Starting phenix.real_space_refine
on Sat Aug 23 04:59:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8utw_42552/08_2025/8utw_42552.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8utw_42552/08_2025/8utw_42552.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8utw_42552/08_2025/8utw_42552.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8utw_42552/08_2025/8utw_42552.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8utw_42552/08_2025/8utw_42552.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8utw_42552/08_2025/8utw_42552.map"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.004
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       5      5.49       5
     Mg      1      5.21       5
     S      65      5.16       5
     C    6120      2.51       5
     N    1677      2.21       5
     O    1919      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9787
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "K"
      Number of atoms: 2782
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 354, 2782
          Classifications: {'peptide': 354}
          Link IDs: {'PTRANS': 11, 'TRANS': 342}
    Chain: "A"
      Number of atoms: 3437
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 440, 3437
          Classifications: {'peptide': 440}
          Link IDs: {'PTRANS': 20, 'TRANS': 419}
    Chain: "B"
      Number of atoms: 3445
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 433, 3407
          Classifications: {'peptide': 433}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 412}
      Conformer: "B"
        Number of residues, atoms: 433, 3407
          Classifications: {'peptide': 433}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 412}
          bond proxies already assigned to first conformer: 3444
    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: "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}
  Residues with excluded nonbonded symmetry interactions: 5
    residue:
      pdb=" N  ATHR B 429 " occ=0.50
      ... (12 atoms not shown)
      pdb=" CG2BTHR B 429 " occ=0.50
    residue:
      pdb=" N  AALA B 430 " occ=0.50
      ... (8 atoms not shown)
      pdb=" CB BALA B 430 " occ=0.50
    residue:
      pdb=" N  AASP B 431 " occ=0.50
      ... (14 atoms not shown)
      pdb=" OD2BASP B 431 " occ=0.50
    residue:
      pdb=" N  AGLU B 432 " occ=0.50
      ... (16 atoms not shown)
      pdb=" OE2BGLU B 432 " occ=0.50
    residue:
      pdb=" N  AGLN B 433 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NE2BGLN B 433 " occ=0.50
  Time building chain proxies: 3.20, per 1000 atoms: 0.33
  Number of scatterers: 9787
  At special positions: 0
  Unit cell: (111.408, 74.272, 114.784, 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      65     16.00
     P       5     15.00
     Mg      1     11.99
     O    1919      8.00
     N    1677      7.00
     C    6120      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=0, symmetry=0
  Time building additional restraints: 1.00
  Conformation dependent library (CDL) restraints added in 514.8 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2294

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 10 sheets defined
      46.5% alpha, 18.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'K' and resid 16 through 22
    Processing helix  chain 'K' and resid 69 through 77
    Processing helix  chain 'K' and resid 77 through 87
      removed outlier: 3.605A  pdb=" N   GLU K  87 " --> pdb=" O   GLN K  83 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 102 through 108
    Processing helix  chain 'K' and resid 117 through 134
      removed outlier: 3.518A  pdb=" N   GLN K 121 " --> pdb=" O   GLY K 117 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 188 through 202
      removed outlier: 3.536A  pdb=" N   ILE K 192 " --> pdb=" O   SER K 188 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   MET K 196 " --> pdb=" O   ILE K 192 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ALA K 202 " --> pdb=" O   SER K 198 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 262 through 294
      removed outlier: 3.811A  pdb=" N   GLY K 268 " --> pdb=" O   ARG K 264 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   GLY K 279 " --> pdb=" O   LEU K 275 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLU K 287 " --> pdb=" O   SER K 283 " (cutoff:3.500A)
      Proline residue:  K 292  - end of helix
    Processing helix  chain 'K' and resid 309 through 315
      removed outlier: 3.601A  pdb=" N   TRP K 313 " --> pdb=" O   SER K 309 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 315 through 320
      removed outlier: 3.622A  pdb=" N   GLY K 320 " --> pdb=" O   ARG K 316 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 337 through 350
      removed outlier: 3.588A  pdb=" N   ARG K 350 " --> pdb=" O   ARG K 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 10 through 29
    Processing helix  chain 'A' and resid 36 through 43
      removed outlier: 4.011A  pdb=" N   LYS A  40 " --> pdb=" O   MET A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 80
      removed outlier: 3.882A  pdb=" N   ILE A  75 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   GLU A  77 " --> pdb=" O   THR A  73 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   VAL A  78 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 108
    Processing helix  chain 'A' and resid 114 through 128
      removed outlier: 3.720A  pdb=" N   GLN A 128 " --> pdb=" O   LYS A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 161
      removed outlier: 3.717A  pdb=" N   GLY A 148 " --> pdb=" O   GLY A 144 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   VAL A 159 " --> pdb=" O   GLU A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 198
      removed outlier: 4.400A  pdb=" N   HIS A 192 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   THR A 193 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
      removed outlier: 4.769A  pdb=" N   GLU A 196 " --> pdb=" O   HIS A 192 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   HIS A 197 " --> pdb=" O   THR A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 216
    Processing helix  chain 'A' and resid 223 through 240
      removed outlier: 3.799A  pdb=" N   LEU A 227 " --> pdb=" O   THR A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 243
      No H-bonds generated for 'chain 'A' and resid 241 through 243'
    Processing helix  chain 'A' and resid 251 through 259
    Processing helix  chain 'A' and resid 287 through 296
      removed outlier: 3.990A  pdb=" N   PHE A 296 " --> pdb=" O   THR A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 301
    Processing helix  chain 'A' and resid 306 through 310
    Processing helix  chain 'A' and resid 324 through 338
      removed outlier: 3.559A  pdb=" N   VAL A 328 " --> pdb=" O   VAL A 324 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   THR A 337 " --> pdb=" O   ALA A 333 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   LYS A 338 " --> pdb=" O   THR A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 399
      removed outlier: 3.888A  pdb=" N   ALA A 387 " --> pdb=" O   ALA A 383 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ARG A 390 " --> pdb=" O   GLU A 386 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   LEU A 391 " --> pdb=" O   ALA A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 4.229A  pdb=" N   TYR A 408 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 436
      removed outlier: 3.554A  pdb=" N   GLU A 420 " --> pdb=" O   GLY A 416 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 29
    Processing helix  chain 'B' and resid 40 through 49
      removed outlier: 3.609A  pdb=" N   GLN B  43 " --> pdb=" O   SER B  40 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   ARG B  46 " --> pdb=" O   GLN B  43 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ILE B  47 " --> pdb=" O   LEU B  44 " (cutoff:3.500A)
      removed outlier: 5.894A  pdb=" N   ASN B  48 " --> pdb=" O   GLU B  45 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   VAL B  49 " --> pdb=" O   ARG B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 78
      removed outlier: 4.082A  pdb=" N   MET B  73 " --> pdb=" O   GLU B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 85
      removed outlier: 4.019A  pdb=" N   PHE B  85 " --> pdb=" O   GLY B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 90
    Processing helix  chain 'B' and resid 100 through 106
    Processing helix  chain 'B' and resid 108 through 127
      removed outlier: 4.017A  pdb=" N   LEU B 112 " --> pdb=" O   GLU B 108 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   ASP B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   SER B 115 " --> pdb=" O   GLU B 111 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   CYS B 127 " --> pdb=" O   GLU B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 159
      removed outlier: 3.530A  pdb=" N   MET B 147 " --> pdb=" O   THR B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 194
      removed outlier: 3.594A  pdb=" N   ASN B 184 " --> pdb=" O   VAL B 180 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   GLU B 194 " --> pdb=" O   HIS B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 214
    Processing helix  chain 'B' and resid 221 through 238
      removed outlier: 3.841A  pdb=" N   LEU B 225 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 239 through 241
      No H-bonds generated for 'chain 'B' and resid 239 through 241'
    Processing helix  chain 'B' and resid 249 through 258
      removed outlier: 3.835A  pdb=" N   VAL B 258 " --> pdb=" O   ALA B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 285 through 294
    Processing helix  chain 'B' and resid 322 through 337
      removed outlier: 4.026A  pdb=" N   VAL B 326 " --> pdb=" O   SER B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 341
    Processing helix  chain 'B' and resid 371 through 373
      No H-bonds generated for 'chain 'B' and resid 371 through 373'
    Processing helix  chain 'B' and resid 374 through 390
      removed outlier: 3.742A  pdb=" N   ARG B 380 " --> pdb=" O   GLU B 376 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 400
    Processing helix  chain 'B' and resid 405 through 425
      removed outlier: 3.631A  pdb=" N   THR B 409 " --> pdb=" O   GLU B 405 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   TYR B 425 " --> pdb=" O   GLU B 421 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'K' and resid 54 through 56
      removed outlier: 8.641A  pdb=" N   TYR K  54 " --> pdb=" O   VAL K   6 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   VAL K   8 " --> pdb=" O   TYR K  54 " (cutoff:3.500A)
      removed outlier: 8.284A  pdb=" N   TYR K  56 " --> pdb=" O   VAL K   8 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   VAL K  10 " --> pdb=" O   TYR K  56 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   SER K   5 " --> pdb=" O   THR K 325 " (cutoff:3.500A)
      removed outlier: 7.837A  pdb=" N   MET K 327 " --> pdb=" O   SER K   5 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   LYS K   7 " --> pdb=" O   MET K 327 " (cutoff:3.500A)
      removed outlier: 7.912A  pdb=" N   ALA K 329 " --> pdb=" O   LYS K   7 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   ALA K   9 " --> pdb=" O   ALA K 329 " (cutoff:3.500A)
      removed outlier: 7.841A  pdb=" N   LEU K 331 " --> pdb=" O   ALA K   9 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   ARG K  11 " --> pdb=" O   LEU K 331 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   CYS K  92 " --> pdb=" O   ALA K 326 " (cutoff:3.500A)
      removed outlier: 8.158A  pdb=" N   VAL K 328 " --> pdb=" O   CYS K  92 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   PHE K  94 " --> pdb=" O   VAL K 328 " (cutoff:3.500A)
      removed outlier: 7.900A  pdb=" N   ALA K 330 " --> pdb=" O   PHE K  94 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   TYR K  96 " --> pdb=" O   ALA K 330 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   VAL K  91 " --> pdb=" O   SER K 245 " (cutoff:3.500A)
      removed outlier: 7.983A  pdb=" N   VAL K 247 " --> pdb=" O   VAL K  91 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ILE K  93 " --> pdb=" O   VAL K 247 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'K' and resid 54 through 56
      removed outlier: 8.641A  pdb=" N   TYR K  54 " --> pdb=" O   VAL K   6 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   VAL K   8 " --> pdb=" O   TYR K  54 " (cutoff:3.500A)
      removed outlier: 8.284A  pdb=" N   TYR K  56 " --> pdb=" O   VAL K   8 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   VAL K  10 " --> pdb=" O   TYR K  56 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   SER K   5 " --> pdb=" O   THR K 325 " (cutoff:3.500A)
      removed outlier: 7.837A  pdb=" N   MET K 327 " --> pdb=" O   SER K   5 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   LYS K   7 " --> pdb=" O   MET K 327 " (cutoff:3.500A)
      removed outlier: 7.912A  pdb=" N   ALA K 329 " --> pdb=" O   LYS K   7 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   ALA K   9 " --> pdb=" O   ALA K 329 " (cutoff:3.500A)
      removed outlier: 7.841A  pdb=" N   LEU K 331 " --> pdb=" O   ALA K   9 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   ARG K  11 " --> pdb=" O   LEU K 331 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   CYS K  92 " --> pdb=" O   ALA K 326 " (cutoff:3.500A)
      removed outlier: 8.158A  pdb=" N   VAL K 328 " --> pdb=" O   CYS K  92 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   PHE K  94 " --> pdb=" O   VAL K 328 " (cutoff:3.500A)
      removed outlier: 7.900A  pdb=" N   ALA K 330 " --> pdb=" O   PHE K  94 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   TYR K  96 " --> pdb=" O   ALA K 330 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   VAL K  91 " --> pdb=" O   SER K 245 " (cutoff:3.500A)
      removed outlier: 7.983A  pdb=" N   VAL K 247 " --> pdb=" O   VAL K  91 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ILE K  93 " --> pdb=" O   VAL K 247 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'K' and resid 28 through 31
    Processing sheet with id=AA4, first strand: chain 'K' and resid 168 through 171
    Processing sheet with id=AA5, first strand: chain 'K' and resid 205 through 206
      removed outlier: 3.743A  pdb=" N   ALA K 206 " --> pdb=" O   SER K 214 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   SER K 214 " --> pdb=" O   ALA K 206 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 65 through 68
      removed outlier: 4.812A  pdb=" N   SER A 140 " --> pdb=" O   VAL A   9 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   PHE A 135 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.491A  pdb=" N   PHE A 169 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   VAL A 137 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 7.724A  pdb=" N   ILE A 171 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 7.186A  pdb=" N   HIS A 139 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   LYS A 166 " --> pdb=" O   CYS A 200 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   PHE A 202 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   GLU A 168 " --> pdb=" O   PHE A 202 " (cutoff:3.500A)
      removed outlier: 7.756A  pdb=" N   VAL A 204 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   SER A 170 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 53 through 55
    Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 272
      removed outlier: 3.864A  pdb=" N   MET A 377 " --> pdb=" O   THR A 271 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ALA A 314 " --> pdb=" O   ASN A 380 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 91 through 92
      removed outlier: 6.193A  pdb=" N   LEU B  65 " --> pdb=" O   VAL B  91 " (cutoff:3.500A)
      removed outlier: 9.091A  pdb=" N   ILE B  64 " --> pdb=" O   ILE B   4 " (cutoff:3.500A)
      removed outlier: 7.165A  pdb=" N   HIS B   6 " --> pdb=" O   ILE B  64 " (cutoff:3.500A)
      removed outlier: 7.715A  pdb=" N   VAL B  66 " --> pdb=" O   HIS B   6 " (cutoff:3.500A)
      removed outlier: 5.902A  pdb=" N   GLN B   8 " --> pdb=" O   VAL B  66 " (cutoff:3.500A)
      removed outlier: 7.111A  pdb=" N   GLU B   3 " --> pdb=" O   GLN B 131 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   PHE B 133 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   VAL B   5 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 5.737A  pdb=" N   LEU B 135 " --> pdb=" O   VAL B   5 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   ILE B   7 " --> pdb=" O   LEU B 135 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   HIS B 137 " --> pdb=" O   ILE B   7 " (cutoff:3.500A)
      removed outlier: 7.714A  pdb=" N   ALA B   9 " --> pdb=" O   HIS B 137 " (cutoff:3.500A)
      removed outlier: 9.877A  pdb=" N   ILE B 163 " --> pdb=" O   CYS B 129 " (cutoff:3.500A)
      removed outlier: 7.344A  pdb=" N   GLN B 131 " --> pdb=" O   ILE B 163 " (cutoff:3.500A)
      removed outlier: 7.758A  pdb=" N   ASN B 165 " --> pdb=" O   GLN B 131 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   PHE B 133 " --> pdb=" O   ASN B 165 " (cutoff:3.500A)
      removed outlier: 7.499A  pdb=" N   PHE B 167 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   LEU B 135 " --> pdb=" O   PHE B 167 " (cutoff:3.500A)
      removed outlier: 7.695A  pdb=" N   VAL B 169 " --> pdb=" O   LEU B 135 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   HIS B 137 " --> pdb=" O   VAL B 169 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   MET B 164 " --> pdb=" O   GLU B 198 " (cutoff:3.500A)
      removed outlier: 8.062A  pdb=" N   TYR B 200 " --> pdb=" O   MET B 164 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   THR B 166 " --> pdb=" O   TYR B 200 " (cutoff:3.500A)
      removed outlier: 7.687A  pdb=" N   ILE B 202 " --> pdb=" O   THR B 166 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   SER B 168 " --> pdb=" O   ILE B 202 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   THR B 199 " --> pdb=" O   PHE B 266 " (cutoff:3.500A)
      removed outlier: 7.493A  pdb=" N   CYS B 201 " --> pdb=" O   PRO B 268 " (cutoff:3.500A)
      removed outlier: 10.050A  pdb=" N   PHE B 270 " --> pdb=" O   CYS B 201 " (cutoff:3.500A)
      removed outlier: 13.588A  pdb=" N   ASP B 203 " --> pdb=" O   PHE B 270 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 51 through 53

    430 hydrogen bonds defined for protein.
    1227 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.66

  Time building geometry restraints manager: 1.27 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: 1745
        1.32 -     1.45: 2594
        1.45 -     1.57: 5538
        1.57 -     1.69: 10
        1.69 -     1.82: 105
  Bond restraints: 9992
  Sorted by residual:
  bond pdb=" CA  SER K 309 "
       pdb=" CB  SER K 309 "
    ideal  model  delta    sigma   weight residual
    1.532  1.467  0.065 1.69e-02 3.50e+03 1.47e+01
  bond pdb=" CA  SER K 188 "
       pdb=" CB  SER K 188 "
    ideal  model  delta    sigma   weight residual
    1.534  1.487  0.047 1.34e-02 5.57e+03 1.23e+01
  bond pdb=" N   ASP B 161 "
       pdb=" CA  ASP B 161 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 9.10e-03 1.21e+04 9.94e+00
  bond pdb=" N   LEU K 319 "
       pdb=" CA  LEU K 319 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.038 1.22e-02 6.72e+03 9.90e+00
  bond pdb=" N   LEU B 361 "
       pdb=" CA  LEU B 361 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.032 1.18e-02 7.18e+03 7.53e+00
  ... (remaining 9987 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.37: 13177
        2.37 -     4.75: 321
        4.75 -     7.12: 51
        7.12 -     9.50: 3
        9.50 -    11.87: 3
  Bond angle restraints: 13555
  Sorted by residual:
  angle pdb=" N   PRO B 160 "
        pdb=" CA  PRO B 160 "
        pdb=" CB  PRO B 160 "
      ideal   model   delta    sigma   weight residual
     103.25   97.45    5.80 1.05e+00 9.07e-01 3.05e+01
  angle pdb=" C   VAL A 324 "
        pdb=" N   PRO A 325 "
        pdb=" CA  PRO A 325 "
      ideal   model   delta    sigma   weight residual
     119.28  124.28   -5.00 1.10e+00 8.26e-01 2.07e+01
  angle pdb=" C   ARG K 316 "
        pdb=" CA  ARG K 316 "
        pdb=" CB  ARG K 316 "
      ideal   model   delta    sigma   weight residual
     110.90  103.92    6.98 1.58e+00 4.01e-01 1.95e+01
  angle pdb=" N   ARG B 251 "
        pdb=" CA  ARG B 251 "
        pdb=" C   ARG B 251 "
      ideal   model   delta    sigma   weight residual
     111.82  106.82    5.00 1.16e+00 7.43e-01 1.85e+01
  angle pdb=" N   GLU B 421 "
        pdb=" CA  GLU B 421 "
        pdb=" C   GLU B 421 "
      ideal   model   delta    sigma   weight residual
     111.36  106.83    4.53 1.09e+00 8.42e-01 1.73e+01
  ... (remaining 13550 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.18: 5636
       27.18 -    54.35: 368
       54.35 -    81.53: 49
       81.53 -   108.70: 17
      108.70 -   135.88: 12
  Dihedral angle restraints: 6082
    sinusoidal: 2510
      harmonic: 3572
  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  -55.36  124.63     1      2.00e+01 2.50e-03 3.76e+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  -15.37  119.96     1      2.00e+01 2.50e-03 3.60e+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  173.41  100.72     1      2.00e+01 2.50e-03 2.85e+01
  ... (remaining 6079 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.102: 1399
       0.102 -    0.204: 87
       0.204 -    0.306: 3
       0.306 -    0.408: 0
       0.408 -    0.509: 1
  Chirality restraints: 1490
  Sorted by residual:
  chirality pdb=" C18 TA1 B 502 "
            pdb=" C10 TA1 B 502 "
            pdb=" C17 TA1 B 502 "
            pdb=" C20 TA1 B 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -3.16   -2.65   -0.51 2.00e-01 2.50e+01 6.49e+00
  chirality pdb=" CA  ILE K 304 "
            pdb=" N   ILE K 304 "
            pdb=" C   ILE K 304 "
            pdb=" CB  ILE K 304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.68   -0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CA  LEU K 305 "
            pdb=" N   LEU K 305 "
            pdb=" C   LEU K 305 "
            pdb=" CB  LEU K 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.30e+00
  ... (remaining 1487 not shown)

  Planarity restraints: 1764
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C29 TA1 B 502 "    0.316 2.00e-02 2.50e+03   2.67e-01 8.89e+02
        pdb=" C30 TA1 B 502 "   -0.084 2.00e-02 2.50e+03
        pdb=" C31 TA1 B 502 "    0.188 2.00e-02 2.50e+03
        pdb=" N01 TA1 B 502 "   -0.461 2.00e-02 2.50e+03
        pdb=" O14 TA1 B 502 "    0.041 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU K 311 "    0.020 2.00e-02 2.50e+03   4.08e-02 1.67e+01
        pdb=" C   LEU K 311 "   -0.071 2.00e-02 2.50e+03
        pdb=" O   LEU K 311 "    0.027 2.00e-02 2.50e+03
        pdb=" N   THR K 312 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 319 "    0.019 2.00e-02 2.50e+03   3.72e-02 1.39e+01
        pdb=" C   TYR A 319 "   -0.064 2.00e-02 2.50e+03
        pdb=" O   TYR A 319 "    0.024 2.00e-02 2.50e+03
        pdb=" N   ARG A 320 "    0.022 2.00e-02 2.50e+03
  ... (remaining 1761 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 56
        2.53 -     3.12: 7401
        3.12 -     3.72: 14632
        3.72 -     4.31: 19453
        4.31 -     4.90: 33019
  Nonbonded interactions: 74561
  Sorted by model distance:
  nonbonded pdb=" O1G GTP A 501 "
            pdb="MG    MG A 502 "
     model   vdw
     1.938 2.170
  nonbonded pdb=" O3B GTP A 501 "
            pdb="MG    MG A 502 "
     model   vdw
     1.987 2.170
  nonbonded pdb=" O1B GTP A 501 "
            pdb="MG    MG A 502 "
     model   vdw
     2.005 2.170
  nonbonded pdb=" OH  TYR K 150 "
            pdb=" OE2 GLU K 267 "
     model   vdw
     2.094 3.040
  nonbonded pdb=" OG  SER A 147 "
            pdb=" OG1 THR A 190 "
     model   vdw
     2.150 3.040
  ... (remaining 74556 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.510
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6976
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      :  0.005   0.065   9992  Z= 0.279
  Angle     :  0.867  11.872  13555  Z= 0.491
  Chirality :  0.051   0.509   1490
  Planarity :  0.009   0.267   1764
  Dihedral  : 19.457 135.878   3788
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.47 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 17.74 %
    Favored  : 80.38 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.80 (0.24), residues: 1226
  helix:  0.65 (0.23), residues: 497
  sheet: -0.46 (0.36), residues: 223
  loop : -1.75 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 402 
 TYR   0.022   0.002   TYR K 306 
 PHE   0.016   0.002   PHE K  86 
 TRP   0.012   0.001   TRP B 344 
 HIS   0.003   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 ( 9992)
  covalent geometry    : angle       0.86691 (13555)
  hydrogen bonds       : bond        0.15609 (  410)
  hydrogen bonds       : angle       6.28116 ( 1227)

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 172
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  159 ASN cc_start: 0.7246 (t0) cc_final: 0.7007 (t0)
REVERT: K  301 THR cc_start: 0.6308 (OUTLIER) cc_final: 0.5747 (p)
REVERT: A  411 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6848 (mm-30)
REVERT: B   23 VAL cc_start: 0.7353 (OUTLIER) cc_final: 0.7090 (p)
REVERT: B   76 VAL cc_start: 0.6428 (t) cc_final: 0.5494 (m)
REVERT: B  161 ASP cc_start: 0.7800 (t0) cc_final: 0.7277 (t0)
REVERT: B  256 ASN cc_start: 0.7771 (m-40) cc_final: 0.7255 (m-40)
REVERT: B  323 MET cc_start: 0.7300 (mtm) cc_final: 0.6887 (mtm)
REVERT: B  347 ASN cc_start: 0.7562 (p0) cc_final: 0.7336 (p0)
  outliers start: 16
  outliers final: 5
  residues processed: 183
  average time/residue: 0.0935
  time to fit residues: 24.0808
Evaluate side-chains
  167 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 160
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  298 LYS
Chi-restraints excluded: chain K residue  299 LYS
Chi-restraints excluded: chain K residue  301 THR
Chi-restraints excluded: chain K residue  303 PHE
Chi-restraints excluded: chain K residue  312 THR
Chi-restraints excluded: chain A residue  396 ASP
Chi-restraints excluded: chain B residue   23 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    0.7980
   chunk 113 optimal weight:    0.0070
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 117 optimal weight:    0.0670
   overall best weight:    0.5336

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

Flipped N/Q/H residues before XYZ refinement:
K  59 HIS
A 258 ASN
B 433 GLN    A

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.140073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.122143 restraints weight = 15637.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3616 rms_B_bonded: 3.46
r_work: 0.3471 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3492
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3492 r_free = 0.3492    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3492 r_free = 0.3492    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3492
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6983
moved from start:          0.1136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9992  Z= 0.127
  Angle     :  0.623  10.530  13555  Z= 0.305
  Chirality :  0.044   0.383   1490
  Planarity :  0.005   0.086   1764
  Dihedral  : 11.398 120.322   1489
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.59 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 16.89 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.03 (0.25), residues: 1226
  helix:  1.42 (0.23), residues: 509
  sheet:  0.08 (0.37), residues: 233
  loop : -1.56 (0.27), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 422 
 TYR   0.015   0.001   TYR A 224 
 PHE   0.017   0.001   PHE B 367 
 TRP   0.014   0.002   TRP B 344 
 HIS   0.003   0.001   HIS B 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 9992)
  covalent geometry    : angle       0.62289 (13555)
  hydrogen bonds       : bond        0.04497 (  410)
  hydrogen bonds       : angle       4.33580 ( 1227)

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 158
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: K  307 ARG cc_start: 0.7592 (mtt180) cc_final: 0.7077 (mtt90)
REVERT: A  377 MET cc_start: 0.6821 (tmm) cc_final: 0.6598 (tmm)
REVERT: A  411 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7107 (mm-30)
REVERT: B   23 VAL cc_start: 0.7179 (OUTLIER) cc_final: 0.6871 (p)
REVERT: B   76 VAL cc_start: 0.6384 (t) cc_final: 0.5451 (m)
REVERT: B   91 VAL cc_start: 0.7748 (m) cc_final: 0.7492 (p)
REVERT: B  256 ASN cc_start: 0.7882 (m-40) cc_final: 0.7332 (m-40)
REVERT: B  257 MET cc_start: 0.7447 (mmm) cc_final: 0.6694 (tmm)
REVERT: B  347 ASN cc_start: 0.7550 (p0) cc_final: 0.7264 (p0)
  outliers start: 29
  outliers final: 13
  residues processed: 176
  average time/residue: 0.0857
  time to fit residues: 21.5656
Evaluate side-chains
  165 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 151
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   31 SER
Chi-restraints excluded: chain K residue   86 PHE
Chi-restraints excluded: chain K residue  256 ASP
Chi-restraints excluded: chain K residue  288 MET
Chi-restraints excluded: chain K residue  303 PHE
Chi-restraints excluded: chain A residue  108 TYR
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain A residue  160 ASP
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  438 ASP
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue  147 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 76 optimal weight:    0.0770
   chunk 83 optimal weight:    3.9990
   chunk 93 optimal weight:    8.9990
   chunk 4 optimal weight:    3.9990
   chunk 101 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 105 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 117 optimal weight:    1.9990
   chunk 61 optimal weight:    0.5980
   chunk 108 optimal weight:    0.7980
   overall best weight:    0.8940

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

Flipped N/Q/H residues before XYZ refinement:
K  59 HIS
B  89 ASN
B 347 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.139172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.121036 restraints weight = 15481.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 3.46
r_work: 0.3448 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3456
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3456 r_free = 0.3456    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3456 r_free = 0.3456    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3456
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7049
moved from start:          0.1651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9992  Z= 0.144
  Angle     :  0.593   9.019  13555  Z= 0.297
  Chirality :  0.046   0.449   1490
  Planarity :  0.005   0.082   1764
  Dihedral  :  8.712 121.940   1477
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.49 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 18.30 %
    Favored  : 78.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.25), residues: 1226
  helix:  1.56 (0.23), residues: 508
  sheet:  0.41 (0.37), residues: 231
  loop : -1.55 (0.27), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 422 
 TYR   0.031   0.002   TYR A 224 
 PHE   0.020   0.002   PHE B 367 
 TRP   0.015   0.001   TRP B 344 
 HIS   0.005   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 9992)
  covalent geometry    : angle       0.59345 (13555)
  hydrogen bonds       : bond        0.04399 (  410)
  hydrogen bonds       : angle       4.10947 ( 1227)

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 168
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  148 GLU cc_start: 0.7564 (pt0) cc_final: 0.7291 (pt0)
REVERT: K  167 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7672 (mtm110)
REVERT: A   26 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7193 (mm)
REVERT: A  109 THR cc_start: 0.7574 (OUTLIER) cc_final: 0.7316 (p)
REVERT: A  260 VAL cc_start: 0.8595 (m) cc_final: 0.8244 (p)
REVERT: A  377 MET cc_start: 0.6883 (tmm) cc_final: 0.6585 (tmm)
REVERT: A  411 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7185 (mm-30)
REVERT: B   23 VAL cc_start: 0.7185 (OUTLIER) cc_final: 0.6922 (p)
REVERT: B   91 VAL cc_start: 0.7798 (m) cc_final: 0.7512 (p)
REVERT: B  161 ASP cc_start: 0.7912 (t0) cc_final: 0.7332 (t0)
REVERT: B  257 MET cc_start: 0.7491 (mmm) cc_final: 0.7040 (mmm)
REVERT: B  299 MET cc_start: 0.7785 (mmt) cc_final: 0.7426 (mmt)
REVERT: B  318 ARG cc_start: 0.7737 (mtp-110) cc_final: 0.7119 (mmm-85)
REVERT: B  395 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7512 (tt)
  outliers start: 26
  outliers final: 14
  residues processed: 185
  average time/residue: 0.0819
  time to fit residues: 21.6572
Evaluate side-chains
  183 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 164
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   10 VAL
Chi-restraints excluded: chain K residue   59 HIS
Chi-restraints excluded: chain K residue   86 PHE
Chi-restraints excluded: chain K residue  154 VAL
Chi-restraints excluded: chain K residue  167 ARG
Chi-restraints excluded: chain K residue  303 PHE
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue  108 TYR
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain A residue  160 ASP
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  307 HIS
Chi-restraints excluded: chain B residue  395 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 104 optimal weight:    3.9990
   chunk 67 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9980
   chunk 17 optimal weight:    5.9990
   chunk 95 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9980
   chunk 2 optimal weight:    6.9990
   chunk 23 optimal weight:    0.0270
   chunk 9 optimal weight:    3.9990
   overall best weight:    0.7640

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

Flipped N/Q/H residues before XYZ refinement:
K  59 HIS
K 318 ASN
A 258 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.139669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.121898 restraints weight = 14567.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3619 rms_B_bonded: 3.32
r_work: 0.3484 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3483
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3483 r_free = 0.3483    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3483 r_free = 0.3483    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3483
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7030
moved from start:          0.1854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9992  Z= 0.130
  Angle     :  0.560   7.531  13555  Z= 0.281
  Chirality :  0.044   0.379   1490
  Planarity :  0.005   0.080   1764
  Dihedral  :  8.453 120.284   1477
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.16 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 18.11 %
    Favored  : 78.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.35 (0.24), residues: 1226
  helix:  1.71 (0.23), residues: 508
  sheet:  0.49 (0.37), residues: 226
  loop : -1.52 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 221 
 TYR   0.018   0.001   TYR A 224 
 PHE   0.016   0.001   PHE B 367 
 TRP   0.016   0.001   TRP B 344 
 HIS   0.010   0.001   HIS K  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 9992)
  covalent geometry    : angle       0.56048 (13555)
  hydrogen bonds       : bond        0.04009 (  410)
  hydrogen bonds       : angle       3.98602 ( 1227)

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 168
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  148 GLU cc_start: 0.7537 (pt0) cc_final: 0.7223 (pt0)
REVERT: A  109 THR cc_start: 0.7522 (OUTLIER) cc_final: 0.7240 (p)
REVERT: A  260 VAL cc_start: 0.8597 (m) cc_final: 0.8269 (p)
REVERT: A  377 MET cc_start: 0.6846 (tmm) cc_final: 0.6517 (tmm)
REVERT: A  411 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7178 (mm-30)
REVERT: B   23 VAL cc_start: 0.7125 (OUTLIER) cc_final: 0.6900 (p)
REVERT: B   91 VAL cc_start: 0.7781 (m) cc_final: 0.7497 (p)
REVERT: B   94 GLN cc_start: 0.7769 (mp10) cc_final: 0.7500 (mp10)
REVERT: B  161 ASP cc_start: 0.7877 (t0) cc_final: 0.7263 (t0)
REVERT: B  257 MET cc_start: 0.7493 (mmm) cc_final: 0.7206 (mmm)
REVERT: B  299 MET cc_start: 0.7844 (mmt) cc_final: 0.7479 (mmt)
REVERT: B  318 ARG cc_start: 0.7695 (mtp-110) cc_final: 0.7134 (mmm-85)
REVERT: B  395 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7482 (tt)
  outliers start: 32
  outliers final: 19
  residues processed: 188
  average time/residue: 0.0903
  time to fit residues: 24.2888
Evaluate side-chains
  189 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 167
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   10 VAL
Chi-restraints excluded: chain K residue   12 VAL
Chi-restraints excluded: chain K residue   86 PHE
Chi-restraints excluded: chain K residue  154 VAL
Chi-restraints excluded: chain K residue  215 SER
Chi-restraints excluded: chain K residue  256 ASP
Chi-restraints excluded: chain K residue  303 PHE
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  108 TYR
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain A residue  160 ASP
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  307 HIS
Chi-restraints excluded: chain B residue  395 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 113 optimal weight:    0.7980
   chunk 16 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 77 optimal weight:    0.8980
   chunk 73 optimal weight:    0.6980
   chunk 80 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 86 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
K  59 HIS
K 116 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.139175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.121678 restraints weight = 14520.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3602 rms_B_bonded: 3.28
r_work: 0.3460 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3475
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3475 r_free = 0.3475    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3475 r_free = 0.3475    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3475
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7037
moved from start:          0.2114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9992  Z= 0.133
  Angle     :  0.551   6.455  13555  Z= 0.279
  Chirality :  0.044   0.310   1490
  Planarity :  0.005   0.077   1764
  Dihedral  :  8.222 120.137   1477
  Min Nonbonded Distance : 1.881

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.65 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 18.96 %
    Favored  : 77.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.25), residues: 1226
  helix:  1.76 (0.23), residues: 510
  sheet:  0.47 (0.36), residues: 234
  loop : -1.49 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 221 
 TYR   0.028   0.002   TYR A 224 
 PHE   0.016   0.001   PHE B 367 
 TRP   0.015   0.001   TRP B 344 
 HIS   0.004   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 9992)
  covalent geometry    : angle       0.55140 (13555)
  hydrogen bonds       : bond        0.03966 (  410)
  hydrogen bonds       : angle       3.92894 ( 1227)

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 168
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
REVERT: K  307 ARG cc_start: 0.7645 (mtt180) cc_final: 0.7201 (ttm-80)
REVERT: A   26 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7233 (mm)
REVERT: A  109 THR cc_start: 0.7512 (OUTLIER) cc_final: 0.7254 (p)
REVERT: A  260 VAL cc_start: 0.8589 (m) cc_final: 0.8284 (p)
REVERT: A  377 MET cc_start: 0.6783 (tmm) cc_final: 0.6317 (tmm)
REVERT: A  411 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7178 (mm-30)
REVERT: B    3 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.6495 (tt0)
REVERT: B   91 VAL cc_start: 0.7792 (m) cc_final: 0.7494 (p)
REVERT: B   94 GLN cc_start: 0.7864 (mp10) cc_final: 0.7555 (mp10)
REVERT: B  299 MET cc_start: 0.7849 (mmt) cc_final: 0.7442 (mmt)
REVERT: B  318 ARG cc_start: 0.7665 (mtp-110) cc_final: 0.7182 (mmm-85)
REVERT: B  395 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7479 (tt)
  outliers start: 32
  outliers final: 22
  residues processed: 187
  average time/residue: 0.0944
  time to fit residues: 25.5790
Evaluate side-chains
  193 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 167
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   10 VAL
Chi-restraints excluded: chain K residue   12 VAL
Chi-restraints excluded: chain K residue   59 HIS
Chi-restraints excluded: chain K residue   86 PHE
Chi-restraints excluded: chain K residue  133 THR
Chi-restraints excluded: chain K residue  154 VAL
Chi-restraints excluded: chain K residue  174 LEU
Chi-restraints excluded: chain K residue  215 SER
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  108 TYR
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain A residue  160 ASP
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  307 HIS
Chi-restraints excluded: chain B residue  395 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 28 optimal weight:    8.9990
   chunk 102 optimal weight:    0.7980
   chunk 90 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0670
   chunk 23 optimal weight:    0.7980
   chunk 47 optimal weight:    0.4980
   chunk 67 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
K  59 HIS
B 298 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.140349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.122876 restraints weight = 14348.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 3.26
r_work: 0.3483 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3488
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3488 r_free = 0.3488    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3488 r_free = 0.3488    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3488
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7027
moved from start:          0.2227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9992  Z= 0.114
  Angle     :  0.538   7.626  13555  Z= 0.271
  Chirality :  0.044   0.286   1490
  Planarity :  0.005   0.075   1764
  Dihedral  :  8.012 118.237   1474
  Min Nonbonded Distance : 1.899

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.08 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 20.00 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.25), residues: 1226
  helix:  1.87 (0.23), residues: 510
  sheet:  0.73 (0.37), residues: 225
  loop : -1.53 (0.27), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 221 
 TYR   0.022   0.001   TYR A 224 
 PHE   0.014   0.001   PHE B 367 
 TRP   0.016   0.001   TRP B 344 
 HIS   0.011   0.001   HIS K  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 9992)
  covalent geometry    : angle       0.53831 (13555)
  hydrogen bonds       : bond        0.03675 (  410)
  hydrogen bonds       : angle       3.83821 ( 1227)

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 160
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
REVERT: K  210 MET cc_start: 0.5390 (OUTLIER) cc_final: 0.4796 (ptt)
REVERT: K  307 ARG cc_start: 0.7686 (mtt180) cc_final: 0.7202 (ttm-80)
REVERT: A   26 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7241 (mm)
REVERT: A  109 THR cc_start: 0.7533 (OUTLIER) cc_final: 0.7269 (p)
REVERT: A  260 VAL cc_start: 0.8567 (m) cc_final: 0.8259 (p)
REVERT: A  377 MET cc_start: 0.6782 (tmm) cc_final: 0.6413 (tmm)
REVERT: A  397 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7274 (tt)
REVERT: A  411 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7182 (mm-30)
REVERT: B    3 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.6466 (tt0)
REVERT: B   91 VAL cc_start: 0.7812 (m) cc_final: 0.7517 (p)
REVERT: B  299 MET cc_start: 0.7859 (mmt) cc_final: 0.7455 (mmt)
  outliers start: 30
  outliers final: 23
  residues processed: 176
  average time/residue: 0.0922
  time to fit residues: 23.8146
Evaluate side-chains
  183 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 155
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   10 VAL
Chi-restraints excluded: chain K residue   12 VAL
Chi-restraints excluded: chain K residue   31 SER
Chi-restraints excluded: chain K residue   59 HIS
Chi-restraints excluded: chain K residue   86 PHE
Chi-restraints excluded: chain K residue  133 THR
Chi-restraints excluded: chain K residue  154 VAL
Chi-restraints excluded: chain K residue  174 LEU
Chi-restraints excluded: chain K residue  210 MET
Chi-restraints excluded: chain K residue  215 SER
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  108 TYR
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain A residue  160 ASP
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  307 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 28 optimal weight:    0.0870
   chunk 83 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   overall best weight:    1.3764

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

Flipped N/Q/H residues before XYZ refinement:
K  59 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.137207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.119686 restraints weight = 14519.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 3.29
r_work: 0.3452 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3449
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3449 r_free = 0.3449    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3449 r_free = 0.3449    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3449
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7057
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9992  Z= 0.187
  Angle     :  0.603  12.801  13555  Z= 0.303
  Chirality :  0.046   0.288   1490
  Planarity :  0.006   0.077   1764
  Dihedral  :  8.222 126.365   1474
  Min Nonbonded Distance : 1.813

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.90 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 20.00 %
    Favored  : 76.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.24), residues: 1226
  helix:  1.73 (0.23), residues: 511
  sheet:  0.64 (0.37), residues: 226
  loop : -1.59 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 221 
 TYR   0.019   0.002   TYR A 224 
 PHE   0.021   0.002   PHE B 378 
 TRP   0.015   0.002   TRP B 344 
 HIS   0.007   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 9992)
  covalent geometry    : angle       0.60279 (13555)
  hydrogen bonds       : bond        0.04545 (  410)
  hydrogen bonds       : angle       3.96383 ( 1227)

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 165
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
REVERT: K  159 ASN cc_start: 0.7351 (t0) cc_final: 0.7113 (t0)
REVERT: K  307 ARG cc_start: 0.7698 (mtt180) cc_final: 0.7237 (ttm-80)
REVERT: K  322 ASN cc_start: 0.8796 (p0) cc_final: 0.8338 (p0)
REVERT: A   26 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7218 (mm)
REVERT: A  109 THR cc_start: 0.7511 (OUTLIER) cc_final: 0.7256 (p)
REVERT: A  260 VAL cc_start: 0.8587 (m) cc_final: 0.8300 (p)
REVERT: A  377 MET cc_start: 0.6786 (tmm) cc_final: 0.6331 (tmm)
REVERT: A  397 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7443 (tt)
REVERT: A  411 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7161 (mm-30)
REVERT: B    3 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6426 (tt0)
REVERT: B  161 ASP cc_start: 0.7929 (t0) cc_final: 0.7280 (t0)
REVERT: B  299 MET cc_start: 0.7966 (mmt) cc_final: 0.7546 (mmt)
REVERT: B  318 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7266 (mmm-85)
  outliers start: 39
  outliers final: 30
  residues processed: 188
  average time/residue: 0.0910
  time to fit residues: 25.2911
Evaluate side-chains
  199 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 164
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   10 VAL
Chi-restraints excluded: chain K residue   12 VAL
Chi-restraints excluded: chain K residue   24 SER
Chi-restraints excluded: chain K residue   31 SER
Chi-restraints excluded: chain K residue   59 HIS
Chi-restraints excluded: chain K residue   86 PHE
Chi-restraints excluded: chain K residue  133 THR
Chi-restraints excluded: chain K residue  154 VAL
Chi-restraints excluded: chain K residue  174 LEU
Chi-restraints excluded: chain K residue  215 SER
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  108 TYR
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain A residue  160 ASP
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   48 ASN
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  193 VAL
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  307 HIS
Chi-restraints excluded: chain B residue  318 ARG
Chi-restraints excluded: chain B residue  388 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 115 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0970
   chunk 54 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
K  59 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.138382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.120667 restraints weight = 14633.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3592 rms_B_bonded: 3.32
r_work: 0.3450 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3444
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3444 r_free = 0.3444    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3444 r_free = 0.3444    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3444
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7069
moved from start:          0.2394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9992  Z= 0.147
  Angle     :  0.571   8.998  13555  Z= 0.288
  Chirality :  0.045   0.278   1490
  Planarity :  0.005   0.079   1764
  Dihedral  :  8.178 122.633   1474
  Min Nonbonded Distance : 1.844

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.41 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 20.47 %
    Favored  : 75.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.24), residues: 1226
  helix:  1.76 (0.23), residues: 511
  sheet:  0.66 (0.37), residues: 224
  loop : -1.60 (0.27), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 221 
 TYR   0.030   0.002   TYR A 224 
 PHE   0.015   0.002   PHE B 378 
 TRP   0.015   0.001   TRP B 344 
 HIS   0.006   0.001   HIS K  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 9992)
  covalent geometry    : angle       0.57114 (13555)
  hydrogen bonds       : bond        0.04132 (  410)
  hydrogen bonds       : angle       3.90056 ( 1227)

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 166
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
REVERT: K  159 ASN cc_start: 0.7362 (t0) cc_final: 0.7124 (t0)
REVERT: K  180 ASP cc_start: 0.8258 (t0) cc_final: 0.7906 (t0)
REVERT: K  307 ARG cc_start: 0.7724 (mtt180) cc_final: 0.7228 (ttm-80)
REVERT: K  322 ASN cc_start: 0.8802 (p0) cc_final: 0.8352 (p0)
REVERT: A   26 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7291 (mm)
REVERT: A  109 THR cc_start: 0.7522 (OUTLIER) cc_final: 0.7259 (p)
REVERT: A  260 VAL cc_start: 0.8593 (m) cc_final: 0.8311 (p)
REVERT: A  377 MET cc_start: 0.6779 (tmm) cc_final: 0.6341 (tmm)
REVERT: A  397 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7526 (tt)
REVERT: A  411 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7158 (mm-30)
REVERT: B    3 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6437 (tt0)
REVERT: B   26 ASP cc_start: 0.7897 (t0) cc_final: 0.7626 (t0)
REVERT: B  161 ASP cc_start: 0.7918 (t0) cc_final: 0.7287 (t0)
REVERT: B  299 MET cc_start: 0.7946 (mmt) cc_final: 0.7556 (mmt)
REVERT: B  318 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7275 (mmm-85)
REVERT: B  323 MET cc_start: 0.7639 (mtm) cc_final: 0.7434 (mtm)
  outliers start: 35
  outliers final: 30
  residues processed: 183
  average time/residue: 0.0842
  time to fit residues: 22.5519
Evaluate side-chains
  200 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 165
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   10 VAL
Chi-restraints excluded: chain K residue   12 VAL
Chi-restraints excluded: chain K residue   24 SER
Chi-restraints excluded: chain K residue   31 SER
Chi-restraints excluded: chain K residue   59 HIS
Chi-restraints excluded: chain K residue   86 PHE
Chi-restraints excluded: chain K residue  133 THR
Chi-restraints excluded: chain K residue  154 VAL
Chi-restraints excluded: chain K residue  174 LEU
Chi-restraints excluded: chain K residue  210 MET
Chi-restraints excluded: chain K residue  215 SER
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  108 TYR
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain A residue  160 ASP
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   48 ASN
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  158 GLU
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  193 VAL
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  307 HIS
Chi-restraints excluded: chain B residue  318 ARG
Chi-restraints excluded: chain B residue  388 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 39 optimal weight:    9.9990
   chunk 43 optimal weight:    0.9990
   chunk 71 optimal weight:    0.6980
   chunk 1 optimal weight:    4.9990
   chunk 116 optimal weight:    2.9990
   chunk 102 optimal weight:    3.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
K  59 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.138667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.121130 restraints weight = 14442.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3601 rms_B_bonded: 3.28
r_work: 0.3457 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3468
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3468 r_free = 0.3468    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3468 r_free = 0.3468    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3468
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7037
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9992  Z= 0.138
  Angle     :  0.570   8.524  13555  Z= 0.287
  Chirality :  0.045   0.261   1490
  Planarity :  0.005   0.080   1764
  Dihedral  :  8.142 122.464   1474
  Min Nonbonded Distance : 1.853

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.73 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 20.47 %
    Favored  : 75.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.42 (0.24), residues: 1226
  helix:  1.77 (0.23), residues: 511
  sheet:  0.67 (0.37), residues: 224
  loop : -1.60 (0.27), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 221 
 TYR   0.027   0.002   TYR A 224 
 PHE   0.014   0.002   PHE B 367 
 TRP   0.015   0.001   TRP B 344 
 HIS   0.004   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 9992)
  covalent geometry    : angle       0.57023 (13555)
  hydrogen bonds       : bond        0.03991 (  410)
  hydrogen bonds       : angle       3.84752 ( 1227)

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 169
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
REVERT: K  159 ASN cc_start: 0.7339 (t0) cc_final: 0.7086 (t0)
REVERT: K  180 ASP cc_start: 0.8277 (t0) cc_final: 0.7905 (t0)
REVERT: K  307 ARG cc_start: 0.7730 (mtt180) cc_final: 0.7249 (ttm-80)
REVERT: K  322 ASN cc_start: 0.8795 (p0) cc_final: 0.8348 (p0)
REVERT: A   26 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7238 (mm)
REVERT: A  260 VAL cc_start: 0.8564 (m) cc_final: 0.8281 (p)
REVERT: A  377 MET cc_start: 0.6787 (tmm) cc_final: 0.6383 (tmm)
REVERT: A  397 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7534 (tt)
REVERT: A  411 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7185 (mm-30)
REVERT: B    3 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.6415 (tt0)
REVERT: B   26 ASP cc_start: 0.7920 (t0) cc_final: 0.7658 (t0)
REVERT: B  299 MET cc_start: 0.7923 (mmt) cc_final: 0.7536 (mmt)
REVERT: B  318 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7226 (mmm-85)
  outliers start: 35
  outliers final: 29
  residues processed: 184
  average time/residue: 0.0777
  time to fit residues: 21.0052
Evaluate side-chains
  201 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 168
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   10 VAL
Chi-restraints excluded: chain K residue   12 VAL
Chi-restraints excluded: chain K residue   31 SER
Chi-restraints excluded: chain K residue   59 HIS
Chi-restraints excluded: chain K residue   86 PHE
Chi-restraints excluded: chain K residue  133 THR
Chi-restraints excluded: chain K residue  154 VAL
Chi-restraints excluded: chain K residue  174 LEU
Chi-restraints excluded: chain K residue  210 MET
Chi-restraints excluded: chain K residue  215 SER
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  108 TYR
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain A residue  160 ASP
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   48 ASN
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  307 HIS
Chi-restraints excluded: chain B residue  318 ARG
Chi-restraints excluded: chain B residue  364 SER
Chi-restraints excluded: chain B residue  388 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 114 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 87 optimal weight:    0.5980
   chunk 5 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 104 optimal weight:    1.9990
   chunk 29 optimal weight:   10.0000
   chunk 59 optimal weight:    0.3980
   chunk 97 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
K  59 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.139036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.121524 restraints weight = 14194.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.3607 rms_B_bonded: 3.23
r_work: 0.3465 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3473
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3473 r_free = 0.3473    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3473 r_free = 0.3473    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3473
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7031
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9992  Z= 0.131
  Angle     :  0.570   8.270  13555  Z= 0.287
  Chirality :  0.044   0.236   1490
  Planarity :  0.005   0.079   1764
  Dihedral  :  8.103 121.162   1474
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.41 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 20.47 %
    Favored  : 75.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.25), residues: 1226
  helix:  1.81 (0.23), residues: 510
  sheet:  0.70 (0.37), residues: 224
  loop : -1.60 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K 229 
 TYR   0.029   0.001   TYR A 224 
 PHE   0.014   0.001   PHE B 367 
 TRP   0.014   0.001   TRP B 344 
 HIS   0.010   0.001   HIS K  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 9992)
  covalent geometry    : angle       0.57025 (13555)
  hydrogen bonds       : bond        0.03857 (  410)
  hydrogen bonds       : angle       3.83036 ( 1227)

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

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

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2452 Ramachandran restraints generated.
    1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 165
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
REVERT: K  159 ASN cc_start: 0.7338 (t0) cc_final: 0.7087 (t0)
REVERT: K  180 ASP cc_start: 0.8272 (t0) cc_final: 0.7907 (t0)
REVERT: K  307 ARG cc_start: 0.7743 (mtt180) cc_final: 0.7262 (ttm-80)
REVERT: K  322 ASN cc_start: 0.8813 (p0) cc_final: 0.8374 (p0)
REVERT: A   26 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7238 (mm)
REVERT: A  109 THR cc_start: 0.7488 (OUTLIER) cc_final: 0.7226 (p)
REVERT: A  260 VAL cc_start: 0.8596 (m) cc_final: 0.8316 (p)
REVERT: A  377 MET cc_start: 0.6762 (tmm) cc_final: 0.6354 (tmm)
REVERT: A  397 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7571 (tt)
REVERT: A  411 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7168 (mm-30)
REVERT: B    3 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.6410 (tt0)
REVERT: B   26 ASP cc_start: 0.7907 (t0) cc_final: 0.7633 (t0)
REVERT: B  256 ASN cc_start: 0.7936 (t0) cc_final: 0.7671 (t0)
REVERT: B  299 MET cc_start: 0.7921 (mmt) cc_final: 0.7532 (mmt)
REVERT: B  318 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7213 (mmm-85)
  outliers start: 36
  outliers final: 30
  residues processed: 184
  average time/residue: 0.0852
  time to fit residues: 22.7983
Evaluate side-chains
  200 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 165
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   10 VAL
Chi-restraints excluded: chain K residue   12 VAL
Chi-restraints excluded: chain K residue   31 SER
Chi-restraints excluded: chain K residue   59 HIS
Chi-restraints excluded: chain K residue   60 THR
Chi-restraints excluded: chain K residue   86 PHE
Chi-restraints excluded: chain K residue  133 THR
Chi-restraints excluded: chain K residue  154 VAL
Chi-restraints excluded: chain K residue  174 LEU
Chi-restraints excluded: chain K residue  210 MET
Chi-restraints excluded: chain K residue  215 SER
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  108 TYR
Chi-restraints excluded: chain A residue  109 THR
Chi-restraints excluded: chain A residue  160 ASP
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   48 ASN
Chi-restraints excluded: chain B residue  158 GLU
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  193 VAL
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  307 HIS
Chi-restraints excluded: chain B residue  318 ARG
Chi-restraints excluded: chain B residue  364 SER
Chi-restraints excluded: chain B residue  388 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 71 optimal weight:    0.0170
   chunk 49 optimal weight:    2.9990
   chunk 96 optimal weight:    0.0670
   chunk 92 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 107 optimal weight:    0.6980
   chunk 34 optimal weight:    4.9990
   chunk 89 optimal weight:    4.9990
   chunk 79 optimal weight:    0.8980
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.4756

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

Flipped N/Q/H residues before XYZ refinement:
K  59 HIS
A 258 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.140586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.122884 restraints weight = 14395.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 3.27
r_work: 0.3477 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3481
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3481 r_free = 0.3481    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3482 r_free = 0.3482    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3482
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7005
moved from start:          0.2583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9992  Z= 0.108
  Angle     :  0.555   8.510  13555  Z= 0.278
  Chirality :  0.043   0.224   1490
  Planarity :  0.005   0.078   1764
  Dihedral  :  7.966 116.819   1474
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.16 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 20.57 %
    Favored  : 75.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.55 (0.25), residues: 1226
  helix:  1.91 (0.23), residues: 510
  sheet:  0.77 (0.37), residues: 224
  loop : -1.57 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K 229 
 TYR   0.029   0.001   TYR A 224 
 PHE   0.014   0.001   PHE B 367 
 TRP   0.014   0.001   TRP B 344 
 HIS   0.004   0.001   HIS K  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 9992)
  covalent geometry    : angle       0.55504 (13555)
  hydrogen bonds       : bond        0.03516 (  410)
  hydrogen bonds       : angle       3.77013 ( 1227)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2408.59 seconds
wall clock time: 42 minutes 2.99 seconds (2522.99 seconds total)