Starting phenix.real_space_refine
on Wed Sep 17 15:08:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rik_19188/09_2025/8rik_19188.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rik_19188/09_2025/8rik_19188.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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rik_19188/09_2025/8rik_19188.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rik_19188/09_2025/8rik_19188.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rik_19188/09_2025/8rik_19188.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rik_19188/09_2025/8rik_19188.cif"
  }
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       7      5.49       5
     Mg      1      5.21       5
     S      60      5.16       5
     C    5873      2.51       5
     N    1591      2.21       5
     O    1821      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9353
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "B"
      Number of atoms: 3351
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 426, 3351
          Classifications: {'peptide': 426}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405}
    Chain: "A"
      Number of atoms: 3358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 428, 3358
          Classifications: {'peptide': 428}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407}
          Chain breaks: 1
    Chain: "K"
      Number of atoms: 2448
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 312, 2448
          Classifications: {'peptide': 312}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 8, 'TRANS': 303}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "T"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 3, 24
          Classifications: {'peptide': 3}
          Link IDs: {'PTRANS': 1, 'TRANS': 1}
    Chain: "t"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: "B"
        Number of residues, atoms: 3, 22
          Classifications: {'peptide': 3}
          Link IDs: {'TRANS': 2}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'GDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 62
          Unusual residues: {'TA1': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "K"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 6
    residue:
      pdb=" N  ALYS T 922 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NZ ALYS T 922 " occ=0.50
    residue:
      pdb=" N  APRO T 923 " occ=0.50
      ... (5 atoms not shown)
      pdb=" CD APRO T 923 " occ=0.50
    residue:
      pdb=" N  AILE T 924 " occ=0.50
      ... (6 atoms not shown)
      pdb=" CD1AILE T 924 " occ=0.50
    residue:
      pdb=" N  BILE t 920 " occ=0.50
      ... (6 atoms not shown)
      pdb=" CD1BILE t 920 " occ=0.50
    residue:
      pdb=" N  BALA t 921 " occ=0.50
      ... (3 atoms not shown)
      pdb=" CB BALA t 921 " occ=0.50
    residue:
      pdb=" N  BLYS t 922 " occ=0.50
      ... (7 atoms not shown)
      pdb=" NZ BLYS t 922 " occ=0.50
  Time building chain proxies: 2.24, per 1000 atoms: 0.24
  Number of scatterers: 9353
  At special positions: 0
  Unit cell: (70.395, 109.383, 115.881, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      60     16.00
     P       7     15.00
     Mg      1     11.99
     O    1821      8.00
     N    1591      7.00
     C    5873      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.90
  Conformation dependent library (CDL) restraints added in 309.9 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2178

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 10 sheets defined
      46.2% alpha, 19.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'B' and resid 10 through 29
    Processing helix  chain 'B' and resid 40 through 48
      removed outlier: 4.300A  pdb=" N   LEU B  44 " --> pdb=" O   SER B  40 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   ARG B  48 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 51
      No H-bonds generated for 'chain 'B' and resid 49 through 51'
    Processing helix  chain 'B' and resid 71 through 79
      removed outlier: 4.639A  pdb=" N   MET B  75 " --> pdb=" O   GLU B  71 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ASP B  76 " --> pdb=" O   PRO B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 90
      No H-bonds generated for 'chain 'B' and resid 88 through 90'
    Processing helix  chain 'B' and resid 102 through 109
    Processing helix  chain 'B' and resid 114 through 127
    Processing helix  chain 'B' and resid 144 through 161
    Processing helix  chain 'B' and resid 182 through 195
      removed outlier: 3.642A  pdb=" N   ASN B 186 " --> pdb=" O   VAL B 182 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   GLN B 193 " --> pdb=" O   LEU B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 216
    Processing helix  chain 'B' and resid 223 through 239
      removed outlier: 3.819A  pdb=" N   LEU B 227 " --> pdb=" O   THR B 223 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   THR B 239 " --> pdb=" O   MET B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 240 through 243
      removed outlier: 3.701A  pdb=" N   ARG B 243 " --> pdb=" O   THR B 240 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 240 through 243'
    Processing helix  chain 'B' and resid 251 through 260
    Processing helix  chain 'B' and resid 287 through 296
    Processing helix  chain 'B' and resid 324 through 339
      removed outlier: 3.532A  pdb=" N   VAL B 328 " --> pdb=" O   SER B 324 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   GLN B 336 " --> pdb=" O   MET B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 343
      removed outlier: 3.572A  pdb=" N   PHE B 343 " --> pdb=" O   SER B 340 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 340 through 343'
    Processing helix  chain 'B' and resid 384 through 400
      removed outlier: 3.862A  pdb=" N   PHE B 388 " --> pdb=" O   ILE B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 410
    Processing helix  chain 'B' and resid 414 through 435
      removed outlier: 3.980A  pdb=" N   PHE B 418 " --> pdb=" O   ASP B 414 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   TYR B 435 " --> pdb=" O   GLU B 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 10 through 29
    Processing helix  chain 'A' and resid 72 through 80
      removed outlier: 3.613A  pdb=" N   ASP A  76 " --> pdb=" O   PRO A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 108
    Processing helix  chain 'A' and resid 110 through 113
      removed outlier: 3.627A  pdb=" N   GLU A 113 " --> pdb=" O   ILE A 110 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 110 through 113'
    Processing helix  chain 'A' and resid 114 through 128
      removed outlier: 3.630A  pdb=" N   GLN A 128 " --> pdb=" O   LYS A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 161
      removed outlier: 4.739A  pdb=" N   THR A 150 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   SER A 151 " --> pdb=" O   SER A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 198
      removed outlier: 3.606A  pdb=" N   ASN A 186 " --> pdb=" O   VAL A 182 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   LEU A 195 " --> pdb=" O   THR A 191 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   GLU A 196 " --> pdb=" O   HIS A 192 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   HIS A 197 " --> pdb=" O   THR A 193 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   SER A 198 " --> pdb=" O   THR A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 216
      removed outlier: 3.714A  pdb=" N   ILE A 209 " --> pdb=" O   ASP A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 244
      removed outlier: 3.837A  pdb=" N   LEU A 227 " --> pdb=" O   THR A 223 " (cutoff:3.500A)
      removed outlier: 4.631A  pdb=" N   SER A 241 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 5.064A  pdb=" N   LEU A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 260
    Processing helix  chain 'A' and resid 287 through 295
    Processing helix  chain 'A' and resid 306 through 310
      removed outlier: 3.505A  pdb=" N   HIS A 309 " --> pdb=" O   ASP A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 338
      removed outlier: 3.676A  pdb=" N   LYS A 338 " --> pdb=" O   THR A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 401
      removed outlier: 4.086A  pdb=" N   TRP A 388 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   LYS A 401 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
    Processing helix  chain 'A' and resid 415 through 437
      removed outlier: 4.434A  pdb=" N   SER A 419 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   VAL A 437 " --> pdb=" O   GLU A 433 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 19 through 24
      removed outlier: 4.254A  pdb=" N   ASN K  24 " --> pdb=" O   GLU K  20 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 57 through 66
      removed outlier: 3.627A  pdb=" N   VAL K  61 " --> pdb=" O   SER K  57 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 66 through 74
      removed outlier: 3.549A  pdb=" N   LEU K  74 " --> pdb=" O   VAL K  70 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 90 through 96
    Processing helix  chain 'K' and resid 106 through 118
      removed outlier: 4.002A  pdb=" N   ARG K 110 " --> pdb=" O   GLY K 106 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   TYR K 118 " --> pdb=" O   ASP K 114 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 175 through 188
    Processing helix  chain 'K' and resid 237 through 241
    Processing helix  chain 'K' and resid 245 through 271
    Processing helix  chain 'K' and resid 280 through 286
    Processing helix  chain 'K' and resid 305 through 307
      No H-bonds generated for 'chain 'K' and resid 305 through 307'
    Processing helix  chain 'K' and resid 308 through 323
      removed outlier: 3.961A  pdb=" N   ALA K 322 " --> pdb=" O   PHE K 318 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   LYS K 323 " --> pdb=" O   GLY K 319 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 94
      removed outlier: 8.447A  pdb=" N   VAL B  93 " --> pdb=" O   ALA B  65 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   LEU B  67 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 8.430A  pdb=" N   ILE B  66 " --> pdb=" O   ILE B   4 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   HIS B   6 " --> pdb=" O   ILE B  66 " (cutoff:3.500A)
      removed outlier: 7.892A  pdb=" N   VAL B  68 " --> pdb=" O   HIS B   6 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   GLN B   8 " --> pdb=" O   VAL B  68 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   GLU B   3 " --> pdb=" O   GLY B 134 " (cutoff:3.500A)
      removed outlier: 7.842A  pdb=" N   GLN B 136 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   VAL B   5 " --> pdb=" O   GLN B 136 " (cutoff:3.500A)
      removed outlier: 8.115A  pdb=" N   THR B 138 " --> pdb=" O   VAL B   5 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   ILE B   7 " --> pdb=" O   THR B 138 " (cutoff:3.500A)
      removed outlier: 9.196A  pdb=" N   SER B 140 " --> pdb=" O   ILE B   7 " (cutoff:3.500A)
      removed outlier: 8.787A  pdb=" N   ALA B   9 " --> pdb=" O   SER B 140 " (cutoff:3.500A)
      removed outlier: 7.080A  pdb=" N   GLN B 133 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   ASN B 167 " --> pdb=" O   GLN B 133 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   PHE B 135 " --> pdb=" O   ASN B 167 " (cutoff:3.500A)
      removed outlier: 7.826A  pdb=" N   PHE B 169 " --> pdb=" O   PHE B 135 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   LEU B 137 " --> pdb=" O   PHE B 169 " (cutoff:3.500A)
      removed outlier: 7.885A  pdb=" N   VAL B 171 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      removed outlier: 7.422A  pdb=" N   HIS B 139 " --> pdb=" O   VAL B 171 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   THR B 168 " --> pdb=" O   GLU B 200 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 56
      removed outlier: 3.690A  pdb=" N   LYS B  60 " --> pdb=" O   ALA B  56 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 272 through 273
      removed outlier: 3.664A  pdb=" N   THR B 314 " --> pdb=" O   ASN B 380 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 94
      removed outlier: 8.168A  pdb=" N   ILE A  93 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   PHE A  67 " --> pdb=" O   ILE A  93 " (cutoff:3.500A)
      removed outlier: 8.604A  pdb=" N   VAL A  66 " --> pdb=" O   CYS A   4 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   SER A   6 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 7.912A  pdb=" N   VAL A  68 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   HIS A   8 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 6.066A  pdb=" N   GLU A   3 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   GLY A 134 " --> pdb=" O   GLU A   3 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   SER A 140 " --> pdb=" O   VAL A   9 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   SER A 165 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   CYS A 200 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 53 through 55
    Processing sheet with id=AA6, first strand: chain 'A' and resid 269 through 273
      removed outlier: 4.237A  pdb=" N   ALA A 314 " --> pdb=" O   ASN A 380 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'K' and resid 50 through 51
      removed outlier: 3.705A  pdb=" N   ARG K  50 " --> pdb=" O   VAL K  11 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   ASN K  78 " --> pdb=" O   ARG K 295 " (cutoff:3.500A)
      removed outlier: 8.666A  pdb=" N   THR K 297 " --> pdb=" O   ASN K  78 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   THR K  80 " --> pdb=" O   THR K 297 " (cutoff:3.500A)
      removed outlier: 7.898A  pdb=" N   VAL K 299 " --> pdb=" O   THR K  80 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   GLY K  79 " --> pdb=" O   TYR K 228 " (cutoff:3.500A)
      removed outlier: 8.295A  pdb=" N   VAL K 230 " --> pdb=" O   GLY K  79 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ILE K  81 " --> pdb=" O   VAL K 230 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLU K 127 " --> pdb=" O   GLU K 215 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'K' and resid 84 through 85
      removed outlier: 6.890A  pdb=" N   ASN K  78 " --> pdb=" O   ARG K 295 " (cutoff:3.500A)
      removed outlier: 8.666A  pdb=" N   THR K 297 " --> pdb=" O   ASN K  78 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   THR K  80 " --> pdb=" O   THR K 297 " (cutoff:3.500A)
      removed outlier: 7.898A  pdb=" N   VAL K 299 " --> pdb=" O   THR K  80 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   GLY K  79 " --> pdb=" O   TYR K 228 " (cutoff:3.500A)
      removed outlier: 8.295A  pdb=" N   VAL K 230 " --> pdb=" O   GLY K  79 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ILE K  81 " --> pdb=" O   VAL K 230 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLU K 127 " --> pdb=" O   GLU K 215 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'K' and resid 32 through 34
      removed outlier: 3.737A  pdb=" N   THR K  38 " --> pdb=" O   GLN K  34 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'K' and resid 154 through 157
      removed outlier: 4.283A  pdb=" N   SER K 154 " --> pdb=" O   LYS K 166 " (cutoff:3.500A)

    447 hydrogen bonds defined for protein.
    1308 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: 1.67

  Time building geometry restraints manager: 1.14 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1589
        1.32 -     1.44: 2544
        1.44 -     1.56: 5309
        1.56 -     1.69: 17
        1.69 -     1.81: 94
  Bond restraints: 9553
  Sorted by residual:
  bond pdb=" N   ASP K 231 "
       pdb=" CA  ASP K 231 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.38e-02 5.25e+03 5.64e+00
  bond pdb=" N   HIS K 191 "
       pdb=" CA  HIS K 191 "
    ideal  model  delta    sigma   weight residual
    1.458  1.484 -0.027 1.25e-02 6.40e+03 4.63e+00
  bond pdb=" N   ARG K 190 "
       pdb=" CA  ARG K 190 "
    ideal  model  delta    sigma   weight residual
    1.454  1.480 -0.026 1.31e-02 5.83e+03 4.03e+00
  bond pdb=" CG  HIS K 191 "
       pdb=" CD2 HIS K 191 "
    ideal  model  delta    sigma   weight residual
    1.354  1.335  0.019 1.10e-02 8.26e+03 3.13e+00
  bond pdb=" C   ASP K 231 "
       pdb=" N   LEU K 232 "
    ideal  model  delta    sigma   weight residual
    1.331  1.314  0.017 1.41e-02 5.03e+03 1.43e+00
  ... (remaining 9548 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.31: 12812
        2.31 -     4.61: 125
        4.61 -     6.92: 16
        6.92 -     9.23: 4
        9.23 -    11.53: 3
  Bond angle restraints: 12960
  Sorted by residual:
  angle pdb=" CA  HIS K 191 "
        pdb=" CB  HIS K 191 "
        pdb=" CG  HIS K 191 "
      ideal   model   delta    sigma   weight residual
     113.80  118.36   -4.56 1.00e+00 1.00e+00 2.08e+01
  angle pdb=" C10 TA1 B 502 "
        pdb=" C18 TA1 B 502 "
        pdb=" C20 TA1 B 502 "
      ideal   model   delta    sigma   weight residual
     104.78  116.31  -11.53 3.00e+00 1.11e-01 1.48e+01
  angle pdb=" CA  ASP K 231 "
        pdb=" CB  ASP K 231 "
        pdb=" CG  ASP K 231 "
      ideal   model   delta    sigma   weight residual
     112.60  115.98   -3.38 1.00e+00 1.00e+00 1.14e+01
  angle pdb=" C14 TA1 B 502 "
        pdb=" C11 TA1 B 502 "
        pdb=" O04 TA1 B 502 "
      ideal   model   delta    sigma   weight residual
     119.42  109.44    9.98 3.00e+00 1.11e-01 1.11e+01
  angle pdb=" C10 TA1 B 502 "
        pdb=" C18 TA1 B 502 "
        pdb=" C17 TA1 B 502 "
      ideal   model   delta    sigma   weight residual
     114.79  105.44    9.35 3.00e+00 1.11e-01 9.71e+00
  ... (remaining 12955 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.86: 5652
       33.86 -    67.72: 108
       67.72 -   101.57: 7
      101.57 -   135.43: 17
      135.43 -   169.29: 5
  Dihedral angle restraints: 5789
    sinusoidal: 2398
      harmonic: 3391
  Sorted by residual:
  dihedral pdb=" C5' GTP A 501 "
           pdb=" O5' GTP A 501 "
           pdb=" PA  GTP A 501 "
           pdb=" O3A GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -121.44 -169.29     1      2.00e+01 2.50e-03 4.76e+01
  dihedral pdb=" C8  GTP A 501 "
           pdb=" C1' GTP A 501 "
           pdb=" N9  GTP A 501 "
           pdb=" O4' GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -52.74  157.33     1      2.00e+01 2.50e-03 4.61e+01
  dihedral pdb=" O5' GTP A 501 "
           pdb=" O3A GTP A 501 "
           pdb=" PA  GTP A 501 "
           pdb=" PB  GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     274.12  135.38  138.74     1      2.00e+01 2.50e-03 4.20e+01
  ... (remaining 5786 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 996
       0.039 -    0.079: 313
       0.079 -    0.118: 103
       0.118 -    0.158: 12
       0.158 -    0.197: 2
  Chirality restraints: 1426
  Sorted by residual:
  chirality pdb=" C3' GTP A 501 "
            pdb=" C2' GTP A 501 "
            pdb=" C4' GTP A 501 "
            pdb=" O3' GTP A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.67    0.20 2.00e-01 2.50e+01 9.73e-01
  chirality pdb=" C21 TA1 B 502 "
            pdb=" C20 TA1 B 502 "
            pdb=" C24 TA1 B 502 "
            pdb=" O09 TA1 B 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.30   -2.49    0.19 2.00e-01 2.50e+01 8.88e-01
  chirality pdb=" C3' GDP B 501 "
            pdb=" C4' GDP B 501 "
            pdb=" O3' GDP B 501 "
            pdb=" C2' GDP B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.66    0.15 2.00e-01 2.50e+01 5.33e-01
  ... (remaining 1423 not shown)

  Planarity restraints: 1673
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  31 "   -0.040 5.00e-02 4.00e+02   6.12e-02 5.99e+00
        pdb=" N   PRO B  32 "    0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO B  32 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B  32 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 324 "    0.032 5.00e-02 4.00e+02   4.88e-02 3.81e+00
        pdb=" N   PRO A 325 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A 325 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 325 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN K 189 "    0.008 2.00e-02 2.50e+03   1.61e-02 2.58e+00
        pdb=" C   ASN K 189 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   ASN K 189 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ARG K 190 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1670 not shown)

  Histogram of nonbonded interaction distances:
        1.97 -     2.56: 60
        2.56 -     3.14: 7172
        3.14 -     3.73: 13658
        3.73 -     4.31: 19037
        4.31 -     4.90: 33313
  Nonbonded interactions: 73240
  Sorted by model distance:
  nonbonded pdb=" O3G GTP A 501 "
            pdb="MG    MG A 502 "
     model   vdw
     1.971 2.170
  nonbonded pdb=" OD2 ASP B 427 "
            pdb=" NH1 ARG K 278 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" NH1 ARG A 264 "
            pdb=" OD2 ASP A 431 "
     model   vdw
     2.277 3.120
  nonbonded pdb=" NH2 ARG A 215 "
            pdb=" O   ALA A 299 "
     model   vdw
     2.277 3.120
  nonbonded pdb=" O   GLY A 142 "
            pdb=" ND2 ASN A 186 "
     model   vdw
     2.293 3.120
  ... (remaining 73235 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=0.50 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:             1.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.940
  Find NCS groups from input model:        0.030
  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:             0.010
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
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      :  0.009   0.796   9554  Z= 0.827
  Angle     :  0.587  11.535  12960  Z= 0.285
  Chirality :  0.043   0.197   1426
  Planarity :  0.004   0.061   1673
  Dihedral  : 16.280 169.290   3611
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.11 %
    Favored  : 90.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.58 (0.25), residues: 1158
  helix:  1.68 (0.25), residues: 468
  sheet:  0.98 (0.36), residues: 210
  loop : -1.24 (0.27), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  64 
 TYR   0.008   0.001   TYR A 312 
 PHE   0.008   0.001   PHE A 255 
 TRP   0.015   0.001   TRP A  21 
 HIS   0.008   0.001   HIS K 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 9553)
  covalent geometry    : angle       0.58654 (12960)
  hydrogen bonds       : bond        0.17318 (  426)
  hydrogen bonds       : angle       5.60994 ( 1308)
  Misc. bond           : bond        0.79567 (    1)

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   60 LYS cc_start: 0.8824 (tttm) cc_final: 0.8473 (ttpt)
REVERT: B   75 MET cc_start: 0.9010 (mmt) cc_final: 0.8664 (mmt)
REVERT: B  116 ASP cc_start: 0.8735 (m-30) cc_final: 0.8438 (m-30)
REVERT: B  215 ARG cc_start: 0.7970 (ttp-110) cc_final: 0.7728 (ttp-110)
REVERT: B  282 GLN cc_start: 0.8815 (mp10) cc_final: 0.8124 (mp10)
REVERT: A  211 ASP cc_start: 0.8743 (t0) cc_final: 0.8386 (t0)
REVERT: A  280 LYS cc_start: 0.9044 (mtpt) cc_final: 0.8084 (mmtt)
REVERT: A  425 MET cc_start: 0.9028 (mmm) cc_final: 0.8579 (tpp)
REVERT: A  429 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8044 (mt-10)
REVERT: K   72 ASP cc_start: 0.8633 (m-30) cc_final: 0.8429 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 243
  average time/residue: 0.1102
  time to fit residues: 35.2276
Evaluate side-chains
  141 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:   10.0000
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    3.9788

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

Flipped N/Q/H residues before XYZ refinement:
B 167 ASN
B 434 GLN
A 226 ASN
A 249 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.081288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.066619 restraints weight = 18866.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.069199 restraints weight = 9131.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.070950 restraints weight = 5656.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.072108 restraints weight = 4041.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.072960 restraints weight = 3186.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2786
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2786 r_free = 0.2786    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2786 r_free = 0.2786    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2786
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   9554  Z= 0.255
  Angle     :  0.681  11.716  12960  Z= 0.335
  Chirality :  0.048   0.331   1426
  Planarity :  0.005   0.062   1673
  Dihedral  : 13.589 167.329   1413
  Min Nonbonded Distance : 1.848

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 12.57 %
    Favored  : 84.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.25), residues: 1158
  helix:  1.51 (0.24), residues: 479
  sheet:  1.10 (0.36), residues: 199
  loop : -1.11 (0.27), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 243 
 TYR   0.016   0.001   TYR K 118 
 PHE   0.011   0.001   PHE K 128 
 TRP   0.016   0.002   TRP A  21 
 HIS   0.005   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00593 ( 9553)
  covalent geometry    : angle       0.68083 (12960)
  hydrogen bonds       : bond        0.05905 (  426)
  hydrogen bonds       : angle       4.38965 ( 1308)
  Misc. bond           : bond        0.00423 (    1)

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 143
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  110 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8466 (mp0)
REVERT: B  166 MET cc_start: 0.8097 (tpp) cc_final: 0.7745 (mtp)
REVERT: A   26 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9110 (mm)
REVERT: A  168 GLU cc_start: 0.6947 (mp0) cc_final: 0.6348 (mp0)
REVERT: A  211 ASP cc_start: 0.8576 (t0) cc_final: 0.8122 (t0)
REVERT: A  280 LYS cc_start: 0.9244 (mtpt) cc_final: 0.8424 (mmtt)
REVERT: A  286 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.8393 (mt)
REVERT: A  377 MET cc_start: 0.8296 (ttp) cc_final: 0.7986 (ttp)
REVERT: A  381 THR cc_start: 0.9466 (p) cc_final: 0.8757 (t)
REVERT: A  425 MET cc_start: 0.8948 (mmm) cc_final: 0.8399 (tpp)
REVERT: A  432 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.6607 (t80)
REVERT: K   72 ASP cc_start: 0.8435 (m-30) cc_final: 0.8089 (m-30)
REVERT: K  114 ASP cc_start: 0.7969 (m-30) cc_final: 0.7712 (m-30)
REVERT: K  136 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8242 (pt0)
  outliers start: 25
  outliers final: 14
  residues processed: 163
  average time/residue: 0.1045
  time to fit residues: 23.2168
Evaluate side-chains
  137 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  167 ASN
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  374 SER
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  432 TYR
Chi-restraints excluded: chain K residue    9 ILE
Chi-restraints excluded: chain K residue   73 VAL
Chi-restraints excluded: chain K residue  136 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0000
   chunk 112 optimal weight:    7.9990
   chunk 50 optimal weight:    0.3980
   chunk 47 optimal weight:    0.9990
   chunk 30 optimal weight:   10.0000
   chunk 110 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 90 optimal weight:    7.9990
   chunk 25 optimal weight:    3.9990
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.8188

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

Flipped N/Q/H residues before XYZ refinement:
B 167 ASN
A 249 ASN
K  34 GLN
K  63 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.083673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2721 r_free = 0.2721 target = 0.069047 restraints weight = 18389.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.071642 restraints weight = 8921.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.073362 restraints weight = 5541.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.074586 restraints weight = 3981.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.075448 restraints weight = 3113.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2838
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2838 r_free = 0.2838    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2838 r_free = 0.2838    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2838
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9554  Z= 0.109
  Angle     :  0.564   9.563  12960  Z= 0.275
  Chirality :  0.044   0.380   1426
  Planarity :  0.004   0.062   1673
  Dihedral  : 10.791 163.354   1413
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 12.77 %
    Favored  : 84.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.80 (0.25), residues: 1158
  helix:  1.66 (0.24), residues: 486
  sheet:  1.17 (0.36), residues: 204
  loop : -1.00 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 215 
 TYR   0.017   0.001   TYR K 118 
 PHE   0.009   0.001   PHE A 255 
 TRP   0.013   0.001   TRP A  21 
 HIS   0.002   0.001   HIS K 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 9553)
  covalent geometry    : angle       0.56374 (12960)
  hydrogen bonds       : bond        0.04078 (  426)
  hydrogen bonds       : angle       4.05778 ( 1308)
  Misc. bond           : bond        0.00225 (    1)

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 134
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   75 MET cc_start: 0.8917 (mmt) cc_final: 0.8545 (mmt)
REVERT: A   26 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8949 (mm)
REVERT: A  168 GLU cc_start: 0.7013 (mp0) cc_final: 0.6501 (mp0)
REVERT: A  211 ASP cc_start: 0.8608 (t0) cc_final: 0.8134 (t0)
REVERT: A  280 LYS cc_start: 0.9289 (mtpt) cc_final: 0.8362 (mmtt)
REVERT: A  425 MET cc_start: 0.8869 (mmm) cc_final: 0.8514 (tpp)
REVERT: A  432 TYR cc_start: 0.8251 (OUTLIER) cc_final: 0.6803 (t80)
REVERT: K   72 ASP cc_start: 0.8409 (m-30) cc_final: 0.8076 (m-30)
REVERT: K  136 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8148 (pt0)
REVERT: K  220 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7866 (tp30)
REVERT: K  311 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8073 (pm20)
  outliers start: 26
  outliers final: 12
  residues processed: 150
  average time/residue: 0.0923
  time to fit residues: 19.2776
Evaluate side-chains
  135 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  174 SER
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  374 SER
Chi-restraints excluded: chain B residue  425 MET
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  203 MET
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  432 TYR
Chi-restraints excluded: chain K residue  136 GLU
Chi-restraints excluded: chain K residue  219 THR
Chi-restraints excluded: chain K residue  220 GLU
Chi-restraints excluded: chain K residue  311 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 47 optimal weight:    9.9990
   chunk 99 optimal weight:    7.9990
   chunk 100 optimal weight:    3.9990
   chunk 77 optimal weight:    5.9990
   chunk 3 optimal weight:    0.2980
   chunk 9 optimal weight:    0.9990
   chunk 14 optimal weight:   10.0000
   chunk 8 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 71 optimal weight:    7.9990
   overall best weight:    1.2386

-------------------------------------------------------------------------------
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 = 0.2988 r_free = 0.2988 target = 0.083268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2714 r_free = 0.2714 target = 0.068612 restraints weight = 18578.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.071219 restraints weight = 8969.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.073007 restraints weight = 5571.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.074238 restraints weight = 3954.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.075071 restraints weight = 3071.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2839
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2839 r_free = 0.2839    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2839 r_free = 0.2839    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2839
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.2343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9554  Z= 0.112
  Angle     :  0.536   7.644  12960  Z= 0.262
  Chirality :  0.044   0.291   1426
  Planarity :  0.004   0.060   1673
  Dihedral  :  9.950 157.083   1413
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 13.27 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.96 (0.25), residues: 1158
  helix:  1.79 (0.25), residues: 481
  sheet:  1.47 (0.37), residues: 199
  loop : -0.97 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 215 
 TYR   0.013   0.001   TYR K 118 
 PHE   0.009   0.001   PHE B 377 
 TRP   0.012   0.001   TRP A  21 
 HIS   0.002   0.000   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 9553)
  covalent geometry    : angle       0.53557 (12960)
  hydrogen bonds       : bond        0.03943 (  426)
  hydrogen bonds       : angle       3.91569 ( 1308)
  Misc. bond           : bond        0.00188 (    1)

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 119
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  308 ARG cc_start: 0.7634 (mtt180) cc_final: 0.7433 (mtt-85)
REVERT: A   26 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8949 (mm)
REVERT: A  168 GLU cc_start: 0.6994 (mp0) cc_final: 0.6653 (mp0)
REVERT: A  211 ASP cc_start: 0.8603 (t0) cc_final: 0.8102 (t0)
REVERT: A  280 LYS cc_start: 0.9359 (mtpt) cc_final: 0.8466 (mmtt)
REVERT: A  425 MET cc_start: 0.8939 (mmm) cc_final: 0.8295 (tpp)
REVERT: A  432 TYR cc_start: 0.8195 (OUTLIER) cc_final: 0.6796 (t80)
REVERT: K  136 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8170 (pt0)
REVERT: K  311 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7842 (pm20)
  outliers start: 29
  outliers final: 18
  residues processed: 138
  average time/residue: 0.0971
  time to fit residues: 18.6247
Evaluate side-chains
  135 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  174 SER
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  374 SER
Chi-restraints excluded: chain B residue  425 MET
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  203 MET
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  432 TYR
Chi-restraints excluded: chain K residue   73 VAL
Chi-restraints excluded: chain K residue  136 GLU
Chi-restraints excluded: chain K residue  219 THR
Chi-restraints excluded: chain K residue  286 LEU
Chi-restraints excluded: chain K residue  311 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 89 optimal weight:    0.4980
   chunk 90 optimal weight:    4.9990
   chunk 32 optimal weight:    8.9990
   chunk 1 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   chunk 87 optimal weight:    6.9990
   chunk 35 optimal weight:    6.9990
   chunk 105 optimal weight:    7.9990
   chunk 91 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   overall best weight:    3.2988

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

Flipped N/Q/H residues before XYZ refinement:
B 426 ASN
** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.080347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.065911 restraints weight = 18994.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.068470 restraints weight = 9188.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.070198 restraints weight = 5686.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.071348 restraints weight = 4059.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.072175 restraints weight = 3183.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2783
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2783 r_free = 0.2783    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2783 r_free = 0.2783    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2783
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.2435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   9554  Z= 0.208
  Angle     :  0.592   7.507  12960  Z= 0.294
  Chirality :  0.046   0.268   1426
  Planarity :  0.004   0.060   1673
  Dihedral  :  9.862 151.650   1413
  Min Nonbonded Distance : 1.877

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 14.16 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.82 (0.25), residues: 1158
  helix:  1.68 (0.24), residues: 482
  sheet:  1.30 (0.36), residues: 204
  loop : -1.03 (0.27), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K 321 
 TYR   0.015   0.001   TYR K 118 
 PHE   0.012   0.001   PHE B 377 
 TRP   0.012   0.001   TRP A  21 
 HIS   0.005   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 ( 9553)
  covalent geometry    : angle       0.59184 (12960)
  hydrogen bonds       : bond        0.05243 (  426)
  hydrogen bonds       : angle       4.06156 ( 1308)
  Misc. bond           : bond        0.00378 (    1)

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 112
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  159 GLU cc_start: 0.7716 (pt0) cc_final: 0.7344 (pt0)
REVERT: B  308 ARG cc_start: 0.7650 (mtt180) cc_final: 0.7449 (mtt-85)
REVERT: A   26 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9053 (mm)
REVERT: A  211 ASP cc_start: 0.8629 (t0) cc_final: 0.8102 (t0)
REVERT: A  280 LYS cc_start: 0.9374 (mtpt) cc_final: 0.8366 (mmtt)
REVERT: A  425 MET cc_start: 0.8978 (mmm) cc_final: 0.8292 (tpp)
REVERT: A  432 TYR cc_start: 0.8250 (OUTLIER) cc_final: 0.6784 (t80)
REVERT: K  120 TYR cc_start: 0.7906 (m-80) cc_final: 0.7667 (m-80)
REVERT: K  136 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8172 (pt0)
REVERT: K  311 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8143 (pm20)
  outliers start: 32
  outliers final: 24
  residues processed: 135
  average time/residue: 0.0978
  time to fit residues: 18.2593
Evaluate side-chains
  136 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  374 SER
Chi-restraints excluded: chain B residue  425 MET
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   36 MET
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  192 HIS
Chi-restraints excluded: chain A residue  203 MET
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  432 TYR
Chi-restraints excluded: chain K residue   73 VAL
Chi-restraints excluded: chain K residue  136 GLU
Chi-restraints excluded: chain K residue  219 THR
Chi-restraints excluded: chain K residue  286 LEU
Chi-restraints excluded: chain K residue  311 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 67 optimal weight:    6.9990
   chunk 92 optimal weight:    6.9990
   chunk 2 optimal weight:    4.9990
   chunk 30 optimal weight:    9.9990
   chunk 0 optimal weight:    8.9990
   chunk 88 optimal weight:    8.9990
   chunk 51 optimal weight:    0.9990
   chunk 79 optimal weight:    4.9990
   chunk 85 optimal weight:    5.9990
   chunk 84 optimal weight:    4.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.078937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2638 r_free = 0.2638 target = 0.064604 restraints weight = 19101.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2687 r_free = 0.2687 target = 0.067086 restraints weight = 9299.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.068776 restraints weight = 5782.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.069917 restraints weight = 4154.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.070699 restraints weight = 3266.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2750
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2750 r_free = 0.2750    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2750 r_free = 0.2750    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2750
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.2606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   9554  Z= 0.269
  Angle     :  0.640   7.455  12960  Z= 0.322
  Chirality :  0.047   0.259   1426
  Planarity :  0.005   0.060   1673
  Dihedral  :  9.880 149.958   1413
  Min Nonbonded Distance : 1.855

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 14.85 %
    Favored  : 82.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.25), residues: 1158
  helix:  1.43 (0.24), residues: 482
  sheet:  1.09 (0.36), residues: 214
  loop : -1.20 (0.27), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 215 
 TYR   0.016   0.001   TYR K 118 
 PHE   0.015   0.002   PHE B 377 
 TRP   0.013   0.002   TRP A  21 
 HIS   0.005   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00624 ( 9553)
  covalent geometry    : angle       0.63970 (12960)
  hydrogen bonds       : bond        0.05917 (  426)
  hydrogen bonds       : angle       4.27331 ( 1308)
  Misc. bond           : bond        0.00438 (    1)

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 108
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  119 LEU cc_start: 0.9434 (mt) cc_final: 0.9204 (mt)
REVERT: B  308 ARG cc_start: 0.7691 (mtt180) cc_final: 0.7444 (mtt-85)
REVERT: B  369 ARG cc_start: 0.8353 (ttm170) cc_final: 0.8102 (mmm160)
REVERT: A   26 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9118 (mm)
REVERT: A  211 ASP cc_start: 0.8638 (t0) cc_final: 0.8098 (t0)
REVERT: A  280 LYS cc_start: 0.9373 (mtpt) cc_final: 0.8375 (mmtt)
REVERT: A  432 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.6842 (t80)
REVERT: K  120 TYR cc_start: 0.7975 (m-80) cc_final: 0.7695 (m-80)
REVERT: K  136 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8167 (pt0)
  outliers start: 31
  outliers final: 23
  residues processed: 132
  average time/residue: 0.0948
  time to fit residues: 17.3747
Evaluate side-chains
  132 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 106
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  374 SER
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   94 THR
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  192 HIS
Chi-restraints excluded: chain A residue  203 MET
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  432 TYR
Chi-restraints excluded: chain K residue   73 VAL
Chi-restraints excluded: chain K residue  136 GLU
Chi-restraints excluded: chain K residue  219 THR
Chi-restraints excluded: chain K residue  286 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   chunk 97 optimal weight:    3.9990
   chunk 72 optimal weight:    7.9990
   chunk 30 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9990
   chunk 95 optimal weight:    9.9990
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.082794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.068531 restraints weight = 18831.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.071132 restraints weight = 9031.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.072935 restraints weight = 5537.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.074149 restraints weight = 3900.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.074962 restraints weight = 3025.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2836
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2836 r_free = 0.2836    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2835 r_free = 0.2835    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2835
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.2665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9554  Z= 0.107
  Angle     :  0.545   8.394  12960  Z= 0.269
  Chirality :  0.044   0.209   1426
  Planarity :  0.004   0.065   1673
  Dihedral  :  9.384 147.732   1413
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 16.34 %
    Favored  : 81.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.79 (0.25), residues: 1158
  helix:  1.66 (0.24), residues: 482
  sheet:  1.20 (0.36), residues: 204
  loop : -1.01 (0.27), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 215 
 TYR   0.008   0.001   TYR A 108 
 PHE   0.010   0.001   PHE B 377 
 TRP   0.015   0.001   TRP A  21 
 HIS   0.002   0.001   HIS B 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 9553)
  covalent geometry    : angle       0.54547 (12960)
  hydrogen bonds       : bond        0.03799 (  426)
  hydrogen bonds       : angle       3.95872 ( 1308)
  Misc. bond           : bond        0.00184 (    1)

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  166 MET cc_start: 0.8225 (tpp) cc_final: 0.7695 (mtp)
REVERT: B  308 ARG cc_start: 0.7691 (mtt180) cc_final: 0.7461 (mtt-85)
REVERT: A   26 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8940 (mm)
REVERT: A  211 ASP cc_start: 0.8629 (t0) cc_final: 0.7822 (t0)
REVERT: A  215 ARG cc_start: 0.7977 (ttm110) cc_final: 0.7203 (ttm110)
REVERT: A  280 LYS cc_start: 0.9329 (mtpt) cc_final: 0.8372 (mmtt)
REVERT: A  425 MET cc_start: 0.8918 (mmm) cc_final: 0.8386 (tpp)
REVERT: A  432 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.6800 (t80)
REVERT: K  136 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8111 (pt0)
REVERT: K  311 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7834 (pm20)
  outliers start: 19
  outliers final: 12
  residues processed: 135
  average time/residue: 0.0949
  time to fit residues: 17.7204
Evaluate side-chains
  123 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  174 SER
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  374 SER
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue  203 MET
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  432 TYR
Chi-restraints excluded: chain K residue  136 GLU
Chi-restraints excluded: chain K residue  219 THR
Chi-restraints excluded: chain K residue  311 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 106 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 29 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 40 optimal weight:    6.9990
   chunk 71 optimal weight:    0.2980
   chunk 86 optimal weight:   10.0000
   chunk 102 optimal weight:    0.0170
   chunk 54 optimal weight:    8.9990
   overall best weight:    1.6622

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

Flipped N/Q/H residues before XYZ refinement:
** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.081641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2690 r_free = 0.2690 target = 0.067195 restraints weight = 18918.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2739 r_free = 0.2739 target = 0.069779 restraints weight = 9119.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.071531 restraints weight = 5627.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.072675 restraints weight = 4005.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.073533 restraints weight = 3145.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2813
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2813 r_free = 0.2813    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2813 r_free = 0.2813    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2813
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
moved from start:          0.2703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9554  Z= 0.131
  Angle     :  0.574   8.963  12960  Z= 0.283
  Chirality :  0.044   0.221   1426
  Planarity :  0.004   0.061   1673
  Dihedral  :  9.191 144.697   1413
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 16.63 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.96 (0.25), residues: 1158
  helix:  1.75 (0.25), residues: 482
  sheet:  1.49 (0.36), residues: 202
  loop : -0.96 (0.27), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 215 
 TYR   0.009   0.001   TYR K 277 
 PHE   0.011   0.001   PHE B 377 
 TRP   0.013   0.001   TRP A  21 
 HIS   0.003   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 9553)
  covalent geometry    : angle       0.57375 (12960)
  hydrogen bonds       : bond        0.04197 (  426)
  hydrogen bonds       : angle       3.94911 ( 1308)
  Misc. bond           : bond        0.00251 (    1)

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 109
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  308 ARG cc_start: 0.7685 (mtt180) cc_final: 0.7456 (mtt-85)
REVERT: A   26 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8963 (mm)
REVERT: A  211 ASP cc_start: 0.8623 (t0) cc_final: 0.8068 (t0)
REVERT: A  280 LYS cc_start: 0.9337 (mtpt) cc_final: 0.8393 (mmtt)
REVERT: A  432 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.6814 (t80)
REVERT: K  136 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8123 (pt0)
REVERT: K  311 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7848 (pm20)
  outliers start: 25
  outliers final: 16
  residues processed: 130
  average time/residue: 0.0956
  time to fit residues: 17.1695
Evaluate side-chains
  127 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  174 SER
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  374 SER
Chi-restraints excluded: chain B residue  425 MET
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   94 THR
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  203 MET
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  432 TYR
Chi-restraints excluded: chain K residue  136 GLU
Chi-restraints excluded: chain K residue  219 THR
Chi-restraints excluded: chain K residue  311 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 87 optimal weight:    0.6980
   chunk 98 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 63 optimal weight:    0.0270
   chunk 65 optimal weight:    9.9990
   chunk 103 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 28 optimal weight:    0.6980
   chunk 76 optimal weight:   10.0000
   chunk 35 optimal weight:    0.3980
   chunk 10 optimal weight:    8.9990
   overall best weight:    0.9640

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

Flipped N/Q/H residues before XYZ refinement:
B 349 ASN
A 128 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.083355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.068864 restraints weight = 18530.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.071492 restraints weight = 8958.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.073180 restraints weight = 5519.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.074430 restraints weight = 3972.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.075247 restraints weight = 3092.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2844
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2844 r_free = 0.2844    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2844 r_free = 0.2844    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2844
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.2830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   9554  Z= 0.106
  Angle     :  0.560   9.713  12960  Z= 0.274
  Chirality :  0.044   0.203   1426
  Planarity :  0.004   0.060   1673
  Dihedral  :  8.919 142.120   1413
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 17.33 %
    Favored  : 80.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  1.02 (0.25), residues: 1158
  helix:  1.80 (0.25), residues: 482
  sheet:  1.42 (0.35), residues: 213
  loop : -0.92 (0.28), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 215 
 TYR   0.008   0.001   TYR K 277 
 PHE   0.011   0.001   PHE B 377 
 TRP   0.013   0.001   TRP A  21 
 HIS   0.002   0.000   HIS B 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 9553)
  covalent geometry    : angle       0.56008 (12960)
  hydrogen bonds       : bond        0.03637 (  426)
  hydrogen bonds       : angle       3.88281 ( 1308)
  Misc. bond           : bond        0.00178 (    1)

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  308 ARG cc_start: 0.7716 (mtt180) cc_final: 0.7486 (mtt-85)
REVERT: A   26 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8917 (mm)
REVERT: A  211 ASP cc_start: 0.8626 (t0) cc_final: 0.7659 (t0)
REVERT: A  215 ARG cc_start: 0.7945 (ttm110) cc_final: 0.6984 (ttm110)
REVERT: A  280 LYS cc_start: 0.9308 (mtpt) cc_final: 0.8347 (mmtt)
REVERT: A  432 TYR cc_start: 0.8247 (OUTLIER) cc_final: 0.7110 (t80)
REVERT: K  136 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8154 (pt0)
REVERT: K  311 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8109 (pm20)
  outliers start: 22
  outliers final: 16
  residues processed: 129
  average time/residue: 0.0984
  time to fit residues: 17.5207
Evaluate side-chains
  125 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  174 SER
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  374 SER
Chi-restraints excluded: chain B residue  425 MET
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   94 THR
Chi-restraints excluded: chain A residue  128 GLN
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  203 MET
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  432 TYR
Chi-restraints excluded: chain K residue  136 GLU
Chi-restraints excluded: chain K residue  219 THR
Chi-restraints excluded: chain K residue  311 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 39 optimal weight:    4.9990
   chunk 99 optimal weight:    4.9990
   chunk 45 optimal weight:    7.9990
   chunk 71 optimal weight:    6.9990
   chunk 80 optimal weight:    0.1980
   chunk 109 optimal weight:    0.9980
   chunk 58 optimal weight:    0.0370
   chunk 37 optimal weight:    4.9990
   chunk 36 optimal weight:    6.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    2.0462

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

Flipped N/Q/H residues before XYZ refinement:
A 128 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.081924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.067535 restraints weight = 19122.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.070148 restraints weight = 9187.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.071888 restraints weight = 5623.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.073088 restraints weight = 4004.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.073932 restraints weight = 3115.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2818
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2818 r_free = 0.2818    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2818 r_free = 0.2818    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2818
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.2803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9554  Z= 0.145
  Angle     :  0.573   9.814  12960  Z= 0.282
  Chirality :  0.044   0.212   1426
  Planarity :  0.004   0.059   1673
  Dihedral  :  8.911 141.865   1413
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 17.62 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  1.01 (0.25), residues: 1158
  helix:  1.80 (0.24), residues: 482
  sheet:  1.54 (0.36), residues: 202
  loop : -0.95 (0.27), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 215 
 TYR   0.009   0.001   TYR K 277 
 PHE   0.010   0.001   PHE B 377 
 TRP   0.011   0.001   TRP A  21 
 HIS   0.003   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 9553)
  covalent geometry    : angle       0.57336 (12960)
  hydrogen bonds       : bond        0.04159 (  426)
  hydrogen bonds       : angle       3.92843 ( 1308)
  Misc. bond           : bond        0.00261 (    1)

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

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

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2316 Ramachandran restraints generated.
    1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  308 ARG cc_start: 0.7699 (mtt180) cc_final: 0.7470 (mtt-85)
REVERT: A   26 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8968 (mm)
REVERT: A  211 ASP cc_start: 0.8630 (t0) cc_final: 0.8074 (t0)
REVERT: A  280 LYS cc_start: 0.9336 (mtpt) cc_final: 0.8350 (mmtt)
REVERT: A  432 TYR cc_start: 0.8281 (OUTLIER) cc_final: 0.7033 (t80)
REVERT: K  136 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8163 (pt0)
REVERT: K  311 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7945 (pm20)
  outliers start: 20
  outliers final: 16
  residues processed: 120
  average time/residue: 0.0990
  time to fit residues: 16.1679
Evaluate side-chains
  124 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  174 SER
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  374 SER
Chi-restraints excluded: chain B residue  425 MET
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   94 THR
Chi-restraints excluded: chain A residue  128 GLN
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  203 MET
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  432 TYR
Chi-restraints excluded: chain K residue  136 GLU
Chi-restraints excluded: chain K residue  219 THR
Chi-restraints excluded: chain K residue  311 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 111 optimal weight:    4.9990
   chunk 46 optimal weight:   10.0000
   chunk 106 optimal weight:    2.9990
   chunk 35 optimal weight:    8.9990
   chunk 103 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9990
   chunk 34 optimal weight:    0.3980
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
A 128 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.082939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.068429 restraints weight = 18351.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.071042 restraints weight = 8941.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.072818 restraints weight = 5522.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.073984 restraints weight = 3931.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.074847 restraints weight = 3084.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2840
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2840 r_free = 0.2840    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2840 r_free = 0.2840    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2840
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.2869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9554  Z= 0.109
  Angle     :  0.561   9.398  12960  Z= 0.275
  Chirality :  0.044   0.201   1426
  Planarity :  0.004   0.060   1673
  Dihedral  :  8.785 141.857   1413
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 17.23 %
    Favored  : 80.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  1.05 (0.25), residues: 1158
  helix:  1.84 (0.24), residues: 482
  sheet:  1.52 (0.36), residues: 208
  loop : -0.94 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 215 
 TYR   0.009   0.001   TYR K 277 
 PHE   0.009   0.001   PHE B 377 
 TRP   0.012   0.001   TRP A  21 
 HIS   0.002   0.000   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 9553)
  covalent geometry    : angle       0.56075 (12960)
  hydrogen bonds       : bond        0.03741 (  426)
  hydrogen bonds       : angle       3.89362 ( 1308)
  Misc. bond           : bond        0.00188 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1396.82 seconds
wall clock time: 24 minutes 55.34 seconds (1495.34 seconds total)