Starting phenix.real_space_refine
on Tue Feb  3 21:56:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9udx_64074/02_2026/9udx_64074.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9udx_64074/02_2026/9udx_64074.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9udx_64074/02_2026/9udx_64074.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9udx_64074/02_2026/9udx_64074.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9udx_64074/02_2026/9udx_64074.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9udx_64074/02_2026/9udx_64074.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.040
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: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    4700      2.51       5
     N    1156      2.21       5
     O    1236      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7142
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3571
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 465, 3571
          Classifications: {'peptide': 465}
          Link IDs: {'PTRANS': 17, 'TRANS': 447}
          Chain breaks: 1
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.16, per 1000 atoms: 0.30
  Number of scatterers: 7142
  At special positions: 0
  Unit cell: (102.3, 103.4, 99, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      50     16.00
     O    1236      8.00
     N    1156      7.00
     C    4700      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  54 " - pdb=" SG  CYS A  73 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  54 " - pdb=" SG  CYS B  73 " distance=2.03

  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: 0.63
  Conformation dependent library (CDL) restraints added in 278.4 milliseconds
  

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1660

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 0 sheets defined
      70.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 15
      removed outlier: 4.190A  pdb=" N   ALA A  14 " --> pdb=" O   TRP A  10 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   PHE A  15 " --> pdb=" O   PHE A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 17 through 41
      removed outlier: 3.945A  pdb=" N   PHE A  21 " --> pdb=" O   ARG A  17 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ARG A  22 " --> pdb=" O   ASP A  18 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   GLY A  23 " --> pdb=" O   SER A  19 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   LEU A  26 " --> pdb=" O   ARG A  22 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LEU A  27 " --> pdb=" O   GLY A  23 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   LEU A  31 " --> pdb=" O   LEU A  27 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   TYR A  33 " --> pdb=" O   THR A  29 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   TYR A  36 " --> pdb=" O   ILE A  32 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   HIS A  37 " --> pdb=" O   TYR A  33 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   LYS A  41 " --> pdb=" O   HIS A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 50
      removed outlier: 4.270A  pdb=" N   ARG A  49 " --> pdb=" O   ILE A  45 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU A  50 " --> pdb=" O   VAL A  46 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 45 through 50'
    Processing helix  chain 'A' and resid 75 through 79
      removed outlier: 3.912A  pdb=" N   ASP A  79 " --> pdb=" O   ALA A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 82
      No H-bonds generated for 'chain 'A' and resid 80 through 82'
    Processing helix  chain 'A' and resid 83 through 105
      removed outlier: 3.863A  pdb=" N   GLY A  88 " --> pdb=" O   LYS A  84 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   GLY A  89 " --> pdb=" O   GLU A  85 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ALA A  93 " --> pdb=" O   GLY A  89 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   PHE A  94 " --> pdb=" O   VAL A  90 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   ALA A  97 " --> pdb=" O   ALA A  93 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ALA A  99 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLY A 101 " --> pdb=" O   ALA A  97 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   MET A 102 " --> pdb=" O   TYR A  98 " (cutoff:3.500A)
      removed outlier: 4.722A  pdb=" N   PHE A 103 " --> pdb=" O   ALA A  99 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   ILE A 104 " --> pdb=" O   ILE A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 112
      removed outlier: 4.049A  pdb=" N   ARG A 111 " --> pdb=" O   VAL A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 134
      removed outlier: 3.692A  pdb=" N   GLY A 121 " --> pdb=" O   TYR A 117 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   LEU A 124 " --> pdb=" O   ALA A 120 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   GLY A 126 " --> pdb=" O   MET A 122 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   LEU A 127 " --> pdb=" O   LEU A 123 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   SER A 130 " --> pdb=" O   GLY A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 153
      removed outlier: 3.502A  pdb=" N   VAL A 148 " --> pdb=" O   TRP A 144 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE A 149 " --> pdb=" O   TYR A 145 " (cutoff:3.500A)
      removed outlier: 4.828A  pdb=" N   GLN A 150 " --> pdb=" O   PHE A 146 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   CYS A 152 " --> pdb=" O   VAL A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 164
      removed outlier: 3.851A  pdb=" N   VAL A 164 " --> pdb=" O   TRP A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 172
      removed outlier: 3.842A  pdb=" N   TRP A 171 " --> pdb=" O   CYS A 167 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   PHE A 172 " --> pdb=" O   VAL A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 184
      removed outlier: 3.578A  pdb=" N   GLY A 182 " --> pdb=" O   GLY A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 199
      removed outlier: 4.548A  pdb=" N   ASN A 192 " --> pdb=" O   THR A 188 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ILE A 193 " --> pdb=" O   SER A 189 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   LEU A 194 " --> pdb=" O   VAL A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 210
    Processing helix  chain 'A' and resid 211 through 228
      removed outlier: 3.696A  pdb=" N   ALA A 219 " --> pdb=" O   GLY A 215 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   VAL A 223 " --> pdb=" O   ALA A 219 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ILE A 224 " --> pdb=" O   VAL A 220 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   PHE A 226 " --> pdb=" O   GLY A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 292
    Processing helix  chain 'A' and resid 304 through 325
      removed outlier: 3.615A  pdb=" N   LEU A 309 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   VAL A 310 " --> pdb=" O   PHE A 306 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LEU A 315 " --> pdb=" O   SER A 311 " (cutoff:3.500A)
      Proline residue:  A 319  - end of helix
      removed outlier: 4.009A  pdb=" N   ASN A 324 " --> pdb=" O   LEU A 320 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   VAL A 325 " --> pdb=" O   TYR A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 357
      removed outlier: 3.561A  pdb=" N   THR A 338 " --> pdb=" O   GLY A 334 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   ASP A 341 " --> pdb=" O   SER A 337 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ILE A 349 " --> pdb=" O   ILE A 345 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   GLY A 352 " --> pdb=" O   GLY A 348 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   VAL A 354 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   SER A 355 " --> pdb=" O   ALA A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 371
      removed outlier: 3.595A  pdb=" N   VAL A 367 " --> pdb=" O   THR A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 382
    Processing helix  chain 'A' and resid 387 through 399
      removed outlier: 4.009A  pdb=" N   ILE A 391 " --> pdb=" O   ILE A 387 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   VAL A 392 " --> pdb=" O   ALA A 388 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   MET A 393 " --> pdb=" O   SER A 389 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ILE A 396 " --> pdb=" O   VAL A 392 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   CYS A 397 " --> pdb=" O   MET A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 411
      removed outlier: 3.574A  pdb=" N   ALA A 406 " --> pdb=" O   ASN A 402 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   ILE A 408 " --> pdb=" O   PRO A 404 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   THR A 409 " --> pdb=" O   TYR A 405 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ALA A 411 " --> pdb=" O   LEU A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 423
    Processing helix  chain 'A' and resid 431 through 446
      removed outlier: 4.068A  pdb=" N   GLY A 443 " --> pdb=" O   THR A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 455
      removed outlier: 3.673A  pdb=" N   GLY A 452 " --> pdb=" O   PRO A 448 " (cutoff:3.500A)
      removed outlier: 5.026A  pdb=" N   LEU A 453 " --> pdb=" O   LEU A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 474
      removed outlier: 3.556A  pdb=" N   TYR A 464 " --> pdb=" O   ASN A 460 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   CYS A 474 " --> pdb=" O   ASP A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 494
      removed outlier: 3.739A  pdb=" N   LEU A 486 " --> pdb=" O   TYR A 482 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   SER A 491 " --> pdb=" O   ALA A 487 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 15
      removed outlier: 4.190A  pdb=" N   ALA B  14 " --> pdb=" O   TRP B  10 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   PHE B  15 " --> pdb=" O   PHE B  11 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 41
      removed outlier: 3.946A  pdb=" N   PHE B  21 " --> pdb=" O   ARG B  17 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ARG B  22 " --> pdb=" O   ASP B  18 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   GLY B  23 " --> pdb=" O   SER B  19 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   LEU B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LEU B  27 " --> pdb=" O   GLY B  23 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   LEU B  31 " --> pdb=" O   LEU B  27 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   TYR B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   TYR B  36 " --> pdb=" O   ILE B  32 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   HIS B  37 " --> pdb=" O   TYR B  33 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   LYS B  41 " --> pdb=" O   HIS B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 50
      removed outlier: 4.270A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B  45 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LEU B  50 " --> pdb=" O   VAL B  46 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 45 through 50'
    Processing helix  chain 'B' and resid 75 through 79
      removed outlier: 3.912A  pdb=" N   ASP B  79 " --> pdb=" O   ALA B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 82
      No H-bonds generated for 'chain 'B' and resid 80 through 82'
    Processing helix  chain 'B' and resid 83 through 105
      removed outlier: 3.864A  pdb=" N   GLY B  88 " --> pdb=" O   LYS B  84 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   GLY B  89 " --> pdb=" O   GLU B  85 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ALA B  93 " --> pdb=" O   GLY B  89 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   PHE B  94 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   ALA B  97 " --> pdb=" O   ALA B  93 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ALA B  99 " --> pdb=" O   LEU B  95 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLY B 101 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   MET B 102 " --> pdb=" O   TYR B  98 " (cutoff:3.500A)
      removed outlier: 4.722A  pdb=" N   PHE B 103 " --> pdb=" O   ALA B  99 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   ILE B 104 " --> pdb=" O   ILE B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 112
      removed outlier: 4.050A  pdb=" N   ARG B 111 " --> pdb=" O   VAL B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 134
      removed outlier: 3.692A  pdb=" N   GLY B 121 " --> pdb=" O   TYR B 117 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   LEU B 124 " --> pdb=" O   ALA B 120 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   GLY B 126 " --> pdb=" O   MET B 122 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   LEU B 127 " --> pdb=" O   LEU B 123 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   SER B 130 " --> pdb=" O   GLY B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 153
      removed outlier: 3.501A  pdb=" N   VAL B 148 " --> pdb=" O   TRP B 144 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE B 149 " --> pdb=" O   TYR B 145 " (cutoff:3.500A)
      removed outlier: 4.827A  pdb=" N   GLN B 150 " --> pdb=" O   PHE B 146 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   CYS B 152 " --> pdb=" O   VAL B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 164
      removed outlier: 3.852A  pdb=" N   VAL B 164 " --> pdb=" O   TRP B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 172
      removed outlier: 3.843A  pdb=" N   TRP B 171 " --> pdb=" O   CYS B 167 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   PHE B 172 " --> pdb=" O   VAL B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 184
      removed outlier: 3.577A  pdb=" N   GLY B 182 " --> pdb=" O   GLY B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 186 through 199
      removed outlier: 4.547A  pdb=" N   ASN B 192 " --> pdb=" O   THR B 188 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ILE B 193 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   LEU B 194 " --> pdb=" O   VAL B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 210
    Processing helix  chain 'B' and resid 211 through 228
      removed outlier: 3.698A  pdb=" N   ALA B 219 " --> pdb=" O   GLY B 215 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   VAL B 223 " --> pdb=" O   ALA B 219 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ILE B 224 " --> pdb=" O   VAL B 220 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   PHE B 226 " --> pdb=" O   GLY B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 292
    Processing helix  chain 'B' and resid 304 through 325
      removed outlier: 3.615A  pdb=" N   LEU B 309 " --> pdb=" O   LEU B 305 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   VAL B 310 " --> pdb=" O   PHE B 306 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   LEU B 315 " --> pdb=" O   SER B 311 " (cutoff:3.500A)
      Proline residue:  B 319  - end of helix
      removed outlier: 4.009A  pdb=" N   ASN B 324 " --> pdb=" O   LEU B 320 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   VAL B 325 " --> pdb=" O   TYR B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 357
      removed outlier: 3.561A  pdb=" N   THR B 338 " --> pdb=" O   GLY B 334 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   ASP B 341 " --> pdb=" O   SER B 337 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ILE B 349 " --> pdb=" O   ILE B 345 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   GLY B 352 " --> pdb=" O   GLY B 348 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   VAL B 354 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   SER B 355 " --> pdb=" O   ALA B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 361 through 371
      removed outlier: 3.595A  pdb=" N   VAL B 367 " --> pdb=" O   THR B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 382
    Processing helix  chain 'B' and resid 387 through 399
      removed outlier: 4.008A  pdb=" N   ILE B 391 " --> pdb=" O   ILE B 387 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   VAL B 392 " --> pdb=" O   ALA B 388 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   MET B 393 " --> pdb=" O   SER B 389 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ILE B 396 " --> pdb=" O   VAL B 392 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   CYS B 397 " --> pdb=" O   MET B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 402 through 411
      removed outlier: 3.575A  pdb=" N   ALA B 406 " --> pdb=" O   ASN B 402 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   ILE B 408 " --> pdb=" O   PRO B 404 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   THR B 409 " --> pdb=" O   TYR B 405 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ALA B 411 " --> pdb=" O   LEU B 407 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 419 through 423
    Processing helix  chain 'B' and resid 431 through 446
      removed outlier: 4.069A  pdb=" N   GLY B 443 " --> pdb=" O   THR B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 455
      removed outlier: 3.673A  pdb=" N   GLY B 452 " --> pdb=" O   PRO B 448 " (cutoff:3.500A)
      removed outlier: 5.027A  pdb=" N   LEU B 453 " --> pdb=" O   LEU B 449 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 460 through 474
      removed outlier: 3.555A  pdb=" N   TYR B 464 " --> pdb=" O   ASN B 460 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   CYS B 474 " --> pdb=" O   ASP B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 477 through 494
      removed outlier: 3.739A  pdb=" N   LEU B 486 " --> pdb=" O   TYR B 482 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   SER B 491 " --> pdb=" O   ALA B 487 " (cutoff:3.500A)

    298 hydrogen bonds defined for protein.
    852 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.00

  Time building geometry restraints manager: 0.82 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: 2083
        1.34 -     1.45: 1493
        1.45 -     1.57: 3688
        1.57 -     1.69: 0
        1.69 -     1.81: 74
  Bond restraints: 7338
  Sorted by residual:
  bond pdb=" CB  VAL A 164 "
       pdb=" CG1 VAL A 164 "
    ideal  model  delta    sigma   weight residual
    1.521  1.463  0.058 3.30e-02 9.18e+02 3.08e+00
  bond pdb=" CB  VAL B 164 "
       pdb=" CG1 VAL B 164 "
    ideal  model  delta    sigma   weight residual
    1.521  1.464  0.057 3.30e-02 9.18e+02 2.96e+00
  bond pdb=" CB  VAL A 165 "
       pdb=" CG2 VAL A 165 "
    ideal  model  delta    sigma   weight residual
    1.521  1.473  0.048 3.30e-02 9.18e+02 2.14e+00
  bond pdb=" CB  VAL B 165 "
       pdb=" CG2 VAL B 165 "
    ideal  model  delta    sigma   weight residual
    1.521  1.473  0.048 3.30e-02 9.18e+02 2.12e+00
  bond pdb=" CG  LEU B 304 "
       pdb=" CD2 LEU B 304 "
    ideal  model  delta    sigma   weight residual
    1.521  1.474  0.047 3.30e-02 9.18e+02 2.06e+00
  ... (remaining 7333 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 9135
        1.63 -     3.25: 698
        3.25 -     4.88: 101
        4.88 -     6.50: 36
        6.50 -     8.13: 18
  Bond angle restraints: 9988
  Sorted by residual:
  angle pdb=" N   LEU A 429 "
        pdb=" CA  LEU A 429 "
        pdb=" C   LEU A 429 "
      ideal   model   delta    sigma   weight residual
     114.56  108.48    6.08 1.27e+00 6.20e-01 2.29e+01
  angle pdb=" N   LEU B 429 "
        pdb=" CA  LEU B 429 "
        pdb=" C   LEU B 429 "
      ideal   model   delta    sigma   weight residual
     114.56  108.51    6.05 1.27e+00 6.20e-01 2.27e+01
  angle pdb=" N   LYS A  41 "
        pdb=" CA  LYS A  41 "
        pdb=" C   LYS A  41 "
      ideal   model   delta    sigma   weight residual
     112.35  117.48   -5.13 1.34e+00 5.57e-01 1.46e+01
  angle pdb=" N   LYS B  41 "
        pdb=" CA  LYS B  41 "
        pdb=" C   LYS B  41 "
      ideal   model   delta    sigma   weight residual
     112.35  117.44   -5.09 1.34e+00 5.57e-01 1.44e+01
  angle pdb=" C   PHE A 103 "
        pdb=" N   ILE A 104 "
        pdb=" CA  ILE A 104 "
      ideal   model   delta    sigma   weight residual
     122.66  118.98    3.68 9.70e-01 1.06e+00 1.44e+01
  ... (remaining 9983 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.83: 3880
       15.83 -    31.67: 248
       31.67 -    47.50: 38
       47.50 -    63.33: 0
       63.33 -    79.17: 2
  Dihedral angle restraints: 4168
    sinusoidal: 1546
      harmonic: 2622
  Sorted by residual:
  dihedral pdb=" CA  SER A 105 "
           pdb=" C   SER A 105 "
           pdb=" N   GLY A 106 "
           pdb=" CA  GLY A 106 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.96   26.04     0      5.00e+00 4.00e-02 2.71e+01
  dihedral pdb=" CA  SER B 105 "
           pdb=" C   SER B 105 "
           pdb=" N   GLY B 106 "
           pdb=" CA  GLY B 106 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.98   26.02     0      5.00e+00 4.00e-02 2.71e+01
  dihedral pdb=" CA  LYS A  41 "
           pdb=" C   LYS A  41 "
           pdb=" N   PRO A  42 "
           pdb=" CA  PRO A  42 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.65  -24.35     0      5.00e+00 4.00e-02 2.37e+01
  ... (remaining 4165 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 589
       0.042 -    0.083: 375
       0.083 -    0.125: 126
       0.125 -    0.166: 28
       0.166 -    0.208: 18
  Chirality restraints: 1136
  Sorted by residual:
  chirality pdb=" CA  LYS A  41 "
            pdb=" N   LYS A  41 "
            pdb=" C   LYS A  41 "
            pdb=" CB  LYS A  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  LYS B  41 "
            pdb=" N   LYS B  41 "
            pdb=" C   LYS B  41 "
            pdb=" CB  LYS B  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.21 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CB  ILE A 104 "
            pdb=" CA  ILE A 104 "
            pdb=" CG1 ILE A 104 "
            pdb=" CG2 ILE A 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.66e-01
  ... (remaining 1133 not shown)

  Planarity restraints: 1226
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP B 161 "    0.051 5.00e-02 4.00e+02   7.65e-02 9.36e+00
        pdb=" N   PRO B 162 "   -0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO B 162 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO B 162 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A 161 "   -0.051 5.00e-02 4.00e+02   7.61e-02 9.26e+00
        pdb=" N   PRO A 162 "    0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO A 162 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A 162 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 403 "   -0.043 5.00e-02 4.00e+02   6.50e-02 6.76e+00
        pdb=" N   PRO A 404 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO A 404 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 404 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 1223 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2083
        2.80 -     3.33: 6394
        3.33 -     3.85: 11150
        3.85 -     4.38: 12564
        4.38 -     4.90: 21606
  Nonbonded interactions: 53797
  Sorted by model distance:
  nonbonded pdb=" O   SER A 105 "
            pdb=" OH  TYR A 117 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   SER B 105 "
            pdb=" OH  TYR B 117 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" OG1 THR A 166 "
            pdb=" OG  SER A 430 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" OG1 THR B 166 "
            pdb=" OG  SER B 430 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" OG  SER A   3 "
            pdb=" OE2 GLU B 231 "
     model   vdw
     2.350 3.040
  ... (remaining 53792 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: 0.01
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:             1.060
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.690
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
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      :  0.008   0.068   7340  Z= 0.335
  Angle     :  1.010   8.128   9992  Z= 0.547
  Chirality :  0.060   0.208   1136
  Planarity :  0.009   0.076   1226
  Dihedral  : 10.480  79.166   2502
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.06 %
    Favored  : 88.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.08 (0.20), residues: 922
  helix: -3.49 (0.13), residues: 594
  sheet:  None (None), residues: 0
  loop : -2.75 (0.29), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 115 
 TYR   0.017   0.003   TYR A 316 
 PHE   0.027   0.003   PHE A 300 
 TRP   0.017   0.002   TRP A 144 
 HIS   0.019   0.003   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00786 ( 7338)
  covalent geometry    : angle       1.00962 ( 9988)
  SS BOND              : bond        0.00464 (    2)
  SS BOND              : angle       1.82014 (    4)
  hydrogen bonds       : bond        0.17205 (  298)
  hydrogen bonds       : angle       6.22818 (  852)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 ARG cc_start: 0.8029 (ttm170) cc_final: 0.7451 (mmp-170)
REVERT: A   86 LEU cc_start: 0.8475 (mm) cc_final: 0.8069 (mt)
REVERT: A  196 SER cc_start: 0.8506 (m) cc_final: 0.8255 (p)
REVERT: A  202 TRP cc_start: 0.8351 (m-90) cc_final: 0.8115 (m-90)
REVERT: A  369 LEU cc_start: 0.9418 (mt) cc_final: 0.9171 (mm)
REVERT: A  463 PHE cc_start: 0.8306 (t80) cc_final: 0.8081 (t80)
REVERT: B   10 TRP cc_start: 0.8354 (t60) cc_final: 0.7411 (t60)
REVERT: B   13 ARG cc_start: 0.8002 (ttm170) cc_final: 0.7592 (mmp-170)
REVERT: B   51 HIS cc_start: 0.7882 (t70) cc_final: 0.7422 (p-80)
REVERT: B   86 LEU cc_start: 0.8640 (mm) cc_final: 0.8346 (mt)
REVERT: B  122 MET cc_start: 0.8533 (mtp) cc_final: 0.8273 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.0602
  time to fit residues: 16.9706
Evaluate side-chains
  139 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 141 HIS
A 244 HIS
A 384 GLN
B 139 ASN
B 141 HIS
B 244 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.168905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.128415 restraints weight = 10074.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.131979 restraints weight = 5716.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.134299 restraints weight = 4102.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.135455 restraints weight = 3402.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.136250 restraints weight = 3083.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7340  Z= 0.129
  Angle     :  0.596   6.355   9992  Z= 0.310
  Chirality :  0.042   0.149   1136
  Planarity :  0.005   0.051   1226
  Dihedral  :  5.385  21.699    988
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 10.16 %
    Favored  : 88.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.66 (0.24), residues: 922
  helix: -2.34 (0.18), residues: 616
  sheet:  None (None), residues: 0
  loop : -2.24 (0.34), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 293 
 TYR   0.018   0.001   TYR B  83 
 PHE   0.011   0.001   PHE A 289 
 TRP   0.024   0.001   TRP B 202 
 HIS   0.004   0.001   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 7338)
  covalent geometry    : angle       0.59522 ( 9988)
  SS BOND              : bond        0.00369 (    2)
  SS BOND              : angle       1.93469 (    4)
  hydrogen bonds       : bond        0.03650 (  298)
  hydrogen bonds       : angle       4.25624 (  852)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 150
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 TRP cc_start: 0.8321 (t60) cc_final: 0.7366 (t60)
REVERT: A   13 ARG cc_start: 0.7792 (ttm170) cc_final: 0.7369 (mmp-170)
REVERT: A   71 MET cc_start: 0.9132 (mmm) cc_final: 0.8820 (mmm)
REVERT: A  484 GLU cc_start: 0.8213 (tp30) cc_final: 0.7963 (tp30)
REVERT: B   10 TRP cc_start: 0.8265 (t60) cc_final: 0.7341 (t60)
REVERT: B   13 ARG cc_start: 0.7836 (ttm170) cc_final: 0.7398 (mmp-170)
REVERT: B   51 HIS cc_start: 0.7792 (t70) cc_final: 0.7259 (p-80)
REVERT: B  382 ILE cc_start: 0.9464 (mm) cc_final: 0.9209 (tp)
REVERT: B  453 LEU cc_start: 0.8158 (tp) cc_final: 0.7953 (tt)
  outliers start: 11
  outliers final: 8
  residues processed: 156
  average time/residue: 0.0582
  time to fit residues: 13.0027
Evaluate side-chains
  137 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 129
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  415 ASP
Chi-restraints excluded: chain B residue   39 SER
Chi-restraints excluded: chain B residue  130 SER
Chi-restraints excluded: chain B residue  190 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 88 optimal weight:    0.1980
   chunk 35 optimal weight:    3.9990
   chunk 86 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 21 optimal weight:    0.5980
   chunk 52 optimal weight:    0.0030
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.4790

-------------------------------------------------------------------------------
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 = 0.3985 r_free = 0.3985 target = 0.171409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.131751 restraints weight = 9911.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.135293 restraints weight = 5642.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.137545 restraints weight = 4054.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.138719 restraints weight = 3364.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.139536 restraints weight = 3051.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.2933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7340  Z= 0.101
  Angle     :  0.536  10.303   9992  Z= 0.275
  Chirality :  0.040   0.142   1136
  Planarity :  0.004   0.044   1226
  Dihedral  :  4.620  18.351    988
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 12.40 %
    Favored  : 84.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.72 (0.26), residues: 922
  helix: -1.51 (0.20), residues: 598
  sheet:  None (None), residues: 0
  loop : -2.12 (0.35), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 293 
 TYR   0.012   0.001   TYR B 312 
 PHE   0.012   0.001   PHE A 289 
 TRP   0.016   0.001   TRP A 202 
 HIS   0.003   0.001   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 7338)
  covalent geometry    : angle       0.53599 ( 9988)
  SS BOND              : bond        0.00057 (    2)
  SS BOND              : angle       0.79499 (    4)
  hydrogen bonds       : bond        0.03011 (  298)
  hydrogen bonds       : angle       3.70010 (  852)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 149
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 TRP cc_start: 0.8280 (t60) cc_final: 0.7967 (t60)
REVERT: A   13 ARG cc_start: 0.7810 (ttm170) cc_final: 0.7306 (mmp-170)
REVERT: A  356 ASP cc_start: 0.8543 (t0) cc_final: 0.8210 (t0)
REVERT: B   10 TRP cc_start: 0.8238 (t60) cc_final: 0.7281 (t60)
REVERT: B   13 ARG cc_start: 0.7823 (ttm170) cc_final: 0.7398 (mmp-170)
REVERT: B   71 MET cc_start: 0.8782 (tpp) cc_final: 0.8430 (mmm)
REVERT: B  301 SER cc_start: 0.9123 (m) cc_final: 0.8771 (t)
REVERT: B  382 ILE cc_start: 0.9500 (mm) cc_final: 0.9200 (tp)
  outliers start: 21
  outliers final: 16
  residues processed: 160
  average time/residue: 0.0628
  time to fit residues: 14.3099
Evaluate side-chains
  146 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 130
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  415 ASP
Chi-restraints excluded: chain B residue  100 ILE
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  183 ILE
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  355 SER
Chi-restraints excluded: chain B residue  377 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 22 optimal weight:    0.4980
   chunk 14 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 66 optimal weight:    0.4980
   chunk 54 optimal weight:    5.9990
   chunk 79 optimal weight:    2.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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 = 0.3922 r_free = 0.3922 target = 0.165701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.125445 restraints weight = 10146.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.128685 restraints weight = 5897.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.130710 restraints weight = 4291.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.132032 restraints weight = 3589.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.132773 restraints weight = 3240.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.3128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7340  Z= 0.172
  Angle     :  0.601   7.284   9992  Z= 0.312
  Chirality :  0.044   0.147   1136
  Planarity :  0.004   0.042   1226
  Dihedral  :  4.845  18.327    988
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.24 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 14.64 %
    Favored  : 82.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.36 (0.27), residues: 922
  helix: -1.36 (0.20), residues: 616
  sheet:  None (None), residues: 0
  loop : -1.66 (0.38), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 111 
 TYR   0.022   0.002   TYR B 312 
 PHE   0.012   0.001   PHE A 179 
 TRP   0.014   0.001   TRP A 202 
 HIS   0.005   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 7338)
  covalent geometry    : angle       0.60053 ( 9988)
  SS BOND              : bond        0.00257 (    2)
  SS BOND              : angle       0.84390 (    4)
  hydrogen bonds       : bond        0.03600 (  298)
  hydrogen bonds       : angle       3.89690 (  852)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 133
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 TRP cc_start: 0.8342 (t60) cc_final: 0.7941 (t60)
REVERT: A   13 ARG cc_start: 0.7951 (ttm170) cc_final: 0.7385 (mmp-170)
REVERT: A  356 ASP cc_start: 0.8641 (t0) cc_final: 0.8378 (t0)
REVERT: A  382 ILE cc_start: 0.9522 (mm) cc_final: 0.9162 (tp)
REVERT: B   10 TRP cc_start: 0.8331 (t60) cc_final: 0.7324 (t60)
REVERT: B   13 ARG cc_start: 0.7901 (ttm170) cc_final: 0.7458 (mmp-170)
  outliers start: 24
  outliers final: 20
  residues processed: 144
  average time/residue: 0.0542
  time to fit residues: 11.3040
Evaluate side-chains
  139 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  415 ASP
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain B residue  100 ILE
Chi-restraints excluded: chain B residue  130 SER
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  149 ILE
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  301 SER
Chi-restraints excluded: chain B residue  355 SER
Chi-restraints excluded: chain B residue  429 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 72 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 83 optimal weight:    0.6980
   chunk 71 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 76 optimal weight:    4.9990
   chunk 13 optimal weight:    6.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 157 GLN
B 157 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.167581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.127897 restraints weight = 10180.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.131356 restraints weight = 5825.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.133563 restraints weight = 4189.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.134702 restraints weight = 3478.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.135481 restraints weight = 3152.594|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.3382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7340  Z= 0.120
  Angle     :  0.547   7.609   9992  Z= 0.281
  Chirality :  0.042   0.146   1136
  Planarity :  0.004   0.043   1226
  Dihedral  :  4.482  17.997    988
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 16.36 %
    Favored  : 79.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.03 (0.28), residues: 922
  helix: -1.12 (0.20), residues: 622
  sheet:  None (None), residues: 0
  loop : -1.52 (0.39), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 293 
 TYR   0.014   0.001   TYR B  83 
 PHE   0.013   0.001   PHE B 328 
 TRP   0.014   0.001   TRP A 202 
 HIS   0.004   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 7338)
  covalent geometry    : angle       0.54673 ( 9988)
  SS BOND              : bond        0.00275 (    2)
  SS BOND              : angle       0.71799 (    4)
  hydrogen bonds       : bond        0.03107 (  298)
  hydrogen bonds       : angle       3.64812 (  852)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 130
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 TRP cc_start: 0.8212 (t60) cc_final: 0.7896 (t60)
REVERT: A   13 ARG cc_start: 0.7964 (ttm170) cc_final: 0.7383 (mmp-170)
REVERT: A  128 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.7521 (m-10)
REVERT: A  382 ILE cc_start: 0.9529 (mm) cc_final: 0.9174 (tp)
REVERT: B   10 TRP cc_start: 0.8292 (t60) cc_final: 0.7893 (t60)
REVERT: B   13 ARG cc_start: 0.7889 (ttm170) cc_final: 0.7394 (mmp-170)
REVERT: B   83 TYR cc_start: 0.7834 (p90) cc_final: 0.7090 (p90)
REVERT: B  382 ILE cc_start: 0.9477 (mm) cc_final: 0.9050 (tp)
  outliers start: 28
  outliers final: 16
  residues processed: 147
  average time/residue: 0.0694
  time to fit residues: 14.5436
Evaluate side-chains
  138 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  128 PHE
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain B residue   39 SER
Chi-restraints excluded: chain B residue  100 ILE
Chi-restraints excluded: chain B residue  130 SER
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  183 ILE
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  355 SER
Chi-restraints excluded: chain B residue  429 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 35 optimal weight:    9.9990
   chunk 58 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 30 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 56 optimal weight:    0.0870
   chunk 80 optimal weight:    5.9990
   overall best weight:    0.6960

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

Flipped N/Q/H residues before XYZ refinement:
A 157 GLN
B 157 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.168752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.129701 restraints weight = 10069.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.133179 restraints weight = 5735.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.135328 restraints weight = 4102.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.136701 restraints weight = 3393.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.137234 restraints weight = 3052.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.3603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7340  Z= 0.115
  Angle     :  0.551   6.954   9992  Z= 0.284
  Chirality :  0.042   0.161   1136
  Planarity :  0.004   0.040   1226
  Dihedral  :  4.309  17.145    988
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.03 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 16.49 %
    Favored  : 80.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.79 (0.28), residues: 922
  helix: -0.80 (0.21), residues: 602
  sheet:  None (None), residues: 0
  loop : -1.71 (0.37), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 293 
 TYR   0.014   0.001   TYR B 381 
 PHE   0.017   0.001   PHE B 328 
 TRP   0.011   0.001   TRP A 202 
 HIS   0.003   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 7338)
  covalent geometry    : angle       0.55106 ( 9988)
  SS BOND              : bond        0.00254 (    2)
  SS BOND              : angle       0.64213 (    4)
  hydrogen bonds       : bond        0.03013 (  298)
  hydrogen bonds       : angle       3.51455 (  852)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 130
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 TRP cc_start: 0.8144 (t60) cc_final: 0.7796 (t60)
REVERT: A   13 ARG cc_start: 0.7922 (ttm170) cc_final: 0.7357 (mmp-170)
REVERT: A  128 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.7495 (m-10)
REVERT: A  382 ILE cc_start: 0.9533 (mm) cc_final: 0.9327 (tp)
REVERT: B   10 TRP cc_start: 0.8181 (t60) cc_final: 0.7865 (t60)
REVERT: B   13 ARG cc_start: 0.7835 (ttm170) cc_final: 0.7347 (mmp-170)
REVERT: B   51 HIS cc_start: 0.7833 (t-90) cc_final: 0.7582 (t70)
REVERT: B   83 TYR cc_start: 0.7781 (p90) cc_final: 0.7111 (p90)
REVERT: B  128 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7477 (m-10)
REVERT: B  382 ILE cc_start: 0.9478 (mm) cc_final: 0.9080 (tp)
  outliers start: 24
  outliers final: 18
  residues processed: 144
  average time/residue: 0.0669
  time to fit residues: 13.9625
Evaluate side-chains
  137 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  128 PHE
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  415 ASP
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain B residue    5 LEU
Chi-restraints excluded: chain B residue   39 SER
Chi-restraints excluded: chain B residue  100 ILE
Chi-restraints excluded: chain B residue  128 PHE
Chi-restraints excluded: chain B residue  130 SER
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  183 ILE
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  355 SER
Chi-restraints excluded: chain B residue  429 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   chunk 29 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   chunk 6 optimal weight:    0.1980
   chunk 54 optimal weight:    5.9990
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 88 optimal weight:    0.1980
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 384 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.170379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.131379 restraints weight = 9944.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.134841 restraints weight = 5659.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.137065 restraints weight = 4045.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.138295 restraints weight = 3344.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.138974 restraints weight = 3015.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.3746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   7340  Z= 0.106
  Angle     :  0.545   7.321   9992  Z= 0.279
  Chirality :  0.041   0.176   1136
  Planarity :  0.004   0.040   1226
  Dihedral  :  4.167  16.560    988
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 17.15 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.51 (0.28), residues: 922
  helix: -0.56 (0.21), residues: 588
  sheet:  None (None), residues: 0
  loop : -1.64 (0.37), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 293 
 TYR   0.010   0.001   TYR B  83 
 PHE   0.013   0.001   PHE B 328 
 TRP   0.010   0.001   TRP A 202 
 HIS   0.003   0.000   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 7338)
  covalent geometry    : angle       0.54526 ( 9988)
  SS BOND              : bond        0.00203 (    2)
  SS BOND              : angle       0.60489 (    4)
  hydrogen bonds       : bond        0.02904 (  298)
  hydrogen bonds       : angle       3.43692 (  852)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 127
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 TRP cc_start: 0.8078 (t60) cc_final: 0.7741 (t60)
REVERT: A   13 ARG cc_start: 0.7904 (ttm170) cc_final: 0.7332 (mmp-170)
REVERT: A   71 MET cc_start: 0.8765 (mmt) cc_final: 0.8483 (mmm)
REVERT: A  128 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.7530 (m-10)
REVERT: B   10 TRP cc_start: 0.8187 (t60) cc_final: 0.7850 (t60)
REVERT: B   13 ARG cc_start: 0.7830 (ttm170) cc_final: 0.7341 (mmp-170)
REVERT: B   51 HIS cc_start: 0.7897 (t-90) cc_final: 0.7632 (t70)
REVERT: B   83 TYR cc_start: 0.7779 (p90) cc_final: 0.7017 (p90)
REVERT: B  128 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.7539 (m-10)
REVERT: B  174 LYS cc_start: 0.7400 (tptp) cc_final: 0.7178 (tptp)
REVERT: B  382 ILE cc_start: 0.9482 (mm) cc_final: 0.9028 (tp)
  outliers start: 26
  outliers final: 15
  residues processed: 142
  average time/residue: 0.0687
  time to fit residues: 14.0278
Evaluate side-chains
  135 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 HIS
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  128 PHE
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  415 ASP
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain B residue   39 SER
Chi-restraints excluded: chain B residue  100 ILE
Chi-restraints excluded: chain B residue  128 PHE
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  183 ILE
Chi-restraints excluded: chain B residue  301 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 69 optimal weight:   20.0000
   chunk 9 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0010
   chunk 14 optimal weight:    0.0470
   chunk 58 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 51 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 90 optimal weight:    5.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    1.2090

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

Flipped N/Q/H residues before XYZ refinement:
A 384 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.166203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.126106 restraints weight = 10259.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.129434 restraints weight = 5967.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.131543 restraints weight = 4312.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.132622 restraints weight = 3599.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.133554 restraints weight = 3269.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.3729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7340  Z= 0.160
  Angle     :  0.605   7.744   9992  Z= 0.312
  Chirality :  0.044   0.174   1136
  Planarity :  0.004   0.040   1226
  Dihedral  :  4.453  17.310    988
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.13 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 17.15 %
    Favored  : 79.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.63 (0.28), residues: 922
  helix: -0.72 (0.21), residues: 612
  sheet:  None (None), residues: 0
  loop : -1.58 (0.39), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 361 
 TYR   0.018   0.002   TYR A 321 
 PHE   0.013   0.001   PHE B 314 
 TRP   0.017   0.001   TRP B 202 
 HIS   0.005   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 7338)
  covalent geometry    : angle       0.60462 ( 9988)
  SS BOND              : bond        0.00302 (    2)
  SS BOND              : angle       0.78645 (    4)
  hydrogen bonds       : bond        0.03461 (  298)
  hydrogen bonds       : angle       3.70940 (  852)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 122
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 TRP cc_start: 0.8194 (t60) cc_final: 0.7792 (t60)
REVERT: A   13 ARG cc_start: 0.7873 (ttm170) cc_final: 0.7276 (mmp-170)
REVERT: A  128 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.7644 (m-10)
REVERT: B   10 TRP cc_start: 0.8186 (t60) cc_final: 0.7798 (t60)
REVERT: B   13 ARG cc_start: 0.7862 (ttm170) cc_final: 0.7335 (mmp-170)
REVERT: B  128 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.7580 (m-10)
REVERT: B  382 ILE cc_start: 0.9494 (mm) cc_final: 0.9096 (tp)
  outliers start: 24
  outliers final: 19
  residues processed: 137
  average time/residue: 0.0638
  time to fit residues: 12.6900
Evaluate side-chains
  135 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 114
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  128 PHE
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  301 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  415 ASP
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain B residue   39 SER
Chi-restraints excluded: chain B residue  100 ILE
Chi-restraints excluded: chain B residue  128 PHE
Chi-restraints excluded: chain B residue  130 SER
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  183 ILE
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  301 SER
Chi-restraints excluded: chain B residue  409 THR
Chi-restraints excluded: chain B residue  429 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 69 optimal weight:   10.0000
   chunk 67 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 70 optimal weight:    0.6980
   chunk 41 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 89 optimal weight:    8.9990
   chunk 90 optimal weight:    2.9990
   chunk 35 optimal weight:   10.0000
   chunk 91 optimal weight:    0.7980
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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 = 0.3950 r_free = 0.3950 target = 0.167919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.128093 restraints weight = 10163.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.131525 restraints weight = 5776.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.133724 restraints weight = 4148.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.134817 restraints weight = 3428.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.135688 restraints weight = 3121.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.3900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7340  Z= 0.129
  Angle     :  0.580   7.951   9992  Z= 0.300
  Chirality :  0.042   0.171   1136
  Planarity :  0.004   0.041   1226
  Dihedral  :  4.364  22.664    988
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 17.15 %
    Favored  : 79.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.47 (0.28), residues: 922
  helix: -0.58 (0.21), residues: 612
  sheet:  None (None), residues: 0
  loop : -1.55 (0.39), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  13 
 TYR   0.017   0.001   TYR B 381 
 PHE   0.012   0.001   PHE A 463 
 TRP   0.016   0.001   TRP B 202 
 HIS   0.004   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 7338)
  covalent geometry    : angle       0.57923 ( 9988)
  SS BOND              : bond        0.00262 (    2)
  SS BOND              : angle       1.20246 (    4)
  hydrogen bonds       : bond        0.03260 (  298)
  hydrogen bonds       : angle       3.61465 (  852)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 TRP cc_start: 0.8129 (t60) cc_final: 0.7722 (t60)
REVERT: A   13 ARG cc_start: 0.7834 (ttm170) cc_final: 0.7297 (mmp-170)
REVERT: A  128 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.7592 (m-10)
REVERT: B   10 TRP cc_start: 0.8168 (t60) cc_final: 0.7762 (t60)
REVERT: B   13 ARG cc_start: 0.7919 (ttm170) cc_final: 0.7341 (mmp-170)
REVERT: B   51 HIS cc_start: 0.7892 (t70) cc_final: 0.7661 (t-170)
REVERT: B   71 MET cc_start: 0.8774 (tpp) cc_final: 0.8470 (mmm)
REVERT: B   83 TYR cc_start: 0.7885 (p90) cc_final: 0.6915 (p90)
REVERT: B  128 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.7559 (m-10)
REVERT: B  382 ILE cc_start: 0.9509 (mm) cc_final: 0.9147 (tp)
  outliers start: 24
  outliers final: 19
  residues processed: 139
  average time/residue: 0.0653
  time to fit residues: 13.2847
Evaluate side-chains
  140 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  128 PHE
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  368 MET
Chi-restraints excluded: chain A residue  415 ASP
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain B residue   39 SER
Chi-restraints excluded: chain B residue  100 ILE
Chi-restraints excluded: chain B residue  128 PHE
Chi-restraints excluded: chain B residue  130 SER
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  183 ILE
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  301 SER
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  454 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 29 optimal weight:    6.9990
   chunk 84 optimal weight:    0.4980
   chunk 38 optimal weight:    6.9990
   chunk 42 optimal weight:    0.6980
   chunk 79 optimal weight:    6.9990
   chunk 49 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 17 optimal weight:    0.3980
   chunk 44 optimal weight:    5.9990
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3971 r_free = 0.3971 target = 0.169875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.130843 restraints weight = 10022.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.134253 restraints weight = 5728.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.136467 restraints weight = 4100.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.137677 restraints weight = 3385.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.138502 restraints weight = 3055.541|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.4034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7340  Z= 0.115
  Angle     :  0.578  10.600   9992  Z= 0.294
  Chirality :  0.042   0.181   1136
  Planarity :  0.004   0.041   1226
  Dihedral  :  4.217  25.739    988
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 16.62 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.29), residues: 922
  helix: -0.41 (0.21), residues: 614
  sheet:  None (None), residues: 0
  loop : -1.60 (0.40), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 293 
 TYR   0.019   0.001   TYR A 321 
 PHE   0.013   0.001   PHE A 463 
 TRP   0.015   0.001   TRP B 202 
 HIS   0.003   0.001   HIS B  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 7338)
  covalent geometry    : angle       0.57767 ( 9988)
  SS BOND              : bond        0.00249 (    2)
  SS BOND              : angle       0.85708 (    4)
  hydrogen bonds       : bond        0.03016 (  298)
  hydrogen bonds       : angle       3.42539 (  852)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 128
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 TRP cc_start: 0.8134 (t60) cc_final: 0.7745 (t60)
REVERT: A   13 ARG cc_start: 0.7904 (ttm170) cc_final: 0.7354 (mmp-170)
REVERT: A   71 MET cc_start: 0.8712 (mmt) cc_final: 0.8460 (mmm)
REVERT: A  128 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.7533 (m-10)
REVERT: A  382 ILE cc_start: 0.9491 (mm) cc_final: 0.9208 (tp)
REVERT: B   10 TRP cc_start: 0.8094 (t60) cc_final: 0.7703 (t60)
REVERT: B   13 ARG cc_start: 0.7886 (ttm170) cc_final: 0.7376 (mmp-170)
REVERT: B   83 TYR cc_start: 0.7853 (p90) cc_final: 0.7055 (p90)
REVERT: B  128 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.7465 (m-10)
REVERT: B  463 PHE cc_start: 0.8282 (t80) cc_final: 0.7868 (m-80)
  outliers start: 27
  outliers final: 21
  residues processed: 143
  average time/residue: 0.0652
  time to fit residues: 13.4248
Evaluate side-chains
  145 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 122
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 HIS
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  128 PHE
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  301 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  368 MET
Chi-restraints excluded: chain A residue  415 ASP
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain B residue   39 SER
Chi-restraints excluded: chain B residue  100 ILE
Chi-restraints excluded: chain B residue  128 PHE
Chi-restraints excluded: chain B residue  130 SER
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  183 ILE
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  301 SER
Chi-restraints excluded: chain B residue  409 THR
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  454 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 84 optimal weight:    0.3980
   chunk 22 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0870
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
A 384 GLN
B  51 HIS
B 157 GLN
B 384 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.169995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.130346 restraints weight = 10163.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.133704 restraints weight = 5806.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.135945 restraints weight = 4183.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.137199 restraints weight = 3477.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.137923 restraints weight = 3138.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.4189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7340  Z= 0.117
  Angle     :  0.584  10.774   9992  Z= 0.296
  Chirality :  0.042   0.175   1136
  Planarity :  0.004   0.040   1226
  Dihedral  :  4.220  28.601    988
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 18.21 %
    Favored  : 78.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.28), residues: 922
  helix: -0.30 (0.21), residues: 614
  sheet:  None (None), residues: 0
  loop : -1.58 (0.39), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 293 
 TYR   0.031   0.002   TYR B 381 
 PHE   0.012   0.001   PHE A 463 
 TRP   0.015   0.001   TRP B 202 
 HIS   0.013   0.001   HIS B  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 7338)
  covalent geometry    : angle       0.58438 ( 9988)
  SS BOND              : bond        0.00245 (    2)
  SS BOND              : angle       0.75469 (    4)
  hydrogen bonds       : bond        0.03059 (  298)
  hydrogen bonds       : angle       3.38987 (  852)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1134.92 seconds
wall clock time: 20 minutes 16.61 seconds (1216.61 seconds total)