Starting phenix.real_space_refine
on Thu Mar 13 23:13:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rik_19188/03_2025/8rik_19188.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rik_19188/03_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_19188/03_2025/8rik_19188.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rik_19188/03_2025/8rik_19188.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rik_19188/03_2025/8rik_19188.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rik_19188/03_2025/8rik_19188.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.58, per 1000 atoms: 0.60
  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: 2.53
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.98
  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: 2.51

  Time building geometry restraints manager: 2.74 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:             0.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.610
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.450
-------------------------------------------------------------------------------
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      :  0.003   0.033   9553  Z= 0.206
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  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
 TRP   0.015   0.001   TRP A  21 
 HIS   0.008   0.001   HIS K 191 
 PHE   0.008   0.001   PHE A 255 
 TYR   0.008   0.001   TYR A 312 
 ARG   0.002   0.000   ARG B  64 

*********************** 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  : 1.102 
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  239 THR cc_start: 0.9362 (m) cc_final: 0.9162 (p)
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: 0.8045 (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: 0.2791
  time to fit residues: 89.1237
Evaluate side-chains
  142 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 1.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    7.9990
   chunk 87 optimal weight:    0.9980
   chunk 48 optimal weight:    0.0470
   chunk 29 optimal weight:    0.0470
   chunk 58 optimal weight:    8.9990
   chunk 46 optimal weight:    9.9990
   chunk 90 optimal weight:    8.9990
   chunk 34 optimal weight:    3.9990
   chunk 54 optimal weight:    9.9990
   chunk 67 optimal weight:    8.9990
   chunk 104 optimal weight:    5.9990
   overall best weight:    2.2180

-------------------------------------------------------------------------------
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
K  34 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.083724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.069111 restraints weight = 18533.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2764 r_free = 0.2764 target = 0.071786 restraints weight = 8926.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.073566 restraints weight = 5478.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2796
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2796 r_free = 0.2796    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 = 0.2796 r_free = 0.2796    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2796
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.1667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9553  Z= 0.247
  Angle     :  0.622  11.831  12960  Z= 0.303
  Chirality :  0.045   0.268   1426
  Planarity :  0.004   0.062   1673
  Dihedral  : 14.369 168.290   1413
  Min Nonbonded Distance : 1.897

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 12.48 %
    Favored  : 85.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.25), residues: 1158
  helix:  1.70 (0.25), residues: 480
  sheet:  1.18 (0.36), residues: 205
  loop : -1.11 (0.27), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  21 
 HIS   0.003   0.001   HIS A 139 
 PHE   0.009   0.001   PHE K 128 
 TYR   0.015   0.001   TYR K 118 
 ARG   0.008   0.000   ARG B 243 

*********************** 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
  172 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 152
  time to evaluate  : 1.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   75 MET cc_start: 0.8967 (mmt) cc_final: 0.8594 (mmt)
REVERT: B  308 ARG cc_start: 0.7535 (mtt-85) cc_final: 0.7223 (mtt-85)
REVERT: A   26 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9019 (mm)
REVERT: A  128 GLN cc_start: 0.8328 (tt0) cc_final: 0.8055 (tm-30)
REVERT: A  211 ASP cc_start: 0.8606 (t0) cc_final: 0.8176 (t0)
REVERT: A  239 THR cc_start: 0.9213 (m) cc_final: 0.8908 (p)
REVERT: A  280 LYS cc_start: 0.9129 (mtpt) cc_final: 0.8112 (mmtt)
REVERT: A  425 MET cc_start: 0.8857 (mmm) cc_final: 0.8362 (tpp)
REVERT: A  432 TYR cc_start: 0.8169 (OUTLIER) cc_final: 0.6574 (t80)
REVERT: K   72 ASP cc_start: 0.8436 (m-30) cc_final: 0.8123 (m-30)
REVERT: K  136 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8334 (pt0)
  outliers start: 20
  outliers final: 10
  residues processed: 166
  average time/residue: 0.2415
  time to fit residues: 54.4394
Evaluate side-chains
  142 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 129
  time to evaluate  : 1.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  429 VAL
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue  159 VAL
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
Chi-restraints excluded: chain K residue  219 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 90 optimal weight:    8.9990
   chunk 110 optimal weight:    5.9990
   chunk 73 optimal weight:    0.8980
   chunk 2 optimal weight:    5.9990
   chunk 88 optimal weight:    5.9990
   chunk 30 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 249 ASN
K  63 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.080937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.066386 restraints weight = 18933.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.068954 restraints weight = 9157.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.070713 restraints weight = 5659.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2748
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2748 r_free = 0.2748    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2748 r_free = 0.2748    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2748
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.2172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9553  Z= 0.298
  Angle     :  0.600   7.839  12960  Z= 0.298
  Chirality :  0.046   0.382   1426
  Planarity :  0.004   0.062   1673
  Dihedral  : 10.852 163.694   1413
  Min Nonbonded Distance : 1.889

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 12.48 %
    Favored  : 84.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.25), residues: 1158
  helix:  1.58 (0.24), residues: 486
  sheet:  1.15 (0.36), residues: 204
  loop : -1.08 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  21 
 HIS   0.004   0.001   HIS B 192 
 PHE   0.009   0.001   PHE B 377 
 TYR   0.009   0.001   TYR K  62 
 ARG   0.006   0.000   ARG B 215 

*********************** 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
  156 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 124
  time to evaluate  : 1.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9050 (mm)
REVERT: A  211 ASP cc_start: 0.8641 (t0) cc_final: 0.8146 (t0)
REVERT: A  280 LYS cc_start: 0.9255 (mtpt) cc_final: 0.8242 (mmtt)
REVERT: A  425 MET cc_start: 0.8900 (mmm) cc_final: 0.8423 (tpp)
REVERT: A  432 TYR cc_start: 0.8217 (OUTLIER) cc_final: 0.6659 (t80)
REVERT: K  136 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8116 (pt0)
REVERT: K  311 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8112 (pm20)
  outliers start: 32
  outliers final: 20
  residues processed: 148
  average time/residue: 0.2210
  time to fit residues: 45.4839
Evaluate side-chains
  133 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
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  118 VAL
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  151 THR
Chi-restraints excluded: chain B residue  172 VAL
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  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 B residue  429 VAL
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  311 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 91 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 55 optimal weight:   10.0000
   chunk 60 optimal weight:    0.9990
   chunk 90 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 16 optimal weight:    6.9990
   chunk 76 optimal weight:    8.9990
   chunk 23 optimal weight:    1.9990
   chunk 101 optimal weight:    4.9990
   chunk 106 optimal weight:    0.0980
   overall best weight:    0.9786

-------------------------------------------------------------------------------
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 = 0.2987 r_free = 0.2987 target = 0.083182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2714 r_free = 0.2714 target = 0.068680 restraints weight = 18551.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.071282 restraints weight = 8897.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.073084 restraints weight = 5478.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2795
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2795 r_free = 0.2795    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2795 r_free = 0.2795    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2795
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
moved from start:          0.2340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9553  Z= 0.156
  Angle     :  0.551   9.786  12960  Z= 0.269
  Chirality :  0.044   0.296   1426
  Planarity :  0.004   0.061   1673
  Dihedral  : 10.005 157.605   1413
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 14.65 %
    Favored  : 82.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.25), residues: 1158
  helix:  1.73 (0.25), residues: 486
  sheet:  1.45 (0.37), residues: 199
  loop : -0.98 (0.27), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  21 
 HIS   0.002   0.000   HIS K 129 
 PHE   0.010   0.001   PHE B 377 
 TYR   0.009   0.001   TYR K  62 
 ARG   0.004   0.000   ARG B 215 

*********************** 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
  149 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 1.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   75 MET cc_start: 0.8909 (mmt) cc_final: 0.8564 (mmt)
REVERT: A   26 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8955 (mm)
REVERT: A  211 ASP cc_start: 0.8656 (t0) cc_final: 0.7728 (t0)
REVERT: A  215 ARG cc_start: 0.8072 (ttm110) cc_final: 0.7399 (ttm110)
REVERT: A  280 LYS cc_start: 0.9207 (mtpt) cc_final: 0.8403 (mmtt)
REVERT: A  425 MET cc_start: 0.8887 (mmm) cc_final: 0.8464 (tpp)
REVERT: A  432 TYR cc_start: 0.8143 (OUTLIER) cc_final: 0.6733 (t80)
REVERT: K  136 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8145 (pt0)
REVERT: K  311 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7831 (pm20)
  outliers start: 24
  outliers final: 14
  residues processed: 140
  average time/residue: 0.2350
  time to fit residues: 45.6709
Evaluate side-chains
  132 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  314 THR
Chi-restraints excluded: chain B residue  329 ASP
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  239 THR
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  183 ILE
Chi-restraints excluded: chain K residue  219 THR
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 7 optimal weight:    7.9990
   chunk 20 optimal weight:    4.9990
   chunk 4 optimal weight:    7.9990
   chunk 45 optimal weight:    8.9990
   chunk 21 optimal weight:    0.9990
   chunk 62 optimal weight:    7.9990
   chunk 96 optimal weight:    5.9990
   chunk 98 optimal weight:    9.9990
   chunk 71 optimal weight:    6.9990
   chunk 101 optimal weight:    2.9990
   chunk 48 optimal weight:    7.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 426 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.078910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2634 r_free = 0.2634 target = 0.064531 restraints weight = 18921.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2682 r_free = 0.2682 target = 0.067019 restraints weight = 9235.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.068728 restraints weight = 5744.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2721
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2721 r_free = 0.2721    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2721 r_free = 0.2721    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2721
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8539
moved from start:          0.2452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   9553  Z= 0.411
  Angle     :  0.640   8.760  12960  Z= 0.323
  Chirality :  0.047   0.284   1426
  Planarity :  0.004   0.061   1673
  Dihedral  : 10.034 153.403   1413
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 14.55 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.25), residues: 1158
  helix:  1.56 (0.24), residues: 482
  sheet:  1.40 (0.36), residues: 202
  loop : -1.11 (0.26), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  21 
 HIS   0.005   0.001   HIS A  88 
 PHE   0.012   0.001   PHE K 128 
 TYR   0.015   0.001   TYR K 118 
 ARG   0.004   0.000   ARG K 321 

*********************** 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
  141 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 113
  time to evaluate  : 1.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  417 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8087 (mt-10)
REVERT: A   26 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9104 (mm)
REVERT: A  211 ASP cc_start: 0.8650 (t0) cc_final: 0.8136 (t0)
REVERT: A  280 LYS cc_start: 0.9361 (mtpt) cc_final: 0.8400 (mmtt)
REVERT: A  425 MET cc_start: 0.8952 (mmm) cc_final: 0.8322 (tpp)
REVERT: A  432 TYR cc_start: 0.8226 (OUTLIER) cc_final: 0.6768 (t80)
REVERT: K  136 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8218 (pt0)
  outliers start: 28
  outliers final: 19
  residues processed: 133
  average time/residue: 0.2333
  time to fit residues: 42.9015
Evaluate side-chains
  131 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 109
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 ASP
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  314 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  192 HIS
Chi-restraints excluded: chain A residue  203 MET
Chi-restraints excluded: chain A residue  239 THR
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  183 ILE
Chi-restraints excluded: chain K residue  219 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 85 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 113 optimal weight:    9.9990
   chunk 106 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 72 optimal weight:    4.9990
   overall best weight:    1.5384

-------------------------------------------------------------------------------
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 = 0.2963 r_free = 0.2963 target = 0.082149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2692 r_free = 0.2692 target = 0.067689 restraints weight = 18676.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2741 r_free = 0.2741 target = 0.070261 restraints weight = 9014.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.072013 restraints weight = 5564.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2772
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2772 r_free = 0.2772    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2772 r_free = 0.2772    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2772
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.2534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9553  Z= 0.186
  Angle     :  0.547   7.857  12960  Z= 0.270
  Chirality :  0.044   0.233   1426
  Planarity :  0.004   0.068   1673
  Dihedral  :  9.602 149.086   1413
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 14.55 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.25), residues: 1158
  helix:  1.73 (0.25), residues: 482
  sheet:  1.42 (0.36), residues: 199
  loop : -1.04 (0.27), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  21 
 HIS   0.002   0.001   HIS A  88 
 PHE   0.012   0.001   PHE B 377 
 TYR   0.008   0.001   TYR K 277 
 ARG   0.004   0.000   ARG B 215 

*********************** 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
  145 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 116
  time to evaluate  : 1.041 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  330 GLU cc_start: 0.8059 (tp30) cc_final: 0.7803 (tp30)
REVERT: A   26 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8947 (mm)
REVERT: A  211 ASP cc_start: 0.8690 (t0) cc_final: 0.7917 (t0)
REVERT: A  215 ARG cc_start: 0.8014 (ttm110) cc_final: 0.7237 (ttm110)
REVERT: A  280 LYS cc_start: 0.9332 (mtpt) cc_final: 0.8347 (mmtt)
REVERT: A  425 MET cc_start: 0.8918 (mmm) cc_final: 0.8489 (tpp)
REVERT: A  432 TYR cc_start: 0.8167 (OUTLIER) cc_final: 0.6762 (t80)
REVERT: K  136 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8117 (pt0)
REVERT: K  311 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8132 (pm20)
  outliers start: 29
  outliers final: 18
  residues processed: 137
  average time/residue: 0.2246
  time to fit residues: 42.8006
Evaluate side-chains
  137 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 115
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
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  145 THR
Chi-restraints excluded: chain B residue  172 VAL
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   36 MET
Chi-restraints excluded: chain A residue  203 MET
Chi-restraints excluded: chain A residue  239 THR
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  183 ILE
Chi-restraints excluded: chain K residue  219 THR
Chi-restraints excluded: chain K residue  311 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 72 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    3.9990
   chunk 109 optimal weight:    6.9990
   chunk 41 optimal weight:    5.9990
   chunk 62 optimal weight:    2.9990
   chunk 80 optimal weight:    4.9990
   chunk 90 optimal weight:    7.9990
   chunk 31 optimal weight:    7.9990
   chunk 82 optimal weight:    7.9990
   overall best weight:    4.9990

-------------------------------------------------------------------------------
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 = 0.2903 r_free = 0.2903 target = 0.078270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2626 r_free = 0.2626 target = 0.064029 restraints weight = 19433.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2673 r_free = 0.2673 target = 0.066487 restraints weight = 9383.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.068186 restraints weight = 5847.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2702
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2702 r_free = 0.2702    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2702 r_free = 0.2702    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2702
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.2653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.047   9553  Z= 0.462
  Angle     :  0.663   8.905  12960  Z= 0.335
  Chirality :  0.048   0.257   1426
  Planarity :  0.005   0.064   1673
  Dihedral  :  9.824 148.379   1413
  Min Nonbonded Distance : 1.843

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 15.84 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.25), residues: 1158
  helix:  1.45 (0.24), residues: 482
  sheet:  1.29 (0.36), residues: 202
  loop : -1.20 (0.27), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  21 
 HIS   0.006   0.001   HIS A  88 
 PHE   0.013   0.002   PHE K 128 
 TYR   0.011   0.002   TYR K 277 
 ARG   0.004   0.000   ARG K 321 

*********************** 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
  137 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 107
  time to evaluate  : 0.998 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  166 MET cc_start: 0.8275 (tpp) cc_final: 0.7720 (mtp)
REVERT: B  369 ARG cc_start: 0.8378 (ttm170) cc_final: 0.8112 (mmm160)
REVERT: B  417 GLU cc_start: 0.8282 (mm-30) cc_final: 0.8042 (mt-10)
REVERT: A  211 ASP cc_start: 0.8674 (t0) cc_final: 0.8140 (t0)
REVERT: A  280 LYS cc_start: 0.9366 (mtpt) cc_final: 0.8395 (mmtt)
REVERT: A  425 MET cc_start: 0.8940 (mmm) cc_final: 0.8320 (tpp)
REVERT: A  432 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.6695 (t80)
REVERT: K  136 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8211 (pt0)
REVERT: K  311 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8159 (pm20)
  outliers start: 30
  outliers final: 22
  residues processed: 130
  average time/residue: 0.2283
  time to fit residues: 40.8996
Evaluate side-chains
  131 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 106
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   74 THR
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  314 THR
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   82 THR
Chi-restraints excluded: chain A residue   94 THR
Chi-restraints excluded: chain A residue  192 HIS
Chi-restraints excluded: chain A residue  203 MET
Chi-restraints excluded: chain A residue  239 THR
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  183 ILE
Chi-restraints excluded: chain K residue  219 THR
Chi-restraints excluded: chain K residue  300 ILE
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 102 optimal weight:    9.9990
   chunk 51 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   chunk 30 optimal weight:    6.9990
   chunk 70 optimal weight:    1.9990
   chunk 54 optimal weight:    6.9990
   chunk 27 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 109 optimal weight:    0.6980
   chunk 46 optimal weight:    4.9990
   overall best weight:    3.1388

-------------------------------------------------------------------------------
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 = 0.2922 r_free = 0.2922 target = 0.079354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2643 r_free = 0.2643 target = 0.064957 restraints weight = 19264.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.067507 restraints weight = 9273.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2727 r_free = 0.2727 target = 0.069217 restraints weight = 5721.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2729
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2729 r_free = 0.2729    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2729 r_free = 0.2729    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2729
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.2660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   9553  Z= 0.304
  Angle     :  0.602   8.889  12960  Z= 0.300
  Chirality :  0.046   0.232   1426
  Planarity :  0.004   0.065   1673
  Dihedral  :  9.630 145.874   1413
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 16.04 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.25), residues: 1158
  helix:  1.53 (0.24), residues: 482
  sheet:  1.30 (0.36), residues: 202
  loop : -1.17 (0.27), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  21 
 HIS   0.004   0.001   HIS B 266 
 PHE   0.013   0.001   PHE B 377 
 TYR   0.017   0.001   TYR K 118 
 ARG   0.004   0.000   ARG B 215 

*********************** 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
  143 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 112
  time to evaluate  : 1.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  166 MET cc_start: 0.8218 (tpp) cc_final: 0.7700 (mtp)
REVERT: B  369 ARG cc_start: 0.8351 (ttm170) cc_final: 0.8090 (mmm160)
REVERT: B  417 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7998 (mt-10)
REVERT: A  211 ASP cc_start: 0.8682 (t0) cc_final: 0.8133 (t0)
REVERT: A  280 LYS cc_start: 0.9355 (mtpt) cc_final: 0.8380 (mmtt)
REVERT: A  425 MET cc_start: 0.8944 (mmm) cc_final: 0.8505 (tpp)
REVERT: A  432 TYR cc_start: 0.8203 (OUTLIER) cc_final: 0.6750 (t80)
REVERT: K  136 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8192 (pt0)
REVERT: K  311 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8133 (pm20)
  outliers start: 31
  outliers final: 25
  residues processed: 136
  average time/residue: 0.2291
  time to fit residues: 43.0935
Evaluate side-chains
  140 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 112
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue   74 THR
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  257 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   82 THR
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  239 THR
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  140 ASP
Chi-restraints excluded: chain K residue  183 ILE
Chi-restraints excluded: chain K residue  219 THR
Chi-restraints excluded: chain K residue  300 ILE
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 64 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 114 optimal weight:    0.8980
   chunk 99 optimal weight:    1.9990
   chunk 96 optimal weight:    5.9990
   chunk 109 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 49 optimal weight:    8.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.2975 r_free = 0.2975 target = 0.082227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2706 r_free = 0.2706 target = 0.067930 restraints weight = 18525.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.070517 restraints weight = 8951.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.072272 restraints weight = 5520.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2787
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2787 r_free = 0.2787    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2787 r_free = 0.2787    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2787
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.2727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9553  Z= 0.182
  Angle     :  0.577   9.581  12960  Z= 0.282
  Chirality :  0.045   0.260   1426
  Planarity :  0.004   0.064   1673
  Dihedral  :  9.215 144.287   1413
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 16.34 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.25), residues: 1158
  helix:  1.72 (0.25), residues: 482
  sheet:  1.43 (0.36), residues: 202
  loop : -1.05 (0.27), residues: 474

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

*********************** 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
  145 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 120
  time to evaluate  : 1.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  369 ARG cc_start: 0.8315 (ttm170) cc_final: 0.8073 (mmm160)
REVERT: A  211 ASP cc_start: 0.8682 (t0) cc_final: 0.7879 (t0)
REVERT: A  215 ARG cc_start: 0.8068 (ttm110) cc_final: 0.7199 (ttm110)
REVERT: A  280 LYS cc_start: 0.9329 (mtpt) cc_final: 0.8360 (mmtt)
REVERT: A  425 MET cc_start: 0.8880 (mmm) cc_final: 0.8377 (tpp)
REVERT: A  432 TYR cc_start: 0.8148 (OUTLIER) cc_final: 0.6837 (t80)
REVERT: K  136 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8118 (pt0)
REVERT: K  311 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.7866 (pm20)
  outliers start: 25
  outliers final: 19
  residues processed: 138
  average time/residue: 0.2838
  time to fit residues: 54.5704
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  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue   74 THR
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   94 THR
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  203 MET
Chi-restraints excluded: chain A residue  239 THR
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  183 ILE
Chi-restraints excluded: chain K residue  219 THR
Chi-restraints excluded: chain K residue  300 ILE
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 14 optimal weight:    9.9990
   chunk 28 optimal weight:    1.9990
   chunk 54 optimal weight:    7.9990
   chunk 8 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 84 optimal weight:    0.8980
   chunk 5 optimal weight:    6.9990
   chunk 78 optimal weight:    7.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
B 167 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 = 0.2978 r_free = 0.2978 target = 0.082500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2708 r_free = 0.2708 target = 0.068102 restraints weight = 18761.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.070690 restraints weight = 9027.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.072455 restraints weight = 5579.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2789
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2789
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.2802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9553  Z= 0.179
  Angle     :  0.585  10.779  12960  Z= 0.285
  Chirality :  0.045   0.247   1426
  Planarity :  0.004   0.063   1673
  Dihedral  :  9.014 142.032   1413
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 16.44 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.25), residues: 1158
  helix:  1.79 (0.25), residues: 483
  sheet:  1.48 (0.36), residues: 202
  loop : -1.00 (0.27), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  21 
 HIS   0.002   0.001   HIS B 266 
 PHE   0.013   0.001   PHE B 377 
 TYR   0.009   0.001   TYR K 120 
 ARG   0.003   0.000   ARG B 215 

********************** 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
  140 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 1.574 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  369 ARG cc_start: 0.8314 (ttm170) cc_final: 0.8054 (mmm160)
REVERT: A  211 ASP cc_start: 0.8668 (t0) cc_final: 0.7860 (t0)
REVERT: A  215 ARG cc_start: 0.8070 (ttm110) cc_final: 0.7195 (ttm110)
REVERT: A  280 LYS cc_start: 0.9328 (mtpt) cc_final: 0.8379 (mmtt)
REVERT: A  432 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.7088 (t80)
REVERT: K  114 ASP cc_start: 0.8229 (m-30) cc_final: 0.7986 (m-30)
REVERT: K  136 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8123 (pt0)
REVERT: K  311 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7968 (pm20)
  outliers start: 25
  outliers final: 18
  residues processed: 134
  average time/residue: 0.2394
  time to fit residues: 44.4574
Evaluate side-chains
  137 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue   74 THR
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  344 VAL
Chi-restraints excluded: chain B residue  374 SER
Chi-restraints excluded: chain B residue  425 MET
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  239 THR
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  300 ILE
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 17 optimal weight:    4.9990
   chunk 102 optimal weight:    8.9990
   chunk 90 optimal weight:    0.9980
   chunk 111 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0970
   chunk 48 optimal weight:    4.9990
   chunk 57 optimal weight:    5.9990
   chunk 79 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 92 optimal weight:    4.9990
   overall best weight:    2.4184

-------------------------------------------------------------------------------
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 = 0.2952 r_free = 0.2952 target = 0.080838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2678 r_free = 0.2678 target = 0.066517 restraints weight = 18867.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.069056 restraints weight = 9181.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2761 r_free = 0.2761 target = 0.070797 restraints weight = 5706.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.2761
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2760
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2760 r_free = 0.2760    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2760 r_free = 0.2760    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2760
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.2791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9553  Z= 0.258
  Angle     :  0.611  11.651  12960  Z= 0.300
  Chirality :  0.046   0.258   1426
  Planarity :  0.004   0.063   1673
  Dihedral  :  9.058 142.055   1413
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 17.03 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.25), residues: 1158
  helix:  1.73 (0.24), residues: 482
  sheet:  1.43 (0.36), residues: 202
  loop : -1.02 (0.27), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  21 
 HIS   0.003   0.001   HIS B 266 
 PHE   0.013   0.001   PHE B 377 
 TYR   0.009   0.001   TYR K 277 
 ARG   0.003   0.000   ARG K 321 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2818.47 seconds
wall clock time: 50 minutes 9.90 seconds (3009.90 seconds total)