Starting phenix.real_space_refine
on Fri Feb 14 10:34:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6tqe_10549/02_2025/6tqe_10549.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6tqe_10549/02_2025/6tqe_10549.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6tqe_10549/02_2025/6tqe_10549.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6tqe_10549/02_2025/6tqe_10549.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6tqe_10549/02_2025/6tqe_10549.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6tqe_10549/02_2025/6tqe_10549.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
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       6      5.49       5
     Mg      2      5.21       5
     S      24      5.16       5
     C    6478      2.51       5
     N    1766      2.21       5
     O    1800      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10076
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5006
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 634, 5006
          Classifications: {'peptide': 634}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 30, 'TRANS': 603}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 9.38, per 1000 atoms: 0.93
  Number of scatterers: 10076
  At special positions: 0
  Unit cell: (82.6537, 82.6537, 147.413, 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      24     16.00
     P       6     15.00
     Mg      2     11.99
     O    1800      8.00
     N    1766      7.00
     C    6478      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: 2.47
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2348

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 6 sheets defined
      51.7% alpha, 5.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 44
      removed outlier: 4.371A  pdb=" N   THR A  28 " --> pdb=" O   GLY A  24 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   ILE A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   SER A  30 " --> pdb=" O   ALA A  26 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   CYS A  33 " --> pdb=" O   ILE A  29 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   ALA A  36 " --> pdb=" O   ILE A  32 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   TYR A  43 " --> pdb=" O   VAL A  39 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   LEU A  44 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 55
      removed outlier: 3.679A  pdb=" N   TRP A  52 " --> pdb=" O   GLY A  48 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ARG A  53 " --> pdb=" O   ARG A  49 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ILE A  54 " --> pdb=" O   GLN A  50 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   THR A  55 " --> pdb=" O   PHE A  51 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 48 through 55'
    Processing helix  chain 'A' and resid 61 through 65
      removed outlier: 3.692A  pdb=" N   SER A  64 " --> pdb=" O   GLY A  61 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   VAL A  65 " --> pdb=" O   PRO A  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 61 through 65'
    Processing helix  chain 'A' and resid 66 through 109
      removed outlier: 4.020A  pdb=" N   VAL A  73 " --> pdb=" O   LEU A  69 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   LEU A  74 " --> pdb=" O   MET A  70 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   LEU A  75 " --> pdb=" O   LEU A  71 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   LEU A  76 " --> pdb=" O   GLY A  72 " (cutoff:3.500A)
      removed outlier: 4.722A  pdb=" N   ALA A  81 " --> pdb=" O   SER A  77 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   LEU A  84 " --> pdb=" O   LEU A  80 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LEU A  87 " --> pdb=" O   ARG A  83 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   SER A  89 " --> pdb=" O   ASN A  85 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   ASP A  94 " --> pdb=" O   TYR A  90 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   MET A  95 " --> pdb=" O   GLN A  91 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   TYR A  96 " --> pdb=" O   GLY A  92 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   GLN A 100 " --> pdb=" O   TYR A  96 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LYS A 101 " --> pdb=" O   THR A  97 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   PHE A 103 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   ILE A 106 " --> pdb=" O   ALA A 102 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ALA A 107 " --> pdb=" O   PHE A 103 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLY A 109 " --> pdb=" O   GLY A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 122
      removed outlier: 3.972A  pdb=" N   PHE A 121 " --> pdb=" O   GLY A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 128
      removed outlier: 3.812A  pdb=" N   PHE A 128 " --> pdb=" O   SER A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 140
      removed outlier: 3.816A  pdb=" N   VAL A 136 " --> pdb=" O   ALA A 132 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   VAL A 139 " --> pdb=" O   HIS A 135 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   MET A 140 " --> pdb=" O   VAL A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 147
    Processing helix  chain 'A' and resid 150 through 166
      removed outlier: 4.175A  pdb=" N   TRP A 156 " --> pdb=" O   ALA A 152 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   HIS A 159 " --> pdb=" O   VAL A 155 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   THR A 162 " --> pdb=" O   THR A 158 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLN A 163 " --> pdb=" O   HIS A 159 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ASP A 164 " --> pdb=" O   HIS A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 177
      removed outlier: 3.567A  pdb=" N   LEU A 175 " --> pdb=" O   TYR A 172 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ILE A 177 " --> pdb=" O   ASP A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 190
      removed outlier: 3.615A  pdb=" N   GLN A 189 " --> pdb=" O   ASP A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 198
    Processing helix  chain 'A' and resid 209 through 213
      removed outlier: 3.624A  pdb=" N   SER A 212 " --> pdb=" O   GLY A 209 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   THR A 213 " --> pdb=" O   THR A 210 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 209 through 213'
    Processing helix  chain 'A' and resid 215 through 227
      removed outlier: 3.641A  pdb=" N   VAL A 219 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   GLN A 220 " --> pdb=" O   PHE A 216 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   SER A 221 " --> pdb=" O   GLY A 217 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   SER A 224 " --> pdb=" O   GLN A 220 " (cutoff:3.500A)
      removed outlier: 5.046A  pdb=" N   VAL A 225 " --> pdb=" O   SER A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 265
      removed outlier: 3.677A  pdb=" N   TRP A 252 " --> pdb=" O   ARG A 248 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   VAL A 254 " --> pdb=" O   MET A 250 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   LEU A 255 " --> pdb=" O   PHE A 251 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   VAL A 256 " --> pdb=" O   TRP A 252 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   PHE A 259 " --> pdb=" O   LEU A 255 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   VAL A 260 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ALA A 261 " --> pdb=" O   TYR A 257 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   VAL A 263 " --> pdb=" O   PHE A 259 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ILE A 264 " --> pdb=" O   VAL A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 283
      removed outlier: 3.571A  pdb=" N   LYS A 281 " --> pdb=" O   PHE A 277 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ASN A 283 " --> pdb=" O   ASN A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 295
      removed outlier: 3.865A  pdb=" N   VAL A 291 " --> pdb=" O   ARG A 287 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   LEU A 293 " --> pdb=" O   ALA A 289 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ASP A 295 " --> pdb=" O   VAL A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 304
      removed outlier: 3.826A  pdb=" N   VAL A 300 " --> pdb=" O   ALA A 296 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   GLY A 301 " --> pdb=" O   ALA A 297 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   PHE A 302 " --> pdb=" O   GLU A 298 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   TYR A 303 " --> pdb=" O   ALA A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 323
      removed outlier: 3.605A  pdb=" N   LEU A 313 " --> pdb=" O   GLU A 309 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   GLN A 314 " --> pdb=" O   GLY A 310 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   THR A 318 " --> pdb=" O   GLN A 314 " (cutoff:3.500A)
      Proline residue:  A 319  - end of helix
    Processing helix  chain 'A' and resid 348 through 353
      removed outlier: 3.506A  pdb=" N   GLN A 353 " --> pdb=" O   PRO A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 359
      removed outlier: 3.625A  pdb=" N   PHE A 358 " --> pdb=" O   ALA A 354 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ALA A 359 " --> pdb=" O   PRO A 355 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 354 through 359'
    Processing helix  chain 'A' and resid 364 through 382
      removed outlier: 4.095A  pdb=" N   GLY A 368 " --> pdb=" O   PHE A 364 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   SER A 373 " --> pdb=" O   GLN A 369 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ASN A 376 " --> pdb=" O   THR A 372 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   HIS A 378 " --> pdb=" O   PHE A 374 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   ASP A 379 " --> pdb=" O   GLY A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 387
    Processing helix  chain 'A' and resid 388 through 396
      removed outlier: 4.159A  pdb=" N   PHE A 394 " --> pdb=" O   ALA A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 406
      removed outlier: 4.303A  pdb=" N   LEU A 404 " --> pdb=" O   ARG A 400 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   VAL A 405 " --> pdb=" O   LEU A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 473
    Processing helix  chain 'A' and resid 521 through 525
      removed outlier: 3.579A  pdb=" N   LEU A 525 " --> pdb=" O   ASP A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 526 through 531
      removed outlier: 3.666A  pdb=" N   THR A 530 " --> pdb=" O   ARG A 526 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   LYS A 531 " --> pdb=" O   ASP A 527 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 526 through 531'
    Processing helix  chain 'A' and resid 532 through 533
      No H-bonds generated for 'chain 'A' and resid 532 through 533'
    Processing helix  chain 'A' and resid 534 through 538
      removed outlier: 3.831A  pdb=" N   LEU A 537 " --> pdb=" O   LEU A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 566
      removed outlier: 3.549A  pdb=" N   LEU A 565 " --> pdb=" O   PHE A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 597
    Processing helix  chain 'A' and resid 611 through 615
      removed outlier: 3.778A  pdb=" N   HIS A 615 " --> pdb=" O   GLU A 612 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 44
      removed outlier: 4.371A  pdb=" N   THR B  28 " --> pdb=" O   GLY B  24 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   ILE B  29 " --> pdb=" O   LYS B  25 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   SER B  30 " --> pdb=" O   ALA B  26 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   CYS B  33 " --> pdb=" O   ILE B  29 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   ALA B  36 " --> pdb=" O   ILE B  32 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   TYR B  43 " --> pdb=" O   VAL B  39 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   LEU B  44 " --> pdb=" O   LEU B  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 48 through 55
      removed outlier: 3.679A  pdb=" N   TRP B  52 " --> pdb=" O   GLY B  48 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   ARG B  53 " --> pdb=" O   ARG B  49 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ILE B  54 " --> pdb=" O   GLN B  50 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   THR B  55 " --> pdb=" O   PHE B  51 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 48 through 55'
    Processing helix  chain 'B' and resid 61 through 65
      removed outlier: 3.692A  pdb=" N   SER B  64 " --> pdb=" O   GLY B  61 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   VAL B  65 " --> pdb=" O   PRO B  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 61 through 65'
    Processing helix  chain 'B' and resid 66 through 109
      removed outlier: 4.020A  pdb=" N   VAL B  73 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   LEU B  74 " --> pdb=" O   MET B  70 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   LEU B  75 " --> pdb=" O   LEU B  71 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   LEU B  76 " --> pdb=" O   GLY B  72 " (cutoff:3.500A)
      removed outlier: 4.722A  pdb=" N   ALA B  81 " --> pdb=" O   SER B  77 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   LEU B  84 " --> pdb=" O   LEU B  80 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LEU B  87 " --> pdb=" O   ARG B  83 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   SER B  89 " --> pdb=" O   ASN B  85 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   ASP B  94 " --> pdb=" O   TYR B  90 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   MET B  95 " --> pdb=" O   GLN B  91 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   TYR B  96 " --> pdb=" O   GLY B  92 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   GLN B 100 " --> pdb=" O   TYR B  96 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LYS B 101 " --> pdb=" O   THR B  97 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   PHE B 103 " --> pdb=" O   LEU B  99 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   ILE B 106 " --> pdb=" O   ALA B 102 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ALA B 107 " --> pdb=" O   PHE B 103 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLY B 109 " --> pdb=" O   GLY B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 122
      removed outlier: 3.971A  pdb=" N   PHE B 121 " --> pdb=" O   GLY B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 128
      removed outlier: 3.813A  pdb=" N   PHE B 128 " --> pdb=" O   SER B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 140
      removed outlier: 3.815A  pdb=" N   VAL B 136 " --> pdb=" O   ALA B 132 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   VAL B 139 " --> pdb=" O   HIS B 135 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   MET B 140 " --> pdb=" O   VAL B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 147
    Processing helix  chain 'B' and resid 150 through 166
      removed outlier: 4.176A  pdb=" N   TRP B 156 " --> pdb=" O   ALA B 152 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   HIS B 159 " --> pdb=" O   VAL B 155 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   THR B 162 " --> pdb=" O   THR B 158 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLN B 163 " --> pdb=" O   HIS B 159 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ASP B 164 " --> pdb=" O   HIS B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 177
      removed outlier: 3.569A  pdb=" N   LEU B 175 " --> pdb=" O   TYR B 172 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ILE B 177 " --> pdb=" O   ASP B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 185 through 190
      removed outlier: 3.614A  pdb=" N   GLN B 189 " --> pdb=" O   ASP B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 198
    Processing helix  chain 'B' and resid 209 through 213
      removed outlier: 3.623A  pdb=" N   SER B 212 " --> pdb=" O   GLY B 209 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   THR B 213 " --> pdb=" O   THR B 210 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 209 through 213'
    Processing helix  chain 'B' and resid 215 through 227
      removed outlier: 3.640A  pdb=" N   VAL B 219 " --> pdb=" O   LEU B 215 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   GLN B 220 " --> pdb=" O   PHE B 216 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   SER B 221 " --> pdb=" O   GLY B 217 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   SER B 224 " --> pdb=" O   GLN B 220 " (cutoff:3.500A)
      removed outlier: 5.046A  pdb=" N   VAL B 225 " --> pdb=" O   SER B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 265
      removed outlier: 3.678A  pdb=" N   TRP B 252 " --> pdb=" O   ARG B 248 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   VAL B 254 " --> pdb=" O   MET B 250 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   LEU B 255 " --> pdb=" O   PHE B 251 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   VAL B 256 " --> pdb=" O   TRP B 252 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   PHE B 259 " --> pdb=" O   LEU B 255 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   VAL B 260 " --> pdb=" O   VAL B 256 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ALA B 261 " --> pdb=" O   TYR B 257 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   VAL B 263 " --> pdb=" O   PHE B 259 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ILE B 264 " --> pdb=" O   VAL B 260 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 277 through 283
      removed outlier: 3.572A  pdb=" N   LYS B 281 " --> pdb=" O   PHE B 277 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ASN B 283 " --> pdb=" O   ASN B 279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 295
      removed outlier: 3.866A  pdb=" N   VAL B 291 " --> pdb=" O   ARG B 287 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   LEU B 293 " --> pdb=" O   ALA B 289 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ASP B 295 " --> pdb=" O   VAL B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 304
      removed outlier: 3.826A  pdb=" N   VAL B 300 " --> pdb=" O   ALA B 296 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   GLY B 301 " --> pdb=" O   ALA B 297 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   PHE B 302 " --> pdb=" O   GLU B 298 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   TYR B 303 " --> pdb=" O   ALA B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 323
      removed outlier: 3.605A  pdb=" N   LEU B 313 " --> pdb=" O   GLU B 309 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   GLN B 314 " --> pdb=" O   GLY B 310 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   THR B 318 " --> pdb=" O   GLN B 314 " (cutoff:3.500A)
      Proline residue:  B 319  - end of helix
    Processing helix  chain 'B' and resid 348 through 353
      removed outlier: 3.506A  pdb=" N   GLN B 353 " --> pdb=" O   PRO B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 359
      removed outlier: 3.625A  pdb=" N   PHE B 358 " --> pdb=" O   ALA B 354 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ALA B 359 " --> pdb=" O   PRO B 355 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 354 through 359'
    Processing helix  chain 'B' and resid 364 through 382
      removed outlier: 4.096A  pdb=" N   GLY B 368 " --> pdb=" O   PHE B 364 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   SER B 373 " --> pdb=" O   GLN B 369 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ASN B 376 " --> pdb=" O   THR B 372 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   HIS B 378 " --> pdb=" O   PHE B 374 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   ASP B 379 " --> pdb=" O   GLY B 375 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 382 through 387
    Processing helix  chain 'B' and resid 388 through 396
      removed outlier: 4.159A  pdb=" N   PHE B 394 " --> pdb=" O   ALA B 390 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 398 through 406
      removed outlier: 4.301A  pdb=" N   LEU B 404 " --> pdb=" O   ARG B 400 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   VAL B 405 " --> pdb=" O   LEU B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 467 through 473
    Processing helix  chain 'B' and resid 521 through 525
      removed outlier: 3.579A  pdb=" N   LEU B 525 " --> pdb=" O   ASP B 522 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 526 through 531
      removed outlier: 3.666A  pdb=" N   THR B 530 " --> pdb=" O   ARG B 526 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   LYS B 531 " --> pdb=" O   ASP B 527 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 526 through 531'
    Processing helix  chain 'B' and resid 532 through 533
      No H-bonds generated for 'chain 'B' and resid 532 through 533'
    Processing helix  chain 'B' and resid 534 through 538
      removed outlier: 3.829A  pdb=" N   LEU B 537 " --> pdb=" O   LEU B 534 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 559 through 566
      removed outlier: 3.548A  pdb=" N   LEU B 565 " --> pdb=" O   PHE B 561 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 585 through 597
    Processing helix  chain 'B' and resid 611 through 615
      removed outlier: 3.779A  pdb=" N   HIS B 615 " --> pdb=" O   GLU B 612 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 418 through 421
      removed outlier: 6.598A  pdb=" N   LEU A 418 " --> pdb=" O   LEU A 484 " (cutoff:3.500A)
      removed outlier: 7.592A  pdb=" N   ARG A 486 " --> pdb=" O   LEU A 418 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   ARG A 420 " --> pdb=" O   ARG A 486 " (cutoff:3.500A)
      removed outlier: 7.210A  pdb=" N   VAL A 434 " --> pdb=" O   LEU A 442 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   LEU A 442 " --> pdb=" O   VAL A 434 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 427 through 429
    Processing sheet with id=AA3, first strand: chain 'A' and resid 573 through 575
      removed outlier: 3.605A  pdb=" N   VAL A 605 " --> pdb=" O   LEU A 574 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   LEU A 456 " --> pdb=" O   SER A 604 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   SER A 455 " --> pdb=" O   ASN A 617 " (cutoff:3.500A)
      removed outlier: 7.973A  pdb=" N   LEU A 619 " --> pdb=" O   SER A 455 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   VAL A 457 " --> pdb=" O   LEU A 619 " (cutoff:3.500A)
      removed outlier: 7.906A  pdb=" N   LEU A 621 " --> pdb=" O   VAL A 457 " (cutoff:3.500A)
      removed outlier: 7.245A  pdb=" N   THR A 459 " --> pdb=" O   LEU A 621 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 418 through 421
      removed outlier: 6.597A  pdb=" N   LEU B 418 " --> pdb=" O   LEU B 484 " (cutoff:3.500A)
      removed outlier: 7.592A  pdb=" N   ARG B 486 " --> pdb=" O   LEU B 418 " (cutoff:3.500A)
      removed outlier: 6.185A  pdb=" N   ARG B 420 " --> pdb=" O   ARG B 486 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   VAL B 434 " --> pdb=" O   LEU B 442 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   LEU B 442 " --> pdb=" O   VAL B 434 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 427 through 429
    Processing sheet with id=AA6, first strand: chain 'B' and resid 573 through 575
      removed outlier: 3.605A  pdb=" N   VAL B 605 " --> pdb=" O   LEU B 574 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   LEU B 456 " --> pdb=" O   SER B 604 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   SER B 455 " --> pdb=" O   ASN B 617 " (cutoff:3.500A)
      removed outlier: 7.974A  pdb=" N   LEU B 619 " --> pdb=" O   SER B 455 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   VAL B 457 " --> pdb=" O   LEU B 619 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   LEU B 621 " --> pdb=" O   VAL B 457 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   THR B 459 " --> pdb=" O   LEU B 621 " (cutoff:3.500A)

    248 hydrogen bonds defined for protein.
    708 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: 2.66

  Time building geometry restraints manager: 2.84 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3257
        1.34 -     1.46: 2248
        1.46 -     1.57: 4771
        1.57 -     1.69: 10
        1.69 -     1.81: 40
  Bond restraints: 10326
  Sorted by residual:
  bond pdb=" C4  ATP A 701 "
       pdb=" C5  ATP A 701 "
    ideal  model  delta    sigma   weight residual
    1.388  1.467 -0.079 1.00e-02 1.00e+04 6.18e+01
  bond pdb=" C4  ATP B 701 "
       pdb=" C5  ATP B 701 "
    ideal  model  delta    sigma   weight residual
    1.388  1.465 -0.077 1.00e-02 1.00e+04 6.01e+01
  bond pdb=" C5  ATP A 701 "
       pdb=" C6  ATP A 701 "
    ideal  model  delta    sigma   weight residual
    1.409  1.472 -0.063 1.00e-02 1.00e+04 3.94e+01
  bond pdb=" C5  ATP B 701 "
       pdb=" C6  ATP B 701 "
    ideal  model  delta    sigma   weight residual
    1.409  1.472 -0.063 1.00e-02 1.00e+04 3.93e+01
  bond pdb=" C5  ATP A 701 "
       pdb=" N7  ATP A 701 "
    ideal  model  delta    sigma   weight residual
    1.387  1.339  0.048 1.00e-02 1.00e+04 2.27e+01
  ... (remaining 10321 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.65: 14006
        4.65 -     9.31: 72
        9.31 -    13.96: 6
       13.96 -    18.62: 0
       18.62 -    23.27: 4
  Bond angle restraints: 14088
  Sorted by residual:
  angle pdb=" PB  ATP A 701 "
        pdb=" O3B ATP A 701 "
        pdb=" PG  ATP A 701 "
      ideal   model   delta    sigma   weight residual
     139.87  116.60   23.27 1.00e+00 1.00e+00 5.42e+02
  angle pdb=" PB  ATP B 701 "
        pdb=" O3B ATP B 701 "
        pdb=" PG  ATP B 701 "
      ideal   model   delta    sigma   weight residual
     139.87  116.62   23.25 1.00e+00 1.00e+00 5.41e+02
  angle pdb=" PA  ATP A 701 "
        pdb=" O3A ATP A 701 "
        pdb=" PB  ATP A 701 "
      ideal   model   delta    sigma   weight residual
     136.83  115.99   20.84 1.00e+00 1.00e+00 4.34e+02
  angle pdb=" PA  ATP B 701 "
        pdb=" O3A ATP B 701 "
        pdb=" PB  ATP B 701 "
      ideal   model   delta    sigma   weight residual
     136.83  116.02   20.81 1.00e+00 1.00e+00 4.33e+02
  angle pdb=" C5  ATP B 701 "
        pdb=" C4  ATP B 701 "
        pdb=" N3  ATP B 701 "
      ideal   model   delta    sigma   weight residual
     126.80  118.05    8.75 1.00e+00 1.00e+00 7.66e+01
  ... (remaining 14083 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.47: 5382
       17.47 -    34.95: 552
       34.95 -    52.42: 124
       52.42 -    69.89: 20
       69.89 -    87.37: 8
  Dihedral angle restraints: 6086
    sinusoidal: 2436
      harmonic: 3650
  Sorted by residual:
  dihedral pdb=" CA  SER B  13 "
           pdb=" C   SER B  13 "
           pdb=" N   ARG B  14 "
           pdb=" CA  ARG B  14 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.68  -26.32     0      5.00e+00 4.00e-02 2.77e+01
  dihedral pdb=" CA  SER A  13 "
           pdb=" C   SER A  13 "
           pdb=" N   ARG A  14 "
           pdb=" CA  ARG A  14 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.72  -26.28     0      5.00e+00 4.00e-02 2.76e+01
  dihedral pdb=" CA  PHE A 358 "
           pdb=" C   PHE A 358 "
           pdb=" N   ALA A 359 "
           pdb=" CA  ALA A 359 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.16   20.84     0      5.00e+00 4.00e-02 1.74e+01
  ... (remaining 6083 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1085
       0.054 -    0.108: 417
       0.108 -    0.162: 74
       0.162 -    0.216: 12
       0.216 -    0.270: 4
  Chirality restraints: 1592
  Sorted by residual:
  chirality pdb=" CA  THR B 318 "
            pdb=" N   THR B 318 "
            pdb=" C   THR B 318 "
            pdb=" CB  THR B 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.26    0.27 2.00e-01 2.50e+01 1.83e+00
  chirality pdb=" CA  THR A 318 "
            pdb=" N   THR A 318 "
            pdb=" C   THR A 318 "
            pdb=" CB  THR A 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.26    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CA  ASN A 183 "
            pdb=" N   ASN A 183 "
            pdb=" C   ASN A 183 "
            pdb=" CB  ASN A 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.24e+00
  ... (remaining 1589 not shown)

  Planarity restraints: 1786
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 436 "    0.034 5.00e-02 4.00e+02   5.15e-02 4.24e+00
        pdb=" N   PRO A 437 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO A 437 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 437 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 436 "   -0.034 5.00e-02 4.00e+02   5.12e-02 4.20e+00
        pdb=" N   PRO B 437 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO B 437 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 437 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 444 "    0.031 5.00e-02 4.00e+02   4.62e-02 3.42e+00
        pdb=" N   PRO B 445 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO B 445 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 445 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1783 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 153
        2.64 -     3.21: 8506
        3.21 -     3.77: 13929
        3.77 -     4.34: 18172
        4.34 -     4.90: 30145
  Nonbonded interactions: 70905
  Sorted by model distance:
  nonbonded pdb=" O2G ATP B 701 "
            pdb="MG    MG B 702 "
     model   vdw
     2.077 2.170
  nonbonded pdb=" O2G ATP A 701 "
            pdb="MG    MG A 702 "
     model   vdw
     2.079 2.170
  nonbonded pdb=" O2B ATP A 701 "
            pdb="MG    MG A 702 "
     model   vdw
     2.109 2.170
  nonbonded pdb=" O2B ATP B 701 "
            pdb="MG    MG B 702 "
     model   vdw
     2.109 2.170
  nonbonded pdb=" OG1 THR A 467 "
            pdb="MG    MG A 702 "
     model   vdw
     2.125 2.170
  ... (remaining 70900 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.520
  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:          0.390
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     27.730
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8804
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      :  0.007   0.082  10326  Z= 0.466
  Angle     :  1.043  23.271  14088  Z= 0.664
  Chirality :  0.057   0.270   1592
  Planarity :  0.006   0.051   1786
  Dihedral  : 14.948  87.368   3738
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 2.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.62 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 10.68 %
    Favored  : 88.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -6.13 (0.15), residues: 1264
  helix: -4.57 (0.09), residues: 654
  sheet: -2.07 (0.42), residues: 120
  loop : -3.59 (0.21), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  12 
 HIS   0.003   0.001   HIS B 615 
 PHE   0.031   0.002   PHE A  88 
 TYR   0.014   0.002   TYR B 327 
 ARG   0.003   0.000   ARG B  49 

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 1.248 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8031 (pp)
REVERT: A  131 MET cc_start: 0.8590 (mtp) cc_final: 0.8258 (ttm)
REVERT: B    5 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8097 (pp)
REVERT: B   14 ARG cc_start: 0.7357 (ttp-110) cc_final: 0.7014 (ttp80)
  outliers start: 8
  outliers final: 4
  residues processed: 72
  average time/residue: 0.2206
  time to fit residues: 23.4180
Evaluate side-chains
  58 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    6.9990
   chunk 95 optimal weight:    0.8980
   chunk 52 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 64 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 98 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 73 optimal weight:    8.9990
   chunk 114 optimal weight:    0.6980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 163 GLN
A 338 ASN
A 618 GLN
B 163 GLN
B 204 ASN
B 338 ASN
B 618 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.078066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.065874 restraints weight = 23969.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.066831 restraints weight = 16964.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.067478 restraints weight = 13190.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.2690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8673
moved from start:          0.1611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  10326  Z= 0.151
  Angle     :  0.587   7.730  14088  Z= 0.292
  Chirality :  0.041   0.165   1592
  Planarity :  0.004   0.059   1786
  Dihedral  :  7.342  69.456   1474
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  3.02 %
    Favored  : 96.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.99 (0.18), residues: 1264
  helix: -3.66 (0.13), residues: 642
  sheet: -1.19 (0.46), residues: 106
  loop : -3.12 (0.23), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 165 
 HIS   0.001   0.000   HIS A 402 
 PHE   0.009   0.001   PHE A 573 
 TYR   0.010   0.001   TYR A 257 
 ARG   0.005   0.000   ARG B 613 

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 95
  time to evaluate  : 1.088 
Fit side-chains
   revert: symmetry clash
REVERT: B   14 ARG cc_start: 0.7245 (ttp-110) cc_final: 0.6973 (ttp80)
  outliers start: 3
  outliers final: 1
  residues processed: 98
  average time/residue: 0.1822
  time to fit residues: 27.4790
Evaluate side-chains
  61 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 1.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 101 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0270
   chunk 111 optimal weight:    9.9990
   chunk 104 optimal weight:    6.9990
   chunk 92 optimal weight:    9.9990
   chunk 88 optimal weight:    1.9990
   chunk 82 optimal weight:    0.0970
   chunk 77 optimal weight:    7.9990
   chunk 24 optimal weight:   20.0000
   chunk 12 optimal weight:    8.9990
   overall best weight:    1.3840

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

Flipped N/Q/H residues before XYZ refinement:
A 353 GLN
A 515 ASN
A 618 GLN
B 353 GLN
B 618 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.077612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2647 r_free = 0.2647 target = 0.065307 restraints weight = 24504.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2666 r_free = 0.2666 target = 0.066287 restraints weight = 17325.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2678 r_free = 0.2678 target = 0.066882 restraints weight = 13416.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.2673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8685
moved from start:          0.1889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10326  Z= 0.164
  Angle     :  0.560   7.383  14088  Z= 0.279
  Chirality :  0.042   0.164   1592
  Planarity :  0.004   0.056   1786
  Dihedral  :  6.829  64.806   1474
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  1.98 %
    Favored  : 97.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.34 (0.19), residues: 1264
  helix: -3.04 (0.16), residues: 654
  sheet: -0.83 (0.48), residues: 106
  loop : -2.94 (0.24), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 274 
 HIS   0.001   0.000   HIS B 378 
 PHE   0.018   0.001   PHE B 103 
 TYR   0.009   0.001   TYR B 257 
 ARG   0.005   0.000   ARG A 385 

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 83
  time to evaluate  : 1.129 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1968
  time to fit residues: 25.5967
Evaluate side-chains
  54 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 1.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 118 optimal weight:    3.9990
   chunk 117 optimal weight:    0.9980
   chunk 98 optimal weight:    8.9990
   chunk 124 optimal weight:   10.0000
   chunk 4 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9980
   chunk 40 optimal weight:   10.0000
   chunk 11 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.9782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.078870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2670 r_free = 0.2670 target = 0.066312 restraints weight = 24062.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2690 r_free = 0.2690 target = 0.067347 restraints weight = 16436.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2706 r_free = 0.2706 target = 0.068143 restraints weight = 12444.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.2703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8655
moved from start:          0.2130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10326  Z= 0.142
  Angle     :  0.535   7.204  14088  Z= 0.264
  Chirality :  0.041   0.162   1592
  Planarity :  0.004   0.054   1786
  Dihedral  :  6.377  65.158   1474
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.82 (0.21), residues: 1264
  helix: -2.55 (0.17), residues: 662
  sheet: -0.59 (0.49), residues: 108
  loop : -2.76 (0.24), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.000   TRP B 274 
 HIS   0.001   0.000   HIS A 615 
 PHE   0.023   0.001   PHE B  88 
 TYR   0.009   0.001   TYR B 257 
 ARG   0.010   0.000   ARG A 115 

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 1.219 
Fit side-chains
REVERT: A  366 ASP cc_start: 0.8243 (m-30) cc_final: 0.8034 (m-30)
REVERT: B  366 ASP cc_start: 0.8219 (m-30) cc_final: 0.8000 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.1844
  time to fit residues: 22.5049
Evaluate side-chains
  56 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 1.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 44 optimal weight:   10.0000
   chunk 8 optimal weight:    5.9990
   chunk 62 optimal weight:    6.9990
   chunk 85 optimal weight:    0.0970
   chunk 97 optimal weight:    0.4980
   chunk 83 optimal weight:    8.9990
   chunk 27 optimal weight:    0.8980
   chunk 71 optimal weight:    5.9990
   chunk 61 optimal weight:    6.9990
   chunk 6 optimal weight:    3.9990
   chunk 73 optimal weight:    6.9990
   overall best weight:    2.2982

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

Flipped N/Q/H residues before XYZ refinement:
A 353 GLN
A 618 GLN
B 353 GLN
B 515 ASN
B 618 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.076356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2626 r_free = 0.2626 target = 0.064120 restraints weight = 24544.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2643 r_free = 0.2643 target = 0.064997 restraints weight = 17640.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.065656 restraints weight = 13881.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.2655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8708
moved from start:          0.2108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10326  Z= 0.216
  Angle     :  0.594   8.391  14088  Z= 0.289
  Chirality :  0.044   0.164   1592
  Planarity :  0.004   0.044   1786
  Dihedral  :  6.388  73.490   1474
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 2.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  2.46 %
    Favored  : 97.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.60 (0.21), residues: 1264
  helix: -2.35 (0.18), residues: 662
  sheet: -0.96 (0.47), residues: 122
  loop : -2.62 (0.26), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 274 
 HIS   0.001   0.000   HIS B 378 
 PHE   0.017   0.001   PHE B  88 
 TYR   0.008   0.001   TYR B 513 
 ARG   0.009   0.000   ARG A 115 

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 72
  time to evaluate  : 1.097 
Fit side-chains
REVERT: B  366 ASP cc_start: 0.8206 (m-30) cc_final: 0.7999 (m-30)
  outliers start: 2
  outliers final: 0
  residues processed: 74
  average time/residue: 0.1957
  time to fit residues: 22.3853
Evaluate side-chains
  50 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 1.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 116 optimal weight:    2.9990
   chunk 60 optimal weight:    7.9990
   chunk 88 optimal weight:    5.9990
   chunk 52 optimal weight:    0.6980
   chunk 14 optimal weight:    0.0980
   chunk 6 optimal weight:    4.9990
   chunk 41 optimal weight:    0.0470
   chunk 112 optimal weight:    0.0470
   chunk 29 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.7778

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.079216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2678 r_free = 0.2678 target = 0.066717 restraints weight = 24040.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.067706 restraints weight = 16692.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2714 r_free = 0.2714 target = 0.068531 restraints weight = 12708.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8642
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  10326  Z= 0.133
  Angle     :  0.537   7.258  14088  Z= 0.261
  Chirality :  0.041   0.160   1592
  Planarity :  0.003   0.057   1786
  Dihedral  :  5.991  74.995   1474
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.15 (0.22), residues: 1264
  helix: -1.94 (0.19), residues: 656
  sheet: -0.29 (0.52), residues: 108
  loop : -2.57 (0.25), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 274 
 HIS   0.001   0.000   HIS A 160 
 PHE   0.012   0.001   PHE A 103 
 TYR   0.015   0.001   TYR B 257 
 ARG   0.003   0.000   ARG A 385 

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 1.211 
Fit side-chains
   revert: symmetry clash
REVERT: A  366 ASP cc_start: 0.8233 (m-30) cc_final: 0.8029 (m-30)
REVERT: B  366 ASP cc_start: 0.8180 (m-30) cc_final: 0.7932 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.1730
  time to fit residues: 21.8116
Evaluate side-chains
  58 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 1.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   chunk 104 optimal weight:    0.6980
   chunk 83 optimal weight:    0.0470
   chunk 68 optimal weight:    6.9990
   chunk 81 optimal weight:    8.9990
   chunk 124 optimal weight:    4.9990
   chunk 90 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0980
   chunk 98 optimal weight:    8.9990
   chunk 121 optimal weight:    0.8980
   overall best weight:    0.7480

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

Flipped N/Q/H residues before XYZ refinement:
A 353 GLN
A 618 GLN
B 353 GLN
B 618 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.079512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2681 r_free = 0.2681 target = 0.067024 restraints weight = 24351.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2701 r_free = 0.2701 target = 0.068073 restraints weight = 16958.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2714 r_free = 0.2714 target = 0.068731 restraints weight = 12882.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.2585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10326  Z= 0.131
  Angle     :  0.532   7.254  14088  Z= 0.256
  Chirality :  0.040   0.160   1592
  Planarity :  0.003   0.059   1786
  Dihedral  :  5.720  73.418   1474
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.85 %
    Favored  : 98.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.84 (0.22), residues: 1264
  helix: -1.65 (0.19), residues: 654
  sheet: -0.20 (0.53), residues: 108
  loop : -2.45 (0.25), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  47 
 HIS   0.001   0.000   HIS A 160 
 PHE   0.012   0.001   PHE B 383 
 TYR   0.012   0.001   TYR B 257 
 ARG   0.013   0.000   ARG A 115 

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 80
  time to evaluate  : 1.115 
Fit side-chains
REVERT: B  366 ASP cc_start: 0.8177 (m-30) cc_final: 0.7894 (m-30)
  outliers start: 2
  outliers final: 0
  residues processed: 82
  average time/residue: 0.1680
  time to fit residues: 21.9916
Evaluate side-chains
  54 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 1.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 19 optimal weight:    6.9990
   chunk 79 optimal weight:    1.9990
   chunk 6 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 25 optimal weight:    6.9990
   chunk 59 optimal weight:    7.9990
   chunk 83 optimal weight:    9.9990
   chunk 97 optimal weight:    0.9980
   chunk 63 optimal weight:   10.0000
   chunk 54 optimal weight:    8.9990
   chunk 44 optimal weight:    6.9990
   overall best weight:    4.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 353 GLN
B 353 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.073516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2573 r_free = 0.2573 target = 0.061272 restraints weight = 25595.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2589 r_free = 0.2589 target = 0.062107 restraints weight = 18616.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2593 r_free = 0.2593 target = 0.062321 restraints weight = 13661.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.2590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8775
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043  10326  Z= 0.393
  Angle     :  0.715  10.238  14088  Z= 0.350
  Chirality :  0.049   0.175   1592
  Planarity :  0.004   0.050   1786
  Dihedral  :  6.775  85.577   1474
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.85 %
    Favored  : 98.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.24 (0.22), residues: 1264
  helix: -2.06 (0.18), residues: 658
  sheet: -0.81 (0.49), residues: 122
  loop : -2.43 (0.26), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  12 
 HIS   0.002   0.001   HIS B 402 
 PHE   0.015   0.002   PHE A 228 
 TYR   0.014   0.002   TYR B 257 
 ARG   0.012   0.001   ARG B 115 

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 65
  time to evaluate  : 1.110 
Fit side-chains
  outliers start: 2
  outliers final: 0
  residues processed: 67
  average time/residue: 0.1776
  time to fit residues: 18.9758
Evaluate side-chains
  42 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 1.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 102 optimal weight:    3.9990
   chunk 67 optimal weight:    5.9990
   chunk 100 optimal weight:    4.9990
   chunk 60 optimal weight:   10.0000
   chunk 47 optimal weight:    1.9990
   chunk 64 optimal weight:    7.9990
   chunk 41 optimal weight:    6.9990
   chunk 31 optimal weight:    3.9990
   chunk 74 optimal weight:    5.9990
   chunk 75 optimal weight:    2.9990
   chunk 108 optimal weight:   10.0000
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 353 GLN
B 353 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.074087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2575 r_free = 0.2575 target = 0.061467 restraints weight = 25336.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2594 r_free = 0.2594 target = 0.062445 restraints weight = 17876.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2608 r_free = 0.2608 target = 0.063129 restraints weight = 13821.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.2607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8761
moved from start:          0.2276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  10326  Z= 0.307
  Angle     :  0.660   8.796  14088  Z= 0.322
  Chirality :  0.046   0.169   1592
  Planarity :  0.004   0.061   1786
  Dihedral  :  6.829  88.790   1474
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.95 %
    Favored  : 98.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.16 (0.22), residues: 1264
  helix: -2.00 (0.18), residues: 658
  sheet: -0.85 (0.50), residues: 122
  loop : -2.37 (0.26), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 274 
 HIS   0.002   0.001   HIS B 402 
 PHE   0.014   0.002   PHE B 573 
 TYR   0.013   0.001   TYR A 257 
 ARG   0.010   0.000   ARG B 115 

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 63
  time to evaluate  : 1.215 
Fit side-chains
  outliers start: 2
  outliers final: 0
  residues processed: 65
  average time/residue: 0.1525
  time to fit residues: 17.1390
Evaluate side-chains
  48 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 1.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 118 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 6 optimal weight:    8.9990
   chunk 3 optimal weight:    0.9990
   chunk 83 optimal weight:    9.9990
   chunk 65 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 89 optimal weight:    9.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 353 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.077823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2648 r_free = 0.2648 target = 0.065307 restraints weight = 24173.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.066294 restraints weight = 16898.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2682 r_free = 0.2682 target = 0.067035 restraints weight = 13000.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.2683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8676
moved from start:          0.2558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10326  Z= 0.141
  Angle     :  0.552   7.439  14088  Z= 0.267
  Chirality :  0.041   0.158   1592
  Planarity :  0.004   0.061   1786
  Dihedral  :  6.070  81.428   1474
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.00 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.69 (0.23), residues: 1264
  helix: -1.57 (0.20), residues: 646
  sheet: -0.30 (0.53), residues: 108
  loop : -2.27 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  47 
 HIS   0.001   0.000   HIS A 160 
 PHE   0.011   0.001   PHE B 573 
 TYR   0.012   0.001   TYR A 257 
 ARG   0.010   0.000   ARG B 115 

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 74
  time to evaluate  : 1.181 
Fit side-chains
REVERT: B   14 ARG cc_start: 0.7387 (ttp-110) cc_final: 0.6967 (ttm170)
  outliers start: 1
  outliers final: 0
  residues processed: 75
  average time/residue: 0.1619
  time to fit residues: 20.0820
Evaluate side-chains
  50 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 1.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 68 optimal weight:    6.9990
   chunk 12 optimal weight:    7.9990
   chunk 10 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 74 optimal weight:    6.9990
   chunk 75 optimal weight:    8.9990
   chunk 32 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:   10.0000
   chunk 86 optimal weight:   10.0000
   overall best weight:    3.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 353 GLN
B 353 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.074269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2585 r_free = 0.2585 target = 0.061976 restraints weight = 24951.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2602 r_free = 0.2602 target = 0.062824 restraints weight = 18229.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2613 r_free = 0.2613 target = 0.063347 restraints weight = 14494.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.2612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8755
moved from start:          0.2388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  10326  Z= 0.327
  Angle     :  0.668   8.919  14088  Z= 0.326
  Chirality :  0.047   0.170   1592
  Planarity :  0.004   0.046   1786
  Dihedral  :  6.536  83.163   1474
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.12 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.09 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.80 (0.23), residues: 1264
  helix: -1.73 (0.19), residues: 648
  sheet: -0.85 (0.50), residues: 122
  loop : -2.11 (0.27), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 274 
 HIS   0.002   0.001   HIS B 402 
 PHE   0.016   0.002   PHE B 103 
 TYR   0.014   0.002   TYR A 257 
 ARG   0.009   0.000   ARG B 115 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2368.37 seconds
wall clock time: 43 minutes 29.39 seconds (2609.39 seconds total)