain: "G"
      Number of atoms: 339
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 339
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 87
          Unresolved non-hydrogen angles: 104
          Unresolved non-hydrogen dihedrals: 72
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 43
    Chain: "R"
      Number of atoms: 2119
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2119
          Classifications: {'peptide': 287}
          Incomplete info: {'truncation_to_alanine': 54}
          Link IDs: {'PTRANS': 7, 'TRANS': 279}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 203
          Unresolved non-hydrogen angles: 254
          Unresolved non-hydrogen dihedrals: 165
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 5, 'GLU:plan': 9, 'TRP:plan': 1, 'GLN:plan1': 6, 'ASN:plan1': 3, 'HIS:plan': 3}
          Unresolved non-hydrogen planarities: 123
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATYR A 360 " occ=0.51
      ... (22 atoms not shown)
      pdb=" OH BTYR A 360 " occ=0.49
  Time building chain proxies: 2.14, per 1000 atoms: 0.32
  Number of scatterers: 6688
  At special positions: 0
  Unit cell: (85.0346, 134.493, 98.9178, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      43     16.00
     P       3     15.00
     O    1190      8.00
     N    1155      7.00
     C    4297      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 184 " - pdb=" SG  CYS R 190 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.63
  Conformation dependent library (CDL) restraints added in 402.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1750

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 8 sheets defined
      47.1% alpha, 17.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 40
      removed outlier: 3.791A  pdb=" N   ARG A  13 " --> pdb=" O   THR A   9 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ASN A  14 " --> pdb=" O   GLU A  10 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLU A  15 " --> pdb=" O   ASP A  11 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ALA A  18 " --> pdb=" O   ASN A  14 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   GLN A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ALA A  39 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   THR A  40 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 61
    Processing helix  chain 'A' and resid 233 through 237
      removed outlier: 3.545A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 302
      removed outlier: 3.700A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ALA A 298 " --> pdb=" O   GLN A 294 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLU A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.938A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
      removed outlier: 3.674A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 313 through 316'
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 3.504A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 5 through 25
      removed outlier: 3.792A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLN B  13 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   LYS B  15 " --> pdb=" O   ALA B  11 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 9 through 24
      removed outlier: 3.908A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.645A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 29 through 61
      removed outlier: 3.518A  pdb=" N   VAL R  39 " --> pdb=" O   GLY R  35 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   LEU R  42 " --> pdb=" O   ILE R  38 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 68 through 97
      removed outlier: 3.758A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
      removed outlier: 3.555A  pdb=" N   CYS R 106 " --> pdb=" O   GLY R 102 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   GLU R 107 " --> pdb=" O   ASN R 103 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   CYS R 125 " --> pdb=" O   ILE R 121 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 3.723A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
    Processing helix  chain 'R' and resid 178 through 187
      removed outlier: 3.768A  pdb=" N   CYS R 184 " --> pdb=" O   GLU R 180 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 196 through 208
    Processing helix  chain 'R' and resid 208 through 238
    Processing helix  chain 'R' and resid 269 through 299
      removed outlier: 3.879A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 4.031A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ILE R 298 " --> pdb=" O   ILE R 294 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
    Processing helix  chain 'R' and resid 317 through 327
      removed outlier: 4.004A  pdb=" N   PHE R 321 " --> pdb=" O   VAL R 317 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ASN R 322 " --> pdb=" O   ASN R 318 " (cutoff:3.500A)
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 329 through 339
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213
      removed outlier: 6.182A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.863A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.902A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.174A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   VAL B  71 " --> pdb=" O   HIS B  62 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.945A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.943A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.231A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.906A  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
      removed outlier: 4.051A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.805A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.674A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.993A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU B 210 " --> pdb=" O   GLN B 220 " (cutoff:3.500A)
      removed outlier: 3.634A  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: 3.757A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.746A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.382A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.031A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    368 hydrogen bonds defined for protein.
    1083 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: 0.95

  Time building geometry restraints manager: 0.79 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2153
        1.34 -     1.46: 1611
        1.46 -     1.59: 3005
        1.59 -     1.71: 5
        1.71 -     1.84: 60
  Bond restraints: 6834
  Sorted by residual:
  bond pdb=" CA  SER A  51 "
       pdb=" CB  SER A  51 "
    ideal  model  delta    sigma   weight residual
    1.526  1.482  0.044 1.36e-02 5.41e+03 1.04e+01
  bond pdb=" N   LYS B 127 "
       pdb=" CA  LYS B 127 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 1.23e-02 6.61e+03 1.02e+01
  bond pdb=" N   ILE A 257 "
       pdb=" CA  ILE A 257 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 1.19e-02 7.06e+03 8.58e+00
  bond pdb=" N   VAL A 256 "
       pdb=" CA  VAL A 256 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.17e-02 7.31e+03 8.22e+00
  bond pdb=" N   GLU A 259 "
       pdb=" CA  GLU A 259 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 1.23e-02 6.61e+03 8.00e+00
  ... (remaining 6829 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.48: 9022
        2.48 -     4.95: 301
        4.95 -     7.43: 25
        7.43 -     9.90: 7
        9.90 -    12.38: 4
  Bond angle restraints: 9359
  Sorted by residual:
  angle pdb=" C   ASN B 132 "
        pdb=" CA  ASN B 132 "
        pdb=" CB  ASN B 132 "
      ideal   model   delta    sigma   weight residual
     116.63  104.25   12.38 1.16e+00 7.43e-01 1.14e+02
  angle pdb=" N   ARG A  13 "
        pdb=" CA  ARG A  13 "
        pdb=" C   ARG A  13 "
      ideal   model   delta    sigma   weight residual
     111.28  104.48    6.80 1.09e+00 8.42e-01 3.89e+01
  angle pdb=" N   ASN A  23 "
        pdb=" CA  ASN A  23 "
        pdb=" C   ASN A  23 "
      ideal   model   delta    sigma   weight residual
     111.28  104.91    6.37 1.09e+00 8.42e-01 3.42e+01
  angle pdb=" N   ARG G  13 "
        pdb=" CA  ARG G  13 "
        pdb=" C   ARG G  13 "
      ideal   model   delta    sigma   weight residual
     111.28  104.97    6.31 1.09e+00 8.42e-01 3.35e+01
  angle pdb=" CA  ASN B 132 "
        pdb=" C   ASN B 132 "
        pdb=" N   VAL B 133 "
      ideal   model   delta    sigma   weight residual
     119.63  115.23    4.40 8.10e-01 1.52e+00 2.95e+01
  ... (remaining 9354 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.82: 3881
       31.82 -    63.64: 61
       63.64 -    95.46: 3
       95.46 -   127.28: 0
      127.28 -   159.10: 4
  Dihedral angle restraints: 3949
    sinusoidal: 1251
      harmonic: 2698
  Sorted by residual:
  dihedral pdb=" C5' GTP A 401 "
           pdb=" O5' GTP A 401 "
           pdb=" PA  GTP A 401 "
           pdb=" O3A GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -131.63 -159.10     1      2.00e+01 2.50e-03 4.64e+01
  dihedral pdb=" O3B GTP A 401 "
           pdb=" O3A GTP A 401 "
           pdb=" PB  GTP A 401 "
           pdb=" PA  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -68.92   83.92 -152.84     1      2.00e+01 2.50e-03 4.54e+01
  dihedral pdb=" C8  GTP A 401 "
           pdb=" C1' GTP A 401 "
           pdb=" N9  GTP A 401 "
           pdb=" O4' GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -43.86  148.46     1      2.00e+01 2.50e-03 4.45e+01
  ... (remaining 3946 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 796
       0.047 -    0.094: 206
       0.094 -    0.141: 78
       0.141 -    0.188: 29
       0.188 -    0.235: 13
  Chirality restraints: 1122
  Sorted by residual:
  chirality pdb=" CA  GLU A  15 "
            pdb=" N   GLU A  15 "
            pdb=" C   GLU A  15 "
            pdb=" CB  GLU A  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.23 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" CA  ILE G   9 "
            pdb=" N   ILE G   9 "
            pdb=" C   ILE G   9 "
            pdb=" CB  ILE G   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CA  ILE R 334 "
            pdb=" N   ILE R 334 "
            pdb=" C   ILE R 334 "
            pdb=" CB  ILE R 334 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.23 2.00e-01 2.50e+01 1.31e+00
  ... (remaining 1119 not shown)

  Planarity restraints: 1176
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 125 "    0.017 2.00e-02 2.50e+03   3.55e-02 1.26e+01
        pdb=" C   ASN B 125 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   ASN B 125 "    0.023 2.00e-02 2.50e+03
        pdb=" N   LEU B 126 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  47 "   -0.013 2.00e-02 2.50e+03   2.61e-02 6.79e+00
        pdb=" C   GLY A  47 "    0.045 2.00e-02 2.50e+03
        pdb=" O   GLY A  47 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ALA A  48 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG R 175 "    0.012 2.00e-02 2.50e+03   2.60e-02 6.75e+00
        pdb=" C   ARG R 175 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   ARG R 175 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ALA R 176 "    0.015 2.00e-02 2.50e+03
  ... (remaining 1173 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 325
        2.72 -     3.27: 6733
        3.27 -     3.81: 10397
        3.81 -     4.36: 11754
        4.36 -     4.90: 21001
  Nonbonded interactions: 50210
  Sorted by model distance:
  nonbonded pdb=" O   LEU R 339 "
            pdb=" CD1 LEU R 339 "
     model   vdw
     2.177 3.460
  nonbonded pdb=" OG1 THR B 143 "
            pdb=" OD2 ASP B 163 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OH  TYR R 185 "
            pdb=" O   PHE R 194 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   ARG B  68 "
            pdb=" OG  SER B  84 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   HIS B  54 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.296 3.040
  ... (remaining 50205 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=0.49 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.550
  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:          0.150
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     8.120
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   6836  Z= 0.403
  Angle     :  0.966  12.378   9363  Z= 0.666
  Chirality :  0.057   0.235   1122
  Planarity :  0.006   0.098   1176
  Dihedral  : 13.805 159.097   2193
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.34 (0.27), residues: 914
  helix:  2.15 (0.26), residues: 392
  sheet:  1.12 (0.42), residues: 169
  loop : -0.69 (0.29), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG R 228 
 TYR   0.020   0.001   TYR R 185 
 PHE   0.017   0.002   PHE A 222 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00591 ( 6834)
  covalent geometry    : angle       0.96446 ( 9359)
  SS BOND              : bond        0.00751 (    2)
  SS BOND              : angle       2.83124 (    4)
  hydrogen bonds       : bond        0.21444 (  368)
  hydrogen bonds       : angle       6.95420 ( 1083)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.238 
Fit side-chains
REVERT: A  253 TYR cc_start: 0.8595 (p90) cc_final: 0.8341 (p90)
REVERT: A  255 MET cc_start: 0.7332 (tpp) cc_final: 0.7016 (mmm)
REVERT: A  308 ILE cc_start: 0.7204 (mm) cc_final: 0.6876 (mm)
REVERT: B  125 ASN cc_start: 0.9072 (t0) cc_final: 0.8832 (t0)
REVERT: R  191 CYS cc_start: 0.6374 (t) cc_final: 0.6135 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.0818
  time to fit residues: 12.0484
Evaluate side-chains
  86 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.3980
   chunk 62 optimal weight:   30.0000
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    8.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.8586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.121082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.092748 restraints weight = 43059.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.098224 restraints weight = 14711.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.101157 restraints weight = 6942.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.101392 restraints weight = 4876.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.101619 restraints weight = 4548.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3221
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3221 r_free = 0.3221    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3221 r_free = 0.3221    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3221
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.1400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6836  Z= 0.192
  Angle     :  0.584   9.793   9363  Z= 0.319
  Chirality :  0.043   0.141   1122
  Planarity :  0.004   0.044   1176
  Dihedral  : 10.594 149.297   1014
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  :  8.74 %
    Favored  : 89.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.31 (0.27), residues: 914
  helix:  2.23 (0.26), residues: 409
  sheet:  0.79 (0.41), residues: 175
  loop : -0.87 (0.29), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R 228 
 TYR   0.010   0.002   TYR R 185 
 PHE   0.016   0.002   PHE A 222 
 TRP   0.011   0.001   TRP B 169 
 HIS   0.005   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 6834)
  covalent geometry    : angle       0.58309 ( 9359)
  SS BOND              : bond        0.00330 (    2)
  SS BOND              : angle       1.72729 (    4)
  hydrogen bonds       : bond        0.06248 (  368)
  hydrogen bonds       : angle       4.81903 ( 1083)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: A  253 TYR cc_start: 0.8837 (p90) cc_final: 0.8469 (p90)
REVERT: A  255 MET cc_start: 0.7957 (tpp) cc_final: 0.7617 (mmm)
REVERT: A  308 ILE cc_start: 0.7296 (mm) cc_final: 0.6957 (mm)
REVERT: R  171 MET cc_start: 0.6987 (mmt) cc_final: 0.6701 (mmt)
REVERT: R  303 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8567 (tt)
  outliers start: 9
  outliers final: 8
  residues processed: 96
  average time/residue: 0.0652
  time to fit residues: 8.8922
Evaluate side-chains
  95 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  272 LEU
Chi-restraints excluded: chain R residue  303 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 85 optimal weight:    0.7980
   chunk 5 optimal weight:   10.0000
   chunk 50 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   chunk 24 optimal weight:   20.0000
   chunk 64 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 72 optimal weight:    0.8980
   chunk 75 optimal weight:    0.6980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.123233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.094671 restraints weight = 44034.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.100177 restraints weight = 14683.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.104455 restraints weight = 6631.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.104440 restraints weight = 4185.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.104674 restraints weight = 4050.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3274
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3274 r_free = 0.3274    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3274 r_free = 0.3274    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3274
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.1677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6836  Z= 0.113
  Angle     :  0.500   8.783   9363  Z= 0.267
  Chirality :  0.040   0.139   1122
  Planarity :  0.003   0.039   1176
  Dihedral  :  9.688 145.297   1014
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 12.10 %
    Favored  : 87.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.50 (0.28), residues: 914
  helix:  2.53 (0.26), residues: 404
  sheet:  0.73 (0.40), residues: 175
  loop : -0.82 (0.30), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG R 228 
 TYR   0.007   0.001   TYR B 111 
 PHE   0.013   0.001   PHE R 104 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.010   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 6834)
  covalent geometry    : angle       0.49909 ( 9359)
  SS BOND              : bond        0.00240 (    2)
  SS BOND              : angle       1.32016 (    4)
  hydrogen bonds       : bond        0.04730 (  368)
  hydrogen bonds       : angle       4.25567 ( 1083)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 MET cc_start: 0.7557 (mtm) cc_final: 0.7335 (mtt)
REVERT: A  253 TYR cc_start: 0.8844 (p90) cc_final: 0.8525 (p90)
REVERT: A  308 ILE cc_start: 0.7351 (mm) cc_final: 0.7044 (mm)
REVERT: R  303 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8531 (tt)
  outliers start: 5
  outliers final: 3
  residues processed: 99
  average time/residue: 0.0747
  time to fit residues: 10.3303
Evaluate side-chains
  89 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 85
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain R residue  303 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 7 optimal weight:    0.3980
   chunk 70 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0050
   chunk 61 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.124040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.095421 restraints weight = 38787.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.100772 restraints weight = 13965.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.103122 restraints weight = 6748.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.104258 restraints weight = 5069.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.104988 restraints weight = 4314.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3282
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3282
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.1937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6836  Z= 0.104
  Angle     :  0.474   7.740   9363  Z= 0.253
  Chirality :  0.039   0.134   1122
  Planarity :  0.003   0.038   1176
  Dihedral  :  9.105 144.069   1014
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 11.93 %
    Favored  : 86.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.58 (0.28), residues: 914
  helix:  2.61 (0.26), residues: 404
  sheet:  0.58 (0.39), residues: 184
  loop : -0.70 (0.31), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG R 228 
 TYR   0.006   0.001   TYR A 339 
 PHE   0.012   0.001   PHE R 104 
 TRP   0.010   0.001   TRP B 169 
 HIS   0.009   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 6834)
  covalent geometry    : angle       0.47394 ( 9359)
  SS BOND              : bond        0.00192 (    2)
  SS BOND              : angle       1.10170 (    4)
  hydrogen bonds       : bond        0.04166 (  368)
  hydrogen bonds       : angle       3.98021 ( 1083)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
REVERT: A  253 TYR cc_start: 0.8869 (p90) cc_final: 0.8566 (p90)
REVERT: A  308 ILE cc_start: 0.7375 (mm) cc_final: 0.7055 (mm)
REVERT: R  303 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8480 (tt)
  outliers start: 11
  outliers final: 7
  residues processed: 108
  average time/residue: 0.0727
  time to fit residues: 10.8961
Evaluate side-chains
  100 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  153 ILE
Chi-restraints excluded: chain R residue  272 LEU
Chi-restraints excluded: chain R residue  303 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 83 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 68 optimal weight:    0.5980
   chunk 9 optimal weight:    0.0870
   chunk 35 optimal weight:    0.9980
   chunk 29 optimal weight:    5.9990
   chunk 65 optimal weight:    0.7980
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
B 142 HIS
R  93 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.124156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.095343 restraints weight = 44078.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.100964 restraints weight = 14517.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.104372 restraints weight = 6697.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.104558 restraints weight = 4562.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.104820 restraints weight = 4308.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3277
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3277 r_free = 0.3277    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3277 r_free = 0.3277    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3277
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.2148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   6836  Z= 0.107
  Angle     :  0.481   7.033   9363  Z= 0.256
  Chirality :  0.039   0.141   1122
  Planarity :  0.003   0.043   1176
  Dihedral  :  8.831 143.435   1014
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 14.79 %
    Favored  : 83.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.58 (0.28), residues: 914
  helix:  2.65 (0.26), residues: 405
  sheet:  0.47 (0.39), residues: 176
  loop : -0.66 (0.30), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG R 228 
 TYR   0.008   0.001   TYR B 111 
 PHE   0.011   0.001   PHE A 222 
 TRP   0.009   0.001   TRP B 169 
 HIS   0.010   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 6834)
  covalent geometry    : angle       0.48024 ( 9359)
  SS BOND              : bond        0.00238 (    2)
  SS BOND              : angle       0.96238 (    4)
  hydrogen bonds       : bond        0.04122 (  368)
  hydrogen bonds       : angle       3.97290 ( 1083)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
REVERT: A  253 TYR cc_start: 0.8872 (p90) cc_final: 0.8569 (p90)
REVERT: A  255 MET cc_start: 0.7869 (tpp) cc_final: 0.7155 (mmm)
REVERT: A  308 ILE cc_start: 0.7337 (mm) cc_final: 0.7050 (mm)
REVERT: A  344 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8095 (tp30)
REVERT: B   88 ASN cc_start: 0.9079 (OUTLIER) cc_final: 0.8849 (p0)
  outliers start: 9
  outliers final: 8
  residues processed: 104
  average time/residue: 0.0767
  time to fit residues: 11.0573
Evaluate side-chains
  103 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue   93 HIS
Chi-restraints excluded: chain R residue  272 LEU
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 58 optimal weight:    5.9990
   chunk 63 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0570
   chunk 2 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 85 optimal weight:    0.7980
   chunk 83 optimal weight:   10.0000
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.7098

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN
B  88 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.124242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.095279 restraints weight = 39122.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.100789 restraints weight = 13814.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.103099 restraints weight = 6632.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.104356 restraints weight = 4949.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.104914 restraints weight = 4244.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3280
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3280 r_free = 0.3280    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3280 r_free = 0.3280    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3280
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.2241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6836  Z= 0.107
  Angle     :  0.472   6.640   9363  Z= 0.254
  Chirality :  0.039   0.144   1122
  Planarity :  0.003   0.049   1176
  Dihedral  :  8.622 142.616   1014
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 16.13 %
    Favored  : 82.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.63 (0.28), residues: 914
  helix:  2.69 (0.26), residues: 405
  sheet:  0.52 (0.39), residues: 174
  loop : -0.65 (0.30), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG R 228 
 TYR   0.009   0.001   TYR B  59 
 PHE   0.017   0.001   PHE A 222 
 TRP   0.009   0.001   TRP B 169 
 HIS   0.008   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 6834)
  covalent geometry    : angle       0.47172 ( 9359)
  SS BOND              : bond        0.00239 (    2)
  SS BOND              : angle       0.88683 (    4)
  hydrogen bonds       : bond        0.04073 (  368)
  hydrogen bonds       : angle       3.94141 ( 1083)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.7968 (tp30) cc_final: 0.6453 (tm-30)
REVERT: A  253 TYR cc_start: 0.8872 (p90) cc_final: 0.8572 (p90)
REVERT: A  255 MET cc_start: 0.7856 (tpp) cc_final: 0.7163 (mmm)
REVERT: A  308 ILE cc_start: 0.7334 (mm) cc_final: 0.7051 (mm)
REVERT: A  344 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8103 (tp30)
REVERT: R  173 TRP cc_start: 0.8017 (m-10) cc_final: 0.7729 (m-10)
REVERT: R  303 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8459 (tt)
  outliers start: 11
  outliers final: 9
  residues processed: 108
  average time/residue: 0.0680
  time to fit residues: 10.2962
Evaluate side-chains
  104 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  155 LEU
Chi-restraints excluded: chain R residue  272 LEU
Chi-restraints excluded: chain R residue  303 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0770
   chunk 23 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 26 optimal weight:    6.9990
   chunk 77 optimal weight:    0.9990
   chunk 49 optimal weight:    0.1980
   chunk 0 optimal weight:   20.0000
   chunk 42 optimal weight:    0.3980
   chunk 62 optimal weight:    7.9990
   overall best weight:    0.5342

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN
R  93 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.124867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.095715 restraints weight = 41948.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.101283 restraints weight = 14366.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.105017 restraints weight = 6812.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.105482 restraints weight = 4286.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.105876 restraints weight = 4080.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3298
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3298 r_free = 0.3298    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3298 r_free = 0.3298    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3298
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.2332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6836  Z= 0.099
  Angle     :  0.460   6.432   9363  Z= 0.248
  Chirality :  0.039   0.149   1122
  Planarity :  0.003   0.052   1176
  Dihedral  :  8.418 141.241   1014
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 16.47 %
    Favored  : 81.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.66 (0.28), residues: 914
  helix:  2.73 (0.26), residues: 404
  sheet:  0.48 (0.39), residues: 174
  loop : -0.61 (0.30), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG R 228 
 TYR   0.008   0.001   TYR B 111 
 PHE   0.012   0.001   PHE A 222 
 TRP   0.009   0.001   TRP B 169 
 HIS   0.010   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 ( 6834)
  covalent geometry    : angle       0.45979 ( 9359)
  SS BOND              : bond        0.00218 (    2)
  SS BOND              : angle       0.83873 (    4)
  hydrogen bonds       : bond        0.03872 (  368)
  hydrogen bonds       : angle       3.89199 ( 1083)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.7926 (tp30) cc_final: 0.6460 (tm-30)
REVERT: A  213 GLN cc_start: 0.8629 (pp30) cc_final: 0.8390 (pp30)
REVERT: A  253 TYR cc_start: 0.8870 (p90) cc_final: 0.8571 (p90)
REVERT: A  255 MET cc_start: 0.7868 (tpp) cc_final: 0.7251 (mmm)
REVERT: A  308 ILE cc_start: 0.7296 (mm) cc_final: 0.7025 (mm)
REVERT: A  344 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8099 (tp30)
REVERT: R  173 TRP cc_start: 0.8015 (m-10) cc_final: 0.7753 (m-10)
REVERT: R  303 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8469 (tt)
  outliers start: 12
  outliers final: 9
  residues processed: 104
  average time/residue: 0.0768
  time to fit residues: 10.9736
Evaluate side-chains
  101 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue   93 HIS
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  272 LEU
Chi-restraints excluded: chain R residue  303 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 88 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0980
   chunk 35 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN
B  88 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.124755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.096051 restraints weight = 35690.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.101437 restraints weight = 13476.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.103801 restraints weight = 6696.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.104646 restraints weight = 5212.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.105056 restraints weight = 4427.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3276
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3276 r_free = 0.3276    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3276 r_free = 0.3276    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3276
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6836  Z= 0.110
  Angle     :  0.467   6.198   9363  Z= 0.253
  Chirality :  0.039   0.155   1122
  Planarity :  0.003   0.054   1176
  Dihedral  :  8.346 140.338   1014
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 16.47 %
    Favored  : 81.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.61 (0.28), residues: 914
  helix:  2.73 (0.26), residues: 403
  sheet:  0.43 (0.38), residues: 172
  loop : -0.68 (0.30), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG R 228 
 TYR   0.007   0.001   TYR B  59 
 PHE   0.018   0.001   PHE A 222 
 TRP   0.008   0.001   TRP B 169 
 HIS   0.014   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 6834)
  covalent geometry    : angle       0.46669 ( 9359)
  SS BOND              : bond        0.00254 (    2)
  SS BOND              : angle       0.84712 (    4)
  hydrogen bonds       : bond        0.04001 (  368)
  hydrogen bonds       : angle       3.87698 ( 1083)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.7937 (tp30) cc_final: 0.6457 (tm-30)
REVERT: A  253 TYR cc_start: 0.8864 (p90) cc_final: 0.8558 (p90)
REVERT: A  255 MET cc_start: 0.7823 (tpp) cc_final: 0.7239 (mmm)
REVERT: A  308 ILE cc_start: 0.7304 (mm) cc_final: 0.7014 (mm)
REVERT: R  173 TRP cc_start: 0.8031 (m-10) cc_final: 0.7789 (m-10)
REVERT: R  303 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8484 (tt)
  outliers start: 12
  outliers final: 11
  residues processed: 99
  average time/residue: 0.0680
  time to fit residues: 9.5135
Evaluate side-chains
  101 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  155 LEU
Chi-restraints excluded: chain R residue  272 LEU
Chi-restraints excluded: chain R residue  303 ILE
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 76 optimal weight:    0.2980
   chunk 40 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9990
   chunk 57 optimal weight:   20.0000
   chunk 62 optimal weight:   20.0000
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN
R  93 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.123941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.094732 restraints weight = 41025.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.100187 restraints weight = 14037.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.102741 restraints weight = 6795.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.104222 restraints weight = 5042.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.104385 restraints weight = 4263.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3276
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3276 r_free = 0.3276    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3276 r_free = 0.3276    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3276
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6836  Z= 0.109
  Angle     :  0.466   6.070   9363  Z= 0.253
  Chirality :  0.039   0.158   1122
  Planarity :  0.003   0.055   1176
  Dihedral  :  8.281 140.826   1014
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 16.81 %
    Favored  : 81.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.67 (0.28), residues: 914
  helix:  2.75 (0.26), residues: 404
  sheet:  0.44 (0.38), residues: 176
  loop : -0.60 (0.31), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG R 228 
 TYR   0.009   0.001   TYR B 111 
 PHE   0.015   0.001   PHE A 222 
 TRP   0.009   0.001   TRP B 169 
 HIS   0.010   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 6834)
  covalent geometry    : angle       0.46579 ( 9359)
  SS BOND              : bond        0.00251 (    2)
  SS BOND              : angle       0.85063 (    4)
  hydrogen bonds       : bond        0.04020 (  368)
  hydrogen bonds       : angle       3.87015 ( 1083)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.7960 (tp30) cc_final: 0.6478 (tm-30)
REVERT: A  253 TYR cc_start: 0.8875 (p90) cc_final: 0.8563 (p90)
REVERT: A  255 MET cc_start: 0.7813 (tpp) cc_final: 0.7243 (mmm)
REVERT: A  308 ILE cc_start: 0.7293 (mm) cc_final: 0.7007 (mm)
REVERT: R  173 TRP cc_start: 0.8053 (m-10) cc_final: 0.7835 (m-10)
  outliers start: 12
  outliers final: 12
  residues processed: 99
  average time/residue: 0.0712
  time to fit residues: 9.9697
Evaluate side-chains
  102 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue   93 HIS
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  155 LEU
Chi-restraints excluded: chain R residue  272 LEU
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 57 optimal weight:    8.9990
   chunk 49 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 3 optimal weight:    0.1980
   chunk 21 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 80 optimal weight:    0.6980
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN
B  88 ASN
R  93 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.124439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.095689 restraints weight = 36907.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.101062 restraints weight = 13674.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.103478 restraints weight = 6760.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.104635 restraints weight = 5187.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.104884 restraints weight = 4411.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3275
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3275 r_free = 0.3275    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3275 r_free = 0.3275    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3275
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.2474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6836  Z= 0.109
  Angle     :  0.467   6.088   9363  Z= 0.254
  Chirality :  0.039   0.160   1122
  Planarity :  0.003   0.055   1176
  Dihedral  :  8.242 144.474   1014
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 16.64 %
    Favored  : 81.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.28), residues: 914
  helix:  2.74 (0.26), residues: 404
  sheet:  0.42 (0.39), residues: 165
  loop : -0.69 (0.30), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG R 228 
 TYR   0.008   0.001   TYR B 111 
 PHE   0.017   0.001   PHE R  49 
 TRP   0.008   0.001   TRP B 169 
 HIS   0.012   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 6834)
  covalent geometry    : angle       0.46630 ( 9359)
  SS BOND              : bond        0.00247 (    2)
  SS BOND              : angle       0.85643 (    4)
  hydrogen bonds       : bond        0.04021 (  368)
  hydrogen bonds       : angle       3.87139 ( 1083)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.7933 (tp30) cc_final: 0.6461 (tm-30)
REVERT: A  253 TYR cc_start: 0.8896 (p90) cc_final: 0.8624 (p90)
REVERT: A  255 MET cc_start: 0.7811 (tpp) cc_final: 0.7265 (mmm)
REVERT: A  308 ILE cc_start: 0.7320 (mm) cc_final: 0.7037 (mm)
  outliers start: 13
  outliers final: 13
  residues processed: 95
  average time/residue: 0.0684
  time to fit residues: 9.1861
Evaluate side-chains
  101 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue   93 HIS
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  155 LEU
Chi-restraints excluded: chain R residue  272 LEU
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0970
   chunk 79 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0870
   chunk 68 optimal weight:    3.9990
   chunk 15 optimal weight:   10.0000
   chunk 27 optimal weight:    1.9990
   chunk 57 optimal weight:   20.0000
   chunk 39 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0980
   overall best weight:    0.4556

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.124558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.095584 restraints weight = 34196.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.099771 restraints weight = 13216.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.102567 restraints weight = 7601.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.104579 restraints weight = 5420.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.105948 restraints weight = 4287.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3299
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3299 r_free = 0.3299    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3299 r_free = 0.3299    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3299
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.133   6836  Z= 0.243
  Angle     :  0.991  59.127   9363  Z= 0.621
  Chirality :  0.065   1.634   1122
  Planarity :  0.007   0.200   1176
  Dihedral  :  8.307 144.518   1014
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 16.81 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.59 (0.28), residues: 914
  helix:  2.73 (0.26), residues: 404
  sheet:  0.42 (0.39), residues: 165
  loop : -0.69 (0.30), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG R 228 
 TYR   0.008   0.001   TYR B 111 
 PHE   0.013   0.001   PHE R  49 
 TRP   0.008   0.001   TRP B 169 
 HIS   0.324   0.012   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 6834)
  covalent geometry    : angle       0.99073 ( 9359)
  SS BOND              : bond        0.00242 (    2)
  SS BOND              : angle       0.82251 (    4)
  hydrogen bonds       : bond        0.04081 (  368)
  hydrogen bonds       : angle       3.87614 ( 1083)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1371.39 seconds
wall clock time: 24 minutes 18.02 seconds (1458.02 seconds total)