Starting phenix.real_space_refine
on Sun Dec 29 05:00:39 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8utw_42552/12_2024/8utw_42552.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8utw_42552/12_2024/8utw_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8utw_42552/12_2024/8utw_42552.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8utw_42552/12_2024/8utw_42552.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8utw_42552/12_2024/8utw_42552.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8utw_42552/12_2024/8utw_42552.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 8.23, per 1000 atoms: 0.84
  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: 2.62
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  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: 1.16
  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: 2.93

  Time building geometry restraints manager: 2.85 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:             4.740
  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:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     27.520
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.870
-------------------------------------------------------------------------------
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= 0.324
  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 : 6.12
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (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
 TRP   0.012   0.001   TRP B 344 
 HIS   0.003   0.001   HIS A  88 
 PHE   0.016   0.002   PHE K  86 
 TYR   0.022   0.002   TYR K 306 
 ARG   0.008   0.001   ARG A 402 

*********************** 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  : 1.102 
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: 0.7091 (p)
REVERT: B   76 VAL cc_start: 0.6428 (t) cc_final: 0.5495 (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: 0.2192
  time to fit residues: 56.6246
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  : 1.097 
-------------------------------------------------------------------------------
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 103 optimal weight:    0.9990
   chunk 92 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 62 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9980
   chunk 95 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   chunk 71 optimal weight:    8.9990
   chunk 110 optimal weight:    0.8980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7008
moved from start:          0.1220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9992  Z= 0.228
  Angle     :  0.640  10.719  13555  Z= 0.314
  Chirality :  0.046   0.451   1490
  Planarity :  0.006   0.086   1764
  Dihedral  : 11.197 123.583   1489
  Min Nonbonded Distance : 1.878

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.16 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 16.89 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.24), residues: 1226
  helix:  1.36 (0.23), residues: 509
  sheet:  0.11 (0.37), residues: 232
  loop : -1.62 (0.27), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 344 
 HIS   0.004   0.001   HIS A  88 
 PHE   0.018   0.002   PHE B 367 
 TYR   0.016   0.002   TYR A 224 
 ARG   0.005   0.001   ARG A 422 

*********************** 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
  205 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 172
  time to evaluate  : 0.958 
Fit side-chains
REVERT: K  167 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7659 (mtm110)
REVERT: A  260 VAL cc_start: 0.8496 (m) cc_final: 0.8187 (p)
REVERT: A  377 MET cc_start: 0.6844 (tmm) cc_final: 0.6545 (tmm)
REVERT: A  411 GLU cc_start: 0.7307 (mm-30) cc_final: 0.6936 (mm-30)
REVERT: B   23 VAL cc_start: 0.7279 (OUTLIER) cc_final: 0.7001 (p)
REVERT: B   76 VAL cc_start: 0.6488 (t) cc_final: 0.5570 (m)
REVERT: B   91 VAL cc_start: 0.7892 (m) cc_final: 0.7646 (p)
REVERT: B  256 ASN cc_start: 0.7925 (m-40) cc_final: 0.7370 (m-40)
REVERT: B  257 MET cc_start: 0.7502 (mmm) cc_final: 0.6986 (mmm)
  outliers start: 33
  outliers final: 16
  residues processed: 190
  average time/residue: 0.2146
  time to fit residues: 57.6387
Evaluate side-chains
  182 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 164
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
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  167 ARG
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  178 SER
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  324 VAL
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
Chi-restraints excluded: chain B residue  176 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 61 optimal weight:    0.0570
   chunk 34 optimal weight:    3.9990
   chunk 92 optimal weight:    0.0670
   chunk 75 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   chunk 110 optimal weight:    2.9990
   chunk 119 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 89 optimal weight:    3.9990
   chunk 109 optimal weight:    5.9990
   overall best weight:    1.2040

-------------------------------------------------------------------------------
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
B  89 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9992  Z= 0.272
  Angle     :  0.624   7.523  13555  Z= 0.313
  Chirality :  0.046   0.461   1490
  Planarity :  0.006   0.088   1764
  Dihedral  :  9.133 126.805   1477
  Min Nonbonded Distance : 1.853

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.98 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 18.40 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.24), residues: 1226
  helix:  1.48 (0.23), residues: 507
  sheet:  0.19 (0.37), residues: 232
  loop : -1.57 (0.27), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 344 
 HIS   0.006   0.001   HIS A  88 
 PHE   0.019   0.002   PHE B 367 
 TYR   0.029   0.002   TYR A 224 
 ARG   0.008   0.001   ARG B 251 

*********************** 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
  225 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 187
  time to evaluate  : 1.027 
Fit side-chains
   revert: symmetry clash
REVERT: K  148 GLU cc_start: 0.7387 (pt0) cc_final: 0.7069 (pt0)
REVERT: K  167 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7662 (mtm110)
REVERT: A   26 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7241 (mm)
REVERT: A   97 GLU cc_start: 0.7565 (pt0) cc_final: 0.7256 (pt0)
REVERT: A  260 VAL cc_start: 0.8522 (m) cc_final: 0.8239 (p)
REVERT: A  377 MET cc_start: 0.6878 (tmm) cc_final: 0.6559 (tmm)
REVERT: A  411 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6946 (mm-30)
REVERT: B   23 VAL cc_start: 0.7251 (OUTLIER) cc_final: 0.7002 (p)
REVERT: B   26 ASP cc_start: 0.7862 (t0) cc_final: 0.7602 (t0)
REVERT: B   91 VAL cc_start: 0.7921 (m) cc_final: 0.7650 (p)
REVERT: B  161 ASP cc_start: 0.7958 (t0) cc_final: 0.7522 (t0)
REVERT: B  299 MET cc_start: 0.7680 (mmt) cc_final: 0.7272 (mmt)
REVERT: B  383 GLU cc_start: 0.7572 (tp30) cc_final: 0.7199 (tt0)
REVERT: B  395 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7499 (tt)
  outliers start: 38
  outliers final: 21
  residues processed: 211
  average time/residue: 0.2166
  time to fit residues: 65.9336
Evaluate side-chains
  206 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 181
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
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  131 ASN
Chi-restraints excluded: chain K residue  167 ARG
Chi-restraints excluded: chain K residue  215 SER
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  341 ILE
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  438 ASP
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  233 MET
Chi-restraints excluded: chain B residue  307 HIS
Chi-restraints excluded: chain B residue  388 MET
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 83 optimal weight:    0.0470
   chunk 57 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 52 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 111 optimal weight:    0.9980
   chunk 117 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9990
   chunk 105 optimal weight:    0.4980
   chunk 31 optimal weight:    0.7980
   chunk 98 optimal weight:    0.8980
   overall best weight:    0.5678

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6999
moved from start:          0.1890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9992  Z= 0.177
  Angle     :  0.563   6.299  13555  Z= 0.286
  Chirality :  0.045   0.397   1490
  Planarity :  0.005   0.081   1764
  Dihedral  :  8.545 120.967   1477
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.08 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 17.55 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.25), residues: 1226
  helix:  1.67 (0.23), residues: 508
  sheet:  0.41 (0.38), residues: 225
  loop : -1.54 (0.26), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 344 
 HIS   0.008   0.001   HIS K  59 
 PHE   0.017   0.001   PHE B 367 
 TYR   0.019   0.001   TYR A 224 
 ARG   0.006   0.000   ARG B 251 

*********************** 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
  204 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 166
  time to evaluate  : 1.039 
Fit side-chains
REVERT: K  307 ARG cc_start: 0.7785 (mtp180) cc_final: 0.7138 (ttm-80)
REVERT: A   26 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7248 (mm)
REVERT: A   97 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7085 (pt0)
REVERT: A  260 VAL cc_start: 0.8537 (m) cc_final: 0.8250 (p)
REVERT: A  377 MET cc_start: 0.6805 (tmm) cc_final: 0.6346 (tmm)
REVERT: A  411 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6956 (mm-30)
REVERT: B    3 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6526 (tt0)
REVERT: B   23 VAL cc_start: 0.7225 (OUTLIER) cc_final: 0.7003 (p)
REVERT: B   76 VAL cc_start: 0.6429 (t) cc_final: 0.6163 (t)
REVERT: B   91 VAL cc_start: 0.7860 (m) cc_final: 0.7583 (p)
REVERT: B   94 GLN cc_start: 0.7815 (mp10) cc_final: 0.7543 (mp10)
REVERT: B  161 ASP cc_start: 0.7921 (t0) cc_final: 0.7438 (t0)
REVERT: B  257 MET cc_start: 0.7604 (mmm) cc_final: 0.7292 (mmm)
REVERT: B  299 MET cc_start: 0.7677 (mmt) cc_final: 0.7283 (mmt)
REVERT: B  318 ARG cc_start: 0.7619 (mtp-110) cc_final: 0.7338 (mmm-85)
REVERT: B  330 MET cc_start: 0.5108 (mmm) cc_final: 0.4703 (mmm)
REVERT: B  383 GLU cc_start: 0.7552 (tp30) cc_final: 0.7187 (tt0)
REVERT: B  395 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7444 (tt)
  outliers start: 38
  outliers final: 19
  residues processed: 192
  average time/residue: 0.2144
  time to fit residues: 58.7270
Evaluate side-chains
  186 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 162
  time to evaluate  : 1.167 
-------------------------------------------------------------------------------
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   60 THR
Chi-restraints excluded: chain K residue   86 PHE
Chi-restraints excluded: chain K residue  131 ASN
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 A residue   26 LEU
Chi-restraints excluded: chain A residue   92 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  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  405 VAL
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   23 VAL
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  395 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 66 optimal weight:    0.6980
   chunk 1 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   chunk 100 optimal weight:    0.5980
   chunk 81 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9990
   chunk 105 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0980
   chunk 39 optimal weight:    7.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6993
moved from start:          0.2112

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= 0.172
  Angle     :  0.554   8.633  13555  Z= 0.278
  Chirality :  0.044   0.327   1490
  Planarity :  0.005   0.078   1764
  Dihedral  :  8.202 120.413   1475
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.24 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 18.58 %
    Favored  : 78.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.25), residues: 1226
  helix:  1.74 (0.23), residues: 510
  sheet:  0.42 (0.36), residues: 233
  loop : -1.45 (0.27), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 344 
 HIS   0.003   0.001   HIS A  61 
 PHE   0.015   0.001   PHE B 367 
 TYR   0.015   0.001   TYR A 224 
 ARG   0.006   0.000   ARG B 251 

*********************** 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
  199 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 168
  time to evaluate  : 1.038 
Fit side-chains
REVERT: K  148 GLU cc_start: 0.7244 (pt0) cc_final: 0.6974 (pt0)
REVERT: A  109 THR cc_start: 0.7443 (OUTLIER) cc_final: 0.7161 (p)
REVERT: A  260 VAL cc_start: 0.8493 (m) cc_final: 0.8254 (p)
REVERT: A  377 MET cc_start: 0.6792 (tmm) cc_final: 0.6336 (tmm)
REVERT: A  397 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7126 (tt)
REVERT: A  411 GLU cc_start: 0.7391 (mm-30) cc_final: 0.6980 (mm-30)
REVERT: B   26 ASP cc_start: 0.7848 (t0) cc_final: 0.7541 (t0)
REVERT: B   76 VAL cc_start: 0.6431 (t) cc_final: 0.6178 (t)
REVERT: B   91 VAL cc_start: 0.7845 (m) cc_final: 0.7565 (p)
REVERT: B   94 GLN cc_start: 0.7863 (mp10) cc_final: 0.7571 (mp10)
REVERT: B  299 MET cc_start: 0.7693 (mmt) cc_final: 0.7264 (mmt)
REVERT: B  318 ARG cc_start: 0.7557 (mtp-110) cc_final: 0.7056 (mmm-85)
REVERT: B  395 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7412 (tt)
  outliers start: 31
  outliers final: 24
  residues processed: 187
  average time/residue: 0.2081
  time to fit residues: 57.6352
Evaluate side-chains
  186 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 159
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
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  154 VAL
Chi-restraints excluded: chain K residue  174 LEU
Chi-restraints excluded: chain K residue  215 SER
Chi-restraints excluded: chain K residue  256 ASP
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  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  375 VAL
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   48 ASN
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  307 HIS
Chi-restraints excluded: chain B residue  388 MET
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 106 optimal weight:    0.9990
   chunk 23 optimal weight:   10.0000
   chunk 69 optimal weight:    0.5980
   chunk 29 optimal weight:    0.2980
   chunk 118 optimal weight:    0.0980
   chunk 97 optimal weight:    0.7980
   chunk 54 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 39 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9980
   chunk 113 optimal weight:    0.0040
   overall best weight:    0.3592

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6971
moved from start:          0.2251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9992  Z= 0.146
  Angle     :  0.533   6.613  13555  Z= 0.268
  Chirality :  0.043   0.289   1490
  Planarity :  0.005   0.076   1764
  Dihedral  :  8.004 120.690   1474
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.08 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 20.09 %
    Favored  : 76.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.25), residues: 1226
  helix:  1.88 (0.23), residues: 511
  sheet:  0.67 (0.37), residues: 225
  loop : -1.44 (0.27), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 344 
 HIS   0.014   0.001   HIS K  59 
 PHE   0.015   0.001   PHE B 367 
 TYR   0.013   0.001   TYR B 310 
 ARG   0.008   0.000   ARG B 251 

*********************** 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
  189 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 157
  time to evaluate  : 1.085 
Fit side-chains
REVERT: K  210 MET cc_start: 0.5317 (OUTLIER) cc_final: 0.4779 (ptt)
REVERT: A   26 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7259 (mm)
REVERT: A  109 THR cc_start: 0.7423 (OUTLIER) cc_final: 0.7163 (p)
REVERT: A  260 VAL cc_start: 0.8534 (m) cc_final: 0.8256 (p)
REVERT: A  377 MET cc_start: 0.6779 (tmm) cc_final: 0.6301 (tmm)
REVERT: A  397 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7239 (tt)
REVERT: A  411 GLU cc_start: 0.7380 (mm-30) cc_final: 0.7025 (mm-30)
REVERT: B   76 VAL cc_start: 0.6405 (t) cc_final: 0.6157 (t)
REVERT: B   91 VAL cc_start: 0.7806 (m) cc_final: 0.7539 (p)
REVERT: B  251 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.5355 (ttp80)
REVERT: B  299 MET cc_start: 0.7711 (mmt) cc_final: 0.7280 (mmt)
  outliers start: 32
  outliers final: 18
  residues processed: 179
  average time/residue: 0.1843
  time to fit residues: 49.1257
Evaluate side-chains
  176 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 153
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
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 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  397 LEU
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain B residue   48 ASN
Chi-restraints excluded: chain B residue  251 ARG
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 13 optimal weight:    6.9990
   chunk 67 optimal weight:    0.5980
   chunk 86 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 117 optimal weight:    0.9990
   chunk 73 optimal weight:    0.5980
   chunk 71 optimal weight:    0.6980
   chunk 54 optimal weight:    6.9990
   chunk 72 optimal weight:    0.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6992
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      :  0.003   0.034   9992  Z= 0.186
  Angle     :  0.560  13.723  13555  Z= 0.277
  Chirality :  0.044   0.282   1490
  Planarity :  0.005   0.076   1764
  Dihedral  :  8.028 120.128   1474
  Min Nonbonded Distance : 1.884

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.41 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 20.57 %
    Favored  : 76.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.25), residues: 1226
  helix:  1.90 (0.23), residues: 511
  sheet:  0.71 (0.37), residues: 225
  loop : -1.45 (0.27), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 344 
 HIS   0.013   0.001   HIS K  59 
 PHE   0.015   0.001   PHE B 367 
 TYR   0.013   0.001   TYR B 425 
 ARG   0.006   0.000   ARG B 251 

*********************** 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
  198 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 167
  time to evaluate  : 1.040 
Fit side-chains
REVERT: K  210 MET cc_start: 0.5250 (OUTLIER) cc_final: 0.4707 (ptt)
REVERT: A   26 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7251 (mm)
REVERT: A  109 THR cc_start: 0.7468 (OUTLIER) cc_final: 0.7208 (p)
REVERT: A  221 ARG cc_start: 0.7842 (mtt-85) cc_final: 0.7630 (mtt-85)
REVERT: A  260 VAL cc_start: 0.8529 (m) cc_final: 0.8264 (p)
REVERT: A  377 MET cc_start: 0.6787 (tmm) cc_final: 0.6420 (tmm)
REVERT: A  397 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7339 (tt)
REVERT: A  411 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6999 (mm-30)
REVERT: B   26 ASP cc_start: 0.7830 (t0) cc_final: 0.7529 (t0)
REVERT: B   76 VAL cc_start: 0.6412 (t) cc_final: 0.6158 (t)
REVERT: B   91 VAL cc_start: 0.7840 (m) cc_final: 0.7556 (p)
REVERT: B  299 MET cc_start: 0.7752 (mmt) cc_final: 0.7335 (mmt)
  outliers start: 31
  outliers final: 22
  residues processed: 185
  average time/residue: 0.1889
  time to fit residues: 51.3600
Evaluate side-chains
  186 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 160
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
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  152 GLU
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 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  160 ASP
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  397 LEU
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain B residue   48 ASN
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  364 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 70 optimal weight:    0.0470
   chunk 35 optimal weight:    4.9990
   chunk 23 optimal weight:    6.9990
   chunk 22 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0170
   chunk 92 optimal weight:    1.9990
   chunk 106 optimal weight:    0.0040
   overall best weight:    0.3728

-------------------------------------------------------------------------------
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 298 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6966
moved from start:          0.2460

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= 0.145
  Angle     :  0.547  13.033  13555  Z= 0.270
  Chirality :  0.043   0.264   1490
  Planarity :  0.005   0.078   1764
  Dihedral  :  7.936 120.155   1474
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.00 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 20.66 %
    Favored  : 76.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.25), residues: 1226
  helix:  1.99 (0.23), residues: 510
  sheet:  0.74 (0.37), residues: 226
  loop : -1.41 (0.27), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 344 
 HIS   0.008   0.001   HIS K  59 
 PHE   0.014   0.001   PHE B 367 
 TYR   0.012   0.001   TYR B 425 
 ARG   0.007   0.000   ARG B 251 

*********************** 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
  187 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 158
  time to evaluate  : 1.028 
Fit side-chains
   revert: symmetry clash
REVERT: K  210 MET cc_start: 0.5239 (OUTLIER) cc_final: 0.4730 (ptt)
REVERT: A   26 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7272 (mm)
REVERT: A  160 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7787 (t70)
REVERT: A  260 VAL cc_start: 0.8524 (m) cc_final: 0.8260 (p)
REVERT: A  397 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7398 (tt)
REVERT: A  411 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6984 (mm-30)
REVERT: A  415 GLU cc_start: 0.7517 (tt0) cc_final: 0.6903 (tt0)
REVERT: B   26 ASP cc_start: 0.7814 (t0) cc_final: 0.7539 (t0)
REVERT: B   91 VAL cc_start: 0.7815 (m) cc_final: 0.7528 (p)
REVERT: B  299 MET cc_start: 0.7755 (mmt) cc_final: 0.7345 (mmt)
REVERT: B  318 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.7019 (mmm-85)
  outliers start: 29
  outliers final: 18
  residues processed: 176
  average time/residue: 0.1955
  time to fit residues: 50.7704
Evaluate side-chains
  175 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 152
  time to evaluate  : 1.061 
-------------------------------------------------------------------------------
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  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  108 TYR
Chi-restraints excluded: chain A residue  109 THR
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  397 LEU
Chi-restraints excluded: chain A residue  405 VAL
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 112 optimal weight:    0.0060
   chunk 102 optimal weight:    6.9990
   chunk 109 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 47 optimal weight:    0.4980
   chunk 86 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 99 optimal weight:    0.5980
   chunk 103 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0980
   chunk 115 optimal weight:    3.9990
   overall best weight:    0.6398

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6981
moved from start:          0.2527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9992  Z= 0.175
  Angle     :  0.557  12.598  13555  Z= 0.276
  Chirality :  0.043   0.237   1490
  Planarity :  0.005   0.077   1764
  Dihedral  :  7.982 119.529   1474
  Min Nonbonded Distance : 1.892

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.57 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 20.28 %
    Favored  : 76.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.25), residues: 1226
  helix:  1.96 (0.23), residues: 510
  sheet:  0.75 (0.37), residues: 226
  loop : -1.40 (0.27), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 344 
 HIS   0.019   0.001   HIS K  59 
 PHE   0.014   0.001   PHE B 367 
 TYR   0.013   0.001   TYR B 310 
 ARG   0.007   0.000   ARG B 251 

*********************** 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
  188 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 157
  time to evaluate  : 0.995 
Fit side-chains
   revert: symmetry clash
REVERT: K  210 MET cc_start: 0.5305 (OUTLIER) cc_final: 0.4799 (ptt)
REVERT: A   26 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7267 (mm)
REVERT: A  109 THR cc_start: 0.7484 (OUTLIER) cc_final: 0.7220 (p)
REVERT: A  160 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7783 (t70)
REVERT: A  260 VAL cc_start: 0.8524 (m) cc_final: 0.8272 (p)
REVERT: A  377 MET cc_start: 0.6746 (tmm) cc_final: 0.6244 (tmm)
REVERT: A  397 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7491 (tt)
REVERT: A  411 GLU cc_start: 0.7323 (mm-30) cc_final: 0.6955 (mm-30)
REVERT: B   26 ASP cc_start: 0.7800 (t0) cc_final: 0.7524 (t0)
REVERT: B  299 MET cc_start: 0.7788 (mmt) cc_final: 0.7350 (mmt)
REVERT: B  318 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.7073 (mmm-85)
REVERT: B  327 ASP cc_start: 0.6622 (OUTLIER) cc_final: 0.6333 (t0)
  outliers start: 31
  outliers final: 22
  residues processed: 177
  average time/residue: 0.1843
  time to fit residues: 48.3723
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  : 1.036 
-------------------------------------------------------------------------------
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  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  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  259 LEU
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  375 VAL
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain B residue   48 ASN
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  327 ASP
Chi-restraints excluded: chain B residue  364 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 70 optimal weight:    0.3980
   chunk 54 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 121 optimal weight:    0.1980
   chunk 111 optimal weight:    0.7980
   chunk 96 optimal weight:    0.0010
   chunk 10 optimal weight:    3.9990
   chunk 74 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9990
   chunk 76 optimal weight:    4.9990
   chunk 103 optimal weight:    1.9990
   overall best weight:    0.4186

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6961
moved from start:          0.2619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9992  Z= 0.148
  Angle     :  0.551  12.567  13555  Z= 0.272
  Chirality :  0.043   0.216   1490
  Planarity :  0.005   0.078   1764
  Dihedral  :  7.933 119.967   1474
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.24 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 20.75 %
    Favored  : 76.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.25), residues: 1226
  helix:  1.99 (0.23), residues: 511
  sheet:  0.78 (0.37), residues: 224
  loop : -1.38 (0.27), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 344 
 HIS   0.010   0.001   HIS K  59 
 PHE   0.014   0.001   PHE B 367 
 TYR   0.026   0.001   TYR A 224 
 ARG   0.007   0.000   ARG B 251 

********************** 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
  191 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 162
  time to evaluate  : 1.102 
Fit side-chains
   revert: symmetry clash
REVERT: K  210 MET cc_start: 0.5439 (OUTLIER) cc_final: 0.4881 (ptt)
REVERT: A   26 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7365 (mm)
REVERT: A  109 THR cc_start: 0.7443 (OUTLIER) cc_final: 0.7184 (p)
REVERT: A  160 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7787 (t70)
REVERT: A  260 VAL cc_start: 0.8528 (m) cc_final: 0.8276 (p)
REVERT: A  377 MET cc_start: 0.6729 (tmm) cc_final: 0.6340 (tmm)
REVERT: A  397 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7524 (tt)
REVERT: A  411 GLU cc_start: 0.7337 (mm-30) cc_final: 0.6965 (mm-30)
REVERT: B   26 ASP cc_start: 0.7817 (t0) cc_final: 0.7536 (t0)
REVERT: B  299 MET cc_start: 0.7765 (mmt) cc_final: 0.7334 (mmt)
REVERT: B  318 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.7028 (mmm-85)
REVERT: B  327 ASP cc_start: 0.6530 (OUTLIER) cc_final: 0.6298 (t0)
  outliers start: 29
  outliers final: 22
  residues processed: 179
  average time/residue: 0.1834
  time to fit residues: 48.9536
Evaluate side-chains
  190 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 161
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
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  174 LEU
Chi-restraints excluded: chain K residue  210 MET
Chi-restraints excluded: chain K residue  215 SER
Chi-restraints excluded: chain K residue  287 GLU
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  160 ASP
Chi-restraints excluded: chain A residue  259 LEU
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  375 VAL
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain B residue   48 ASN
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  327 ASP
Chi-restraints excluded: chain B residue  364 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 89 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 96 optimal weight:    0.5980
   chunk 40 optimal weight:    3.9990
   chunk 99 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 17 optimal weight:    0.3980
   chunk 85 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.3861 r_free = 0.3861 target = 0.140834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.123937 restraints weight = 14165.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 3.02
r_work: 0.3508 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3519
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3519 r_free = 0.3519    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3519 r_free = 0.3519    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3519
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6947
moved from start:          0.2650

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= 0.195
  Angle     :  0.560  10.769  13555  Z= 0.280
  Chirality :  0.044   0.210   1490
  Planarity :  0.005   0.078   1764
  Dihedral  :  7.980 118.557   1474
  Min Nonbonded Distance : 1.871

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.06 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 20.75 %
    Favored  : 76.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.25), residues: 1226
  helix:  1.93 (0.23), residues: 514
  sheet:  0.76 (0.37), residues: 226
  loop : -1.41 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 344 
 HIS   0.012   0.001   HIS K  59 
 PHE   0.028   0.002   PHE B 270 
 TYR   0.039   0.001   TYR A 224 
 ARG   0.007   0.000   ARG B 251 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2443.36 seconds
wall clock time: 45 minutes 17.84 seconds (2717.84 seconds total)