Starting phenix.real_space_refine
on Tue Feb  3 21:30:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9udw_64073/02_2026/9udw_64073.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9udw_64073/02_2026/9udw_64073.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9udw_64073/02_2026/9udw_64073.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9udw_64073/02_2026/9udw_64073.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9udw_64073/02_2026/9udw_64073.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9udw_64073/02_2026/9udw_64073.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.046
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      48      5.16       5
     C    4598      2.51       5
     N    1118      2.21       5
     O    1221      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: 6987
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3475
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 452, 3475
          Classifications: {'peptide': 452}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 16, 'TRANS': 435}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "A"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 16
          Unusual residues: {'G6P': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Classifications: {'water': 5}
          Link IDs: {None: 4}
  Restraints were copied for chains:
    B
  Time building chain proxies: 1.61, per 1000 atoms: 0.23
  Number of scatterers: 6987
  At special positions: 0
  Unit cell: (124.3, 102.3, 90.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      48     16.00
     P       2     15.00
     O    1221      8.00
     N    1118      7.00
     C    4598      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=2.04
    Simple disulfide: pdb=" SG  CYS B  54 " - pdb=" SG  CYS B  73 " distance=2.04

  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: 0.51
  Conformation dependent library (CDL) restraints added in 166.0 milliseconds
  

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1620

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 0 sheets defined
      73.0% 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 13
    Processing helix  chain 'A' and resid 17 through 41
      removed outlier: 3.609A  pdb=" N   PHE A  21 " --> pdb=" O   ARG A  17 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   GLY A  23 " --> pdb=" O   SER A  19 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ILE A  25 " --> pdb=" O   PHE A  21 " (cutoff:3.500A)
      removed outlier: 4.847A  pdb=" N   LEU A  26 " --> pdb=" O   ARG A  22 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   LEU A  27 " --> pdb=" O   GLY A  23 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   THR A  29 " --> pdb=" O   ILE A  25 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU A  31 " --> pdb=" O   LEU A  27 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   TYR A  33 " --> pdb=" O   THR A  29 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   HIS A  37 " --> pdb=" O   TYR A  33 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LYS A  41 " --> pdb=" O   HIS A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 44
      No H-bonds generated for 'chain 'A' and resid 42 through 44'
    Processing helix  chain 'A' and resid 87 through 105
      removed outlier: 3.817A  pdb=" N   ASN A  92 " --> pdb=" O   GLY A  88 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   PHE A  94 " --> pdb=" O   VAL A  90 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   LEU A  95 " --> pdb=" O   ASP A  91 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   ALA A  97 " --> pdb=" O   ALA A  93 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   PHE A 103 " --> pdb=" O   ALA A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 119
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.685A  pdb=" N   LEU A 124 " --> pdb=" O   ALA A 120 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   GLY A 126 " --> pdb=" O   MET A 122 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   PHE A 128 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   THR A 129 " --> pdb=" O   SER A 125 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   SER A 130 " --> pdb=" O   GLY A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 147
      removed outlier: 3.961A  pdb=" N   PHE A 146 " --> pdb=" O   GLU A 142 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   VAL A 147 " --> pdb=" O   LEU A 143 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 142 through 147'
    Processing helix  chain 'A' and resid 147 through 157
      removed outlier: 3.861A  pdb=" N   LEU A 155 " --> pdb=" O   VAL A 151 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   VAL A 156 " --> pdb=" O   CYS A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 173
      removed outlier: 4.199A  pdb=" N   THR A 166 " --> pdb=" O   PRO A 162 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   TRP A 171 " --> pdb=" O   CYS A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 184
    Processing helix  chain 'A' and resid 186 through 194
      removed outlier: 3.757A  pdb=" N   GLY A 191 " --> pdb=" O   HIS A 187 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   ASN A 192 " --> pdb=" O   THR A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 201
      removed outlier: 3.565A  pdb=" N   ILE A 198 " --> pdb=" O   LEU A 194 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ALA A 199 " --> pdb=" O   GLY A 195 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   ILE A 201 " --> pdb=" O   LEU A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 212
      removed outlier: 3.537A  pdb=" N   LEU A 209 " --> pdb=" O   GLN A 206 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   ILE A 212 " --> pdb=" O   LEU A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 228
      removed outlier: 3.950A  pdb=" N   THR A 218 " --> pdb=" O   PRO A 214 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   ALA A 219 " --> pdb=" O   GLY A 215 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   VAL A 223 " --> pdb=" O   ALA A 219 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   PHE A 226 " --> pdb=" O   GLY A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 292
    Processing helix  chain 'A' and resid 296 through 299
    Processing helix  chain 'A' and resid 300 through 327
      removed outlier: 4.449A  pdb=" N   PHE A 306 " --> pdb=" O   LEU A 302 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   LYS A 308 " --> pdb=" O   LEU A 304 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LEU A 309 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   VAL A 310 " --> pdb=" O   PHE A 306 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   PHE A 314 " --> pdb=" O   VAL A 310 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   LEU A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
      Proline residue:  A 319  - end of helix
      removed outlier: 3.979A  pdb=" N   ALA A 323 " --> pdb=" O   PRO A 319 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ALA A 326 " --> pdb=" O   ILE A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 358
      removed outlier: 3.536A  pdb=" N   LEU A 336 " --> pdb=" O   GLU A 332 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   THR A 338 " --> pdb=" O   GLY A 334 " (cutoff:3.500A)
      removed outlier: 4.638A  pdb=" N   LEU A 339 " --> pdb=" O   ASP A 335 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   PHE A 340 " --> pdb=" O   LEU A 336 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   ASP A 341 " --> pdb=" O   SER A 337 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLY A 343 " --> pdb=" O   LEU A 339 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   ILE A 346 " --> pdb=" O   VAL A 342 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLY A 348 " --> pdb=" O   GLY A 344 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ALA A 351 " --> pdb=" O   GLY A 347 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   SER A 355 " --> pdb=" O   ALA A 351 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ASP A 356 " --> pdb=" O   GLY A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 383
      removed outlier: 4.031A  pdb=" N   VAL A 367 " --> pdb=" O   THR A 363 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   MET A 368 " --> pdb=" O   THR A 364 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   ALA A 373 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      Proline residue:  A 374  - end of helix
    Processing helix  chain 'A' and resid 386 through 400
      removed outlier: 3.892A  pdb=" N   VAL A 392 " --> pdb=" O   ALA A 388 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ILE A 395 " --> pdb=" O   ILE A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 406
    Processing helix  chain 'A' and resid 407 through 416
      removed outlier: 3.604A  pdb=" N   ASP A 415 " --> pdb=" O   ALA A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 433
    Processing helix  chain 'A' and resid 435 through 441
      removed outlier: 3.770A  pdb=" N   SER A 441 " --> pdb=" O   ASP A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 455
      removed outlier: 3.712A  pdb=" N   ALA A 445 " --> pdb=" O   SER A 441 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   GLY A 447 " --> pdb=" O   GLY A 443 " (cutoff:3.500A)
      Proline residue:  A 448  - end of helix
      removed outlier: 3.666A  pdb=" N   LEU A 453 " --> pdb=" O   LEU A 449 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ILE A 454 " --> pdb=" O   LEU A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 456 through 458
      No H-bonds generated for 'chain 'A' and resid 456 through 458'
    Processing helix  chain 'A' and resid 459 through 474
      removed outlier: 3.745A  pdb=" N   ASP A 470 " --> pdb=" O   LEU A 466 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   VAL A 471 " --> pdb=" O   ILE A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 485
    Processing helix  chain 'A' and resid 488 through 492
    Processing helix  chain 'B' and resid 6 through 13
    Processing helix  chain 'B' and resid 17 through 41
      removed outlier: 3.610A  pdb=" N   PHE B  21 " --> pdb=" O   ARG B  17 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   GLY B  23 " --> pdb=" O   SER B  19 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ILE B  25 " --> pdb=" O   PHE B  21 " (cutoff:3.500A)
      removed outlier: 4.848A  pdb=" N   LEU B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   LEU B  27 " --> pdb=" O   GLY B  23 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   THR B  29 " --> pdb=" O   ILE B  25 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU B  31 " --> pdb=" O   LEU B  27 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   TYR B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   HIS B  37 " --> pdb=" O   TYR B  33 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LYS B  41 " --> pdb=" O   HIS B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 44
      No H-bonds generated for 'chain 'B' and resid 42 through 44'
    Processing helix  chain 'B' and resid 87 through 105
      removed outlier: 3.818A  pdb=" N   ASN B  92 " --> pdb=" O   GLY B  88 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   PHE B  94 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   LEU B  95 " --> pdb=" O   ASP B  91 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   ALA B  97 " --> pdb=" O   ALA B  93 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   PHE B 103 " --> pdb=" O   ALA B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 119
    Processing helix  chain 'B' and resid 120 through 131
      removed outlier: 3.685A  pdb=" N   LEU B 124 " --> pdb=" O   ALA B 120 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   GLY B 126 " --> pdb=" O   MET B 122 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   PHE B 128 " --> pdb=" O   LEU B 124 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   THR B 129 " --> pdb=" O   SER B 125 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   SER B 130 " --> pdb=" O   GLY B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 147
      removed outlier: 3.960A  pdb=" N   PHE B 146 " --> pdb=" O   GLU B 142 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   VAL B 147 " --> pdb=" O   LEU B 143 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 142 through 147'
    Processing helix  chain 'B' and resid 147 through 157
      removed outlier: 3.861A  pdb=" N   LEU B 155 " --> pdb=" O   VAL B 151 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   VAL B 156 " --> pdb=" O   CYS B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 173
      removed outlier: 4.199A  pdb=" N   THR B 166 " --> pdb=" O   PRO B 162 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   TRP B 171 " --> pdb=" O   CYS B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 184
    Processing helix  chain 'B' and resid 186 through 194
      removed outlier: 3.758A  pdb=" N   GLY B 191 " --> pdb=" O   HIS B 187 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   ASN B 192 " --> pdb=" O   THR B 188 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 201
      removed outlier: 3.565A  pdb=" N   ILE B 198 " --> pdb=" O   LEU B 194 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ALA B 199 " --> pdb=" O   GLY B 195 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   ILE B 201 " --> pdb=" O   LEU B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 212
      removed outlier: 3.537A  pdb=" N   LEU B 209 " --> pdb=" O   GLN B 206 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   ILE B 212 " --> pdb=" O   LEU B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 228
      removed outlier: 3.950A  pdb=" N   THR B 218 " --> pdb=" O   PRO B 214 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   ALA B 219 " --> pdb=" O   GLY B 215 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   VAL B 223 " --> pdb=" O   ALA B 219 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   PHE B 226 " --> pdb=" O   GLY B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 292
    Processing helix  chain 'B' and resid 296 through 299
    Processing helix  chain 'B' and resid 300 through 327
      removed outlier: 4.449A  pdb=" N   PHE B 306 " --> pdb=" O   LEU B 302 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   LYS B 308 " --> pdb=" O   LEU B 304 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LEU B 309 " --> pdb=" O   LEU B 305 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   VAL B 310 " --> pdb=" O   PHE B 306 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   PHE B 314 " --> pdb=" O   VAL B 310 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   LEU B 318 " --> pdb=" O   PHE B 314 " (cutoff:3.500A)
      Proline residue:  B 319  - end of helix
      removed outlier: 3.978A  pdb=" N   ALA B 323 " --> pdb=" O   PRO B 319 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ALA B 326 " --> pdb=" O   ILE B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 358
      removed outlier: 3.536A  pdb=" N   LEU B 336 " --> pdb=" O   GLU B 332 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   THR B 338 " --> pdb=" O   GLY B 334 " (cutoff:3.500A)
      removed outlier: 4.638A  pdb=" N   LEU B 339 " --> pdb=" O   ASP B 335 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   PHE B 340 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   ASP B 341 " --> pdb=" O   SER B 337 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLY B 343 " --> pdb=" O   LEU B 339 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   ILE B 346 " --> pdb=" O   VAL B 342 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLY B 348 " --> pdb=" O   GLY B 344 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ALA B 351 " --> pdb=" O   GLY B 347 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   SER B 355 " --> pdb=" O   ALA B 351 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ASP B 356 " --> pdb=" O   GLY B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 362 through 383
      removed outlier: 4.031A  pdb=" N   VAL B 367 " --> pdb=" O   THR B 363 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   MET B 368 " --> pdb=" O   THR B 364 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   ALA B 373 " --> pdb=" O   LEU B 369 " (cutoff:3.500A)
      Proline residue:  B 374  - end of helix
    Processing helix  chain 'B' and resid 386 through 400
      removed outlier: 3.891A  pdb=" N   VAL B 392 " --> pdb=" O   ALA B 388 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ILE B 395 " --> pdb=" O   ILE B 391 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 406
    Processing helix  chain 'B' and resid 407 through 416
      removed outlier: 3.604A  pdb=" N   ASP B 415 " --> pdb=" O   ALA B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 433
    Processing helix  chain 'B' and resid 435 through 441
      removed outlier: 3.770A  pdb=" N   SER B 441 " --> pdb=" O   ASP B 437 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 441 through 455
      removed outlier: 3.713A  pdb=" N   ALA B 445 " --> pdb=" O   SER B 441 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   GLY B 447 " --> pdb=" O   GLY B 443 " (cutoff:3.500A)
      Proline residue:  B 448  - end of helix
      removed outlier: 3.666A  pdb=" N   LEU B 453 " --> pdb=" O   LEU B 449 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ILE B 454 " --> pdb=" O   LEU B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 456 through 458
      No H-bonds generated for 'chain 'B' and resid 456 through 458'
    Processing helix  chain 'B' and resid 459 through 474
      removed outlier: 3.745A  pdb=" N   ASP B 470 " --> pdb=" O   LEU B 466 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   VAL B 471 " --> pdb=" O   ILE B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 479 through 485
    Processing helix  chain 'B' and resid 488 through 492

    284 hydrogen bonds defined for protein.
    816 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: 0.66

  Time building geometry restraints manager: 0.68 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1178
        1.32 -     1.45: 2012
        1.45 -     1.57: 3908
        1.57 -     1.69: 2
        1.69 -     1.82: 72
  Bond restraints: 7172
  Sorted by residual:
  bond pdb=" O6  G6P A 601 "
       pdb=" P   G6P A 601 "
    ideal  model  delta    sigma   weight residual
    1.722  1.591  0.131 2.00e-02 2.50e+03 4.32e+01
  bond pdb=" O6  G6P B 601 "
       pdb=" P   G6P B 601 "
    ideal  model  delta    sigma   weight residual
    1.722  1.591  0.131 2.00e-02 2.50e+03 4.31e+01
  bond pdb=" C   LYS B  41 "
       pdb=" N   PRO B  42 "
    ideal  model  delta    sigma   weight residual
    1.337  1.394 -0.058 9.80e-03 1.04e+04 3.45e+01
  bond pdb=" C   LYS A  41 "
       pdb=" N   PRO A  42 "
    ideal  model  delta    sigma   weight residual
    1.337  1.393 -0.057 9.80e-03 1.04e+04 3.37e+01
  bond pdb=" CA  LEU B 315 "
       pdb=" C   LEU B 315 "
    ideal  model  delta    sigma   weight residual
    1.524  1.464  0.060 1.29e-02 6.01e+03 2.13e+01
  ... (remaining 7167 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.49: 9272
        2.49 -     4.98: 418
        4.98 -     7.46: 52
        7.46 -     9.95: 20
        9.95 -    12.44: 10
  Bond angle restraints: 9772
  Sorted by residual:
  angle pdb=" N   LYS A 308 "
        pdb=" CA  LYS A 308 "
        pdb=" C   LYS A 308 "
      ideal   model   delta    sigma   weight residual
     112.54  123.02  -10.48 1.22e+00 6.72e-01 7.38e+01
  angle pdb=" N   LYS B 308 "
        pdb=" CA  LYS B 308 "
        pdb=" C   LYS B 308 "
      ideal   model   delta    sigma   weight residual
     112.54  123.01  -10.47 1.22e+00 6.72e-01 7.36e+01
  angle pdb=" C   ALA B 307 "
        pdb=" CA  ALA B 307 "
        pdb=" CB  ALA B 307 "
      ideal   model   delta    sigma   weight residual
     110.88  123.32  -12.44 1.57e+00 4.06e-01 6.28e+01
  angle pdb=" C   ALA A 307 "
        pdb=" CA  ALA A 307 "
        pdb=" CB  ALA A 307 "
      ideal   model   delta    sigma   weight residual
     110.88  123.29  -12.41 1.57e+00 4.06e-01 6.25e+01
  angle pdb=" N   VAL B 203 "
        pdb=" CA  VAL B 203 "
        pdb=" C   VAL B 203 "
      ideal   model   delta    sigma   weight residual
     110.23  118.02   -7.79 1.04e+00 9.25e-01 5.61e+01
  ... (remaining 9767 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.68: 3982
       26.68 -    53.36: 96
       53.36 -    80.04: 4
       80.04 -   106.72: 12
      106.72 -   133.40: 4
  Dihedral angle restraints: 4098
    sinusoidal: 1544
      harmonic: 2554
  Sorted by residual:
  dihedral pdb=" C   ALA B 307 "
           pdb=" N   ALA B 307 "
           pdb=" CA  ALA B 307 "
           pdb=" CB  ALA B 307 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -141.49   18.89     0      2.50e+00 1.60e-01 5.71e+01
  dihedral pdb=" C   ALA A 307 "
           pdb=" N   ALA A 307 "
           pdb=" CA  ALA A 307 "
           pdb=" CB  ALA A 307 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -141.45   18.85     0      2.50e+00 1.60e-01 5.69e+01
  dihedral pdb=" CB  CYS A  54 "
           pdb=" SG  CYS A  54 "
           pdb=" SG  CYS A  73 "
           pdb=" CB  CYS A  73 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  147.93  -54.93     1      1.00e+01 1.00e-02 4.08e+01
  ... (remaining 4095 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.141: 1062
       0.141 -    0.281: 44
       0.281 -    0.422: 10
       0.422 -    0.562: 6
       0.562 -    0.703: 4
  Chirality restraints: 1126
  Sorted by residual:
  chirality pdb=" CA  ALA B 307 "
            pdb=" N   ALA B 307 "
            pdb=" C   ALA B 307 "
            pdb=" CB  ALA B 307 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.78    0.70 2.00e-01 2.50e+01 1.23e+01
  chirality pdb=" CA  ALA A 307 "
            pdb=" N   ALA A 307 "
            pdb=" C   ALA A 307 "
            pdb=" CB  ALA A 307 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.78    0.70 2.00e-01 2.50e+01 1.23e+01
  chirality pdb=" CA  SER A 337 "
            pdb=" N   SER A 337 "
            pdb=" C   SER A 337 "
            pdb=" CB  SER A 337 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.89    0.62 2.00e-01 2.50e+01 9.51e+00
  ... (remaining 1123 not shown)

  Planarity restraints: 1188
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 447 "   -0.045 5.00e-02 4.00e+02   6.88e-02 7.56e+00
        pdb=" N   PRO B 448 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO B 448 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 448 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 447 "    0.045 5.00e-02 4.00e+02   6.87e-02 7.56e+00
        pdb=" N   PRO A 448 "   -0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO A 448 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 448 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 455 "   -0.045 5.00e-02 4.00e+02   6.66e-02 7.10e+00
        pdb=" N   PRO B 456 "    0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO B 456 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 456 "   -0.038 5.00e-02 4.00e+02
  ... (remaining 1185 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1523
        2.76 -     3.30: 6237
        3.30 -     3.83: 10740
        3.83 -     4.37: 12718
        4.37 -     4.90: 21758
  Nonbonded interactions: 52976
  Sorted by model distance:
  nonbonded pdb=" O   GLY B 383 "
            pdb=" OG  SER B 390 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" O   GLY A 383 "
            pdb=" OG  SER A 390 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" O   TRP A 488 "
            pdb=" OG  SER A 491 "
     model   vdw
     2.350 3.040
  nonbonded pdb=" O   TRP B 488 "
            pdb=" OG  SER B 491 "
     model   vdw
     2.351 3.040
  nonbonded pdb=" O   SER B  19 "
            pdb=" OG  SER B  19 "
     model   vdw
     2.387 3.040
  ... (remaining 52971 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:             1.000
  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:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.870
  Find NCS groups from input model:        0.030
  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:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
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      :  0.011   0.131   7174  Z= 0.493
  Angle     :  1.244  12.438   9776  Z= 0.713
  Chirality :  0.089   0.703   1126
  Planarity :  0.008   0.069   1188
  Dihedral  : 13.857 133.399   2472
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  5.92 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  3.51 %
    Favored  : 96.22 %
  Cbeta Deviations :  0.74 %
  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: -6.05 (0.19), residues: 896
  helix: -4.29 (0.10), residues: 618
  sheet:  None (None), residues: 0
  loop : -2.67 (0.35), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.002   ARG A 115 
 TYR   0.025   0.004   TYR A 381 
 PHE   0.023   0.003   PHE B 146 
 TRP   0.032   0.003   TRP B  10 
 HIS   0.018   0.004   HIS B 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.01101 ( 7172)
  covalent geometry    : angle       1.24342 ( 9772)
  SS BOND              : bond        0.00812 (    2)
  SS BOND              : angle       1.93828 (    4)
  hydrogen bonds       : bond        0.22657 (  284)
  hydrogen bonds       : angle       9.25420 (  816)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 193
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6529 (pmm) cc_final: 0.4184 (mmm)
REVERT: A   47 LYS cc_start: 0.8562 (mtmt) cc_final: 0.8233 (mtmm)
REVERT: A   83 TYR cc_start: 0.7790 (p90) cc_final: 0.7383 (p90)
REVERT: A   86 LEU cc_start: 0.8229 (mt) cc_final: 0.7904 (mt)
REVERT: A  193 ILE cc_start: 0.8440 (tt) cc_final: 0.8082 (tt)
REVERT: A  427 LYS cc_start: 0.9127 (mptt) cc_final: 0.8632 (tmmt)
REVERT: A  481 VAL cc_start: 0.9204 (t) cc_final: 0.8958 (p)
REVERT: B    1 MET cc_start: 0.6531 (pmm) cc_final: 0.4119 (mmm)
REVERT: B   10 TRP cc_start: 0.7617 (t60) cc_final: 0.7183 (t60)
REVERT: B   22 ARG cc_start: 0.7063 (ppt170) cc_final: 0.5740 (mtm110)
REVERT: B   47 LYS cc_start: 0.8545 (mtmt) cc_final: 0.8266 (mtmm)
REVERT: B   83 TYR cc_start: 0.7888 (p90) cc_final: 0.7470 (p90)
REVERT: B   86 LEU cc_start: 0.8105 (mt) cc_final: 0.7851 (mt)
REVERT: B  139 ASN cc_start: 0.8106 (p0) cc_final: 0.7834 (p0)
REVERT: B  193 ILE cc_start: 0.8461 (tt) cc_final: 0.8144 (tt)
REVERT: B  400 LEU cc_start: 0.8895 (mp) cc_final: 0.8484 (mp)
REVERT: B  419 HIS cc_start: 0.7457 (t-90) cc_final: 0.7233 (t-90)
REVERT: B  427 LYS cc_start: 0.9103 (mptt) cc_final: 0.8676 (tmmt)
REVERT: B  446 LEU cc_start: 0.8270 (mm) cc_final: 0.8008 (tp)
REVERT: B  481 VAL cc_start: 0.9115 (t) cc_final: 0.8898 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 195
  average time/residue: 0.0798
  time to fit residues: 20.3389
Evaluate side-chains
  129 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    8.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  65 HIS
A 402 ASN
B  65 HIS
B 402 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.147081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.109451 restraints weight = 8925.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.112736 restraints weight = 4960.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.114815 restraints weight = 3555.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.115970 restraints weight = 2966.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.116416 restraints weight = 2695.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.2165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7174  Z= 0.135
  Angle     :  0.645   7.199   9776  Z= 0.333
  Chirality :  0.044   0.231   1126
  Planarity :  0.005   0.038   1188
  Dihedral  :  6.554  36.695   1004
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  :  7.16 %
    Favored  : 89.86 %
  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: -4.40 (0.23), residues: 896
  helix: -3.01 (0.15), residues: 632
  sheet:  None (None), residues: 0
  loop : -2.04 (0.38), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 361 
 TYR   0.024   0.002   TYR B 464 
 PHE   0.010   0.001   PHE B 306 
 TRP   0.014   0.001   TRP A  72 
 HIS   0.003   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 7172)
  covalent geometry    : angle       0.64480 ( 9772)
  SS BOND              : bond        0.00071 (    2)
  SS BOND              : angle       1.10643 (    4)
  hydrogen bonds       : bond        0.04560 (  284)
  hydrogen bonds       : angle       5.34101 (  816)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 149
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A    1 MET cc_start: 0.6374 (pmm) cc_final: 0.3966 (mmm)
REVERT: A   22 ARG cc_start: 0.6360 (ppt170) cc_final: 0.5239 (mtm110)
REVERT: A   52 GLN cc_start: 0.7475 (pt0) cc_final: 0.7214 (pt0)
REVERT: A   83 TYR cc_start: 0.7765 (p90) cc_final: 0.7325 (p90)
REVERT: A   86 LEU cc_start: 0.8052 (mt) cc_final: 0.7740 (mt)
REVERT: A  119 SER cc_start: 0.8695 (t) cc_final: 0.8416 (m)
REVERT: A  232 HIS cc_start: 0.7974 (OUTLIER) cc_final: 0.7569 (m-70)
REVERT: A  407 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8364 (mp)
REVERT: A  427 LYS cc_start: 0.9117 (mptt) cc_final: 0.8622 (tmmt)
REVERT: A  446 LEU cc_start: 0.8445 (tp) cc_final: 0.8018 (tp)
REVERT: A  481 VAL cc_start: 0.9091 (t) cc_final: 0.8849 (p)
REVERT: B    1 MET cc_start: 0.6643 (pmm) cc_final: 0.4095 (mmm)
REVERT: B   10 TRP cc_start: 0.7248 (t60) cc_final: 0.6948 (t60)
REVERT: B   22 ARG cc_start: 0.6693 (ppt170) cc_final: 0.5698 (mtm110)
REVERT: B   47 LYS cc_start: 0.8681 (mtmt) cc_final: 0.8432 (mtpp)
REVERT: B   83 TYR cc_start: 0.7841 (p90) cc_final: 0.7460 (p90)
REVERT: B  119 SER cc_start: 0.8738 (t) cc_final: 0.8363 (m)
REVERT: B  193 ILE cc_start: 0.8305 (tt) cc_final: 0.7826 (tt)
REVERT: B  232 HIS cc_start: 0.7977 (OUTLIER) cc_final: 0.7588 (m-70)
REVERT: B  407 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8351 (mp)
REVERT: B  427 LYS cc_start: 0.9091 (mptt) cc_final: 0.8624 (tmmt)
  outliers start: 22
  outliers final: 8
  residues processed: 161
  average time/residue: 0.0879
  time to fit residues: 18.4130
Evaluate side-chains
  148 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 136
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue   91 ASP
Chi-restraints excluded: chain A residue  103 PHE
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  232 HIS
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain B residue   91 ASP
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  232 HIS
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  407 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 69 optimal weight:    0.6980
   chunk 15 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 34 optimal weight:    7.9990
   chunk 6 optimal weight:    4.9990
   chunk 8 optimal weight:    5.9990
   chunk 52 optimal weight:    0.0970
   chunk 37 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3598 r_free = 0.3598 target = 0.143225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.106958 restraints weight = 9043.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.109967 restraints weight = 5161.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.111823 restraints weight = 3722.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.112748 restraints weight = 3116.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.113434 restraints weight = 2845.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.2579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7174  Z= 0.138
  Angle     :  0.609   7.418   9776  Z= 0.313
  Chirality :  0.042   0.146   1126
  Planarity :  0.004   0.034   1188
  Dihedral  :  5.440  38.238   1004
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  :  8.92 %
    Favored  : 86.49 %
  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: -3.63 (0.25), residues: 896
  helix: -2.40 (0.17), residues: 630
  sheet:  None (None), residues: 0
  loop : -1.87 (0.39), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 361 
 TYR   0.016   0.001   TYR B 464 
 PHE   0.009   0.001   PHE B  94 
 TRP   0.010   0.001   TRP A 207 
 HIS   0.004   0.001   HIS B  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 7172)
  covalent geometry    : angle       0.60675 ( 9772)
  SS BOND              : bond        0.00104 (    2)
  SS BOND              : angle       2.77954 (    4)
  hydrogen bonds       : bond        0.04182 (  284)
  hydrogen bonds       : angle       4.86357 (  816)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 135
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A    1 MET cc_start: 0.6360 (pmm) cc_final: 0.3812 (mmm)
REVERT: A   22 ARG cc_start: 0.6243 (ppt170) cc_final: 0.5014 (mtm110)
REVERT: A   83 TYR cc_start: 0.7796 (p90) cc_final: 0.7313 (p90)
REVERT: A   86 LEU cc_start: 0.7960 (mt) cc_final: 0.7643 (mt)
REVERT: A  119 SER cc_start: 0.8684 (t) cc_final: 0.8359 (m)
REVERT: A  122 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.8075 (ttp)
REVERT: A  232 HIS cc_start: 0.7903 (OUTLIER) cc_final: 0.7566 (m-70)
REVERT: A  407 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8299 (mp)
REVERT: A  425 ASN cc_start: 0.7497 (t0) cc_final: 0.6670 (p0)
REVERT: A  427 LYS cc_start: 0.9118 (mptt) cc_final: 0.8559 (tmmt)
REVERT: A  481 VAL cc_start: 0.9066 (t) cc_final: 0.8842 (p)
REVERT: B    1 MET cc_start: 0.6752 (pmm) cc_final: 0.3999 (mmm)
REVERT: B   10 TRP cc_start: 0.7254 (t60) cc_final: 0.6843 (t60)
REVERT: B   22 ARG cc_start: 0.6386 (ppt170) cc_final: 0.5192 (mtm110)
REVERT: B   47 LYS cc_start: 0.8647 (mtmt) cc_final: 0.8345 (mtpp)
REVERT: B   83 TYR cc_start: 0.7893 (p90) cc_final: 0.7468 (p90)
REVERT: B   86 LEU cc_start: 0.8029 (mt) cc_final: 0.7774 (mt)
REVERT: B  119 SER cc_start: 0.8727 (t) cc_final: 0.8322 (m)
REVERT: B  122 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.8127 (ttp)
REVERT: B  232 HIS cc_start: 0.7934 (OUTLIER) cc_final: 0.7604 (m-70)
REVERT: B  407 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8317 (mp)
REVERT: B  427 LYS cc_start: 0.9087 (mptt) cc_final: 0.8594 (tmmt)
REVERT: B  446 LEU cc_start: 0.8332 (tp) cc_final: 0.7928 (tp)
  outliers start: 34
  outliers final: 19
  residues processed: 153
  average time/residue: 0.0784
  time to fit residues: 15.6942
Evaluate side-chains
  158 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 133
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue   91 ASP
Chi-restraints excluded: chain A residue  122 MET
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  232 HIS
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  402 ASN
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   91 ASP
Chi-restraints excluded: chain B residue  122 MET
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  232 HIS
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  402 ASN
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  433 THR
Chi-restraints excluded: chain B residue  486 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 29 optimal weight:    0.3980
   chunk 51 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
B 461 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.141918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.105342 restraints weight = 9099.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.108310 restraints weight = 5154.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.110255 restraints weight = 3711.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.111181 restraints weight = 3106.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.111842 restraints weight = 2834.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7174  Z= 0.151
  Angle     :  0.605   7.502   9776  Z= 0.311
  Chirality :  0.042   0.146   1126
  Planarity :  0.004   0.032   1188
  Dihedral  :  5.224  35.951   1004
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 10.81 %
    Favored  : 84.05 %
  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: -3.15 (0.25), residues: 896
  helix: -2.05 (0.18), residues: 630
  sheet:  None (None), residues: 0
  loop : -1.66 (0.38), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  22 
 TYR   0.013   0.001   TYR A 464 
 PHE   0.016   0.001   PHE B 179 
 TRP   0.011   0.001   TRP B  72 
 HIS   0.004   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 7172)
  covalent geometry    : angle       0.60354 ( 9772)
  SS BOND              : bond        0.00036 (    2)
  SS BOND              : angle       2.16324 (    4)
  hydrogen bonds       : bond        0.04104 (  284)
  hydrogen bonds       : angle       4.71258 (  816)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 136
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A    1 MET cc_start: 0.6448 (pmm) cc_final: 0.3689 (mmm)
REVERT: A   22 ARG cc_start: 0.6427 (ppt170) cc_final: 0.5205 (mtm110)
REVERT: A   83 TYR cc_start: 0.7807 (p90) cc_final: 0.7322 (p90)
REVERT: A  119 SER cc_start: 0.8837 (t) cc_final: 0.8466 (m)
REVERT: A  231 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7882 (mt-10)
REVERT: A  232 HIS cc_start: 0.8023 (OUTLIER) cc_final: 0.7618 (m-70)
REVERT: A  407 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8379 (mp)
REVERT: A  425 ASN cc_start: 0.7508 (t0) cc_final: 0.6774 (p0)
REVERT: A  427 LYS cc_start: 0.9006 (mptt) cc_final: 0.8529 (tmmt)
REVERT: B    1 MET cc_start: 0.6747 (pmm) cc_final: 0.4113 (mmm)
REVERT: B   10 TRP cc_start: 0.7309 (t60) cc_final: 0.6873 (t60)
REVERT: B   22 ARG cc_start: 0.6610 (ppt170) cc_final: 0.5442 (mtm110)
REVERT: B   80 LYS cc_start: 0.8012 (mmtm) cc_final: 0.7605 (mmtt)
REVERT: B   83 TYR cc_start: 0.7877 (p90) cc_final: 0.7460 (p90)
REVERT: B   86 LEU cc_start: 0.8116 (mt) cc_final: 0.7864 (mt)
REVERT: B  119 SER cc_start: 0.8802 (t) cc_final: 0.8450 (m)
REVERT: B  193 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7626 (tt)
REVERT: B  232 HIS cc_start: 0.8011 (OUTLIER) cc_final: 0.7716 (m-70)
REVERT: B  376 MET cc_start: 0.6383 (OUTLIER) cc_final: 0.6177 (ptp)
REVERT: B  427 LYS cc_start: 0.9096 (mptt) cc_final: 0.8601 (tmmt)
  outliers start: 38
  outliers final: 20
  residues processed: 154
  average time/residue: 0.0758
  time to fit residues: 15.5298
Evaluate side-chains
  153 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 128
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue   91 ASP
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  232 HIS
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  402 ASN
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   91 ASP
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain B residue  232 HIS
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  376 MET
Chi-restraints excluded: chain B residue  402 ASN
Chi-restraints excluded: chain B residue  433 THR
Chi-restraints excluded: chain B residue  486 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 78 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 5 optimal weight:    0.4980
   chunk 40 optimal weight:    0.9990
   chunk 70 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 89 optimal weight:    0.7980
   chunk 79 optimal weight:    0.9980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3588 r_free = 0.3588 target = 0.142708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.106899 restraints weight = 9059.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.109820 restraints weight = 5187.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.111715 restraints weight = 3754.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.112833 restraints weight = 3135.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.113346 restraints weight = 2837.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.3110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7174  Z= 0.128
  Angle     :  0.582  10.314   9776  Z= 0.295
  Chirality :  0.041   0.143   1126
  Planarity :  0.004   0.029   1188
  Dihedral  :  5.051  37.491   1004
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 13.51 %
    Favored  : 82.16 %
  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: -2.73 (0.26), residues: 896
  helix: -1.71 (0.19), residues: 632
  sheet:  None (None), residues: 0
  loop : -1.56 (0.38), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  22 
 TYR   0.011   0.001   TYR B 464 
 PHE   0.012   0.001   PHE B 179 
 TRP   0.010   0.001   TRP B  10 
 HIS   0.003   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 7172)
  covalent geometry    : angle       0.58109 ( 9772)
  SS BOND              : bond        0.00061 (    2)
  SS BOND              : angle       1.44864 (    4)
  hydrogen bonds       : bond        0.03758 (  284)
  hydrogen bonds       : angle       4.50473 (  816)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 136
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A    1 MET cc_start: 0.6447 (pmm) cc_final: 0.3624 (mmm)
REVERT: A   22 ARG cc_start: 0.6365 (ppt170) cc_final: 0.5072 (mtm110)
REVERT: A   83 TYR cc_start: 0.7817 (p90) cc_final: 0.7384 (p90)
REVERT: A   86 LEU cc_start: 0.8027 (mt) cc_final: 0.7721 (mt)
REVERT: A  119 SER cc_start: 0.8796 (t) cc_final: 0.8392 (m)
REVERT: A  193 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7575 (tt)
REVERT: A  232 HIS cc_start: 0.7908 (OUTLIER) cc_final: 0.7639 (m-70)
REVERT: A  407 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8282 (mp)
REVERT: A  425 ASN cc_start: 0.7514 (t0) cc_final: 0.6715 (p0)
REVERT: A  427 LYS cc_start: 0.8995 (mptt) cc_final: 0.8465 (tmmt)
REVERT: B    1 MET cc_start: 0.6697 (pmm) cc_final: 0.3927 (mmm)
REVERT: B   22 ARG cc_start: 0.6430 (ppt170) cc_final: 0.5177 (mtm110)
REVERT: B   80 LYS cc_start: 0.7973 (mmtm) cc_final: 0.7699 (mmtm)
REVERT: B   83 TYR cc_start: 0.7869 (p90) cc_final: 0.7489 (p90)
REVERT: B   86 LEU cc_start: 0.7987 (mt) cc_final: 0.7739 (mt)
REVERT: B  119 SER cc_start: 0.8760 (t) cc_final: 0.8385 (m)
REVERT: B  174 LYS cc_start: 0.8304 (tmmt) cc_final: 0.8090 (ttpt)
REVERT: B  232 HIS cc_start: 0.7891 (OUTLIER) cc_final: 0.7624 (m-70)
REVERT: B  376 MET cc_start: 0.6201 (OUTLIER) cc_final: 0.5985 (ptp)
REVERT: B  427 LYS cc_start: 0.9104 (mptt) cc_final: 0.8550 (tmmt)
REVERT: B  446 LEU cc_start: 0.8493 (tp) cc_final: 0.8014 (tp)
  outliers start: 32
  outliers final: 20
  residues processed: 155
  average time/residue: 0.0709
  time to fit residues: 14.8109
Evaluate side-chains
  157 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 132
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue   91 ASP
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  193 ILE
Chi-restraints excluded: chain A residue  232 HIS
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  402 ASN
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   91 ASP
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  232 HIS
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  376 MET
Chi-restraints excluded: chain B residue  402 ASN
Chi-restraints excluded: chain B residue  433 THR
Chi-restraints excluded: chain B residue  486 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 74 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   chunk 56 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 82 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.3626 r_free = 0.3626 target = 0.145036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.106601 restraints weight = 9077.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.109769 restraints weight = 5113.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.111744 restraints weight = 3717.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.112705 restraints weight = 3133.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.113476 restraints weight = 2877.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.3219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7174  Z= 0.137
  Angle     :  0.583  11.017   9776  Z= 0.296
  Chirality :  0.042   0.144   1126
  Planarity :  0.004   0.029   1188
  Dihedral  :  5.018  37.553   1004
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 14.05 %
    Favored  : 81.76 %
  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: -2.43 (0.27), residues: 896
  helix: -1.53 (0.19), residues: 630
  sheet:  None (None), residues: 0
  loop : -1.35 (0.39), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  22 
 TYR   0.011   0.001   TYR B 117 
 PHE   0.021   0.001   PHE A 179 
 TRP   0.010   0.001   TRP B  10 
 HIS   0.004   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 7172)
  covalent geometry    : angle       0.58287 ( 9772)
  SS BOND              : bond        0.00060 (    2)
  SS BOND              : angle       1.29535 (    4)
  hydrogen bonds       : bond        0.03765 (  284)
  hydrogen bonds       : angle       4.47252 (  816)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 134
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A    1 MET cc_start: 0.6454 (pmm) cc_final: 0.3581 (mmm)
REVERT: A   22 ARG cc_start: 0.6441 (ppt170) cc_final: 0.5162 (mtm110)
REVERT: A   83 TYR cc_start: 0.7829 (p90) cc_final: 0.7362 (p90)
REVERT: A   86 LEU cc_start: 0.8118 (mt) cc_final: 0.7824 (mt)
REVERT: A  119 SER cc_start: 0.8777 (t) cc_final: 0.8459 (m)
REVERT: A  193 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7624 (tt)
REVERT: A  232 HIS cc_start: 0.7932 (OUTLIER) cc_final: 0.7545 (m-70)
REVERT: A  407 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8308 (mp)
REVERT: A  425 ASN cc_start: 0.7428 (t0) cc_final: 0.6726 (p0)
REVERT: A  427 LYS cc_start: 0.9000 (mptt) cc_final: 0.8462 (tmmt)
REVERT: B    1 MET cc_start: 0.6707 (pmm) cc_final: 0.3835 (mmm)
REVERT: B   22 ARG cc_start: 0.6511 (ppt170) cc_final: 0.5273 (mtm110)
REVERT: B   80 LYS cc_start: 0.8021 (mmtm) cc_final: 0.7747 (mmtm)
REVERT: B   83 TYR cc_start: 0.7871 (p90) cc_final: 0.7492 (p90)
REVERT: B   86 LEU cc_start: 0.8045 (mt) cc_final: 0.7811 (mt)
REVERT: B  119 SER cc_start: 0.8775 (t) cc_final: 0.8460 (m)
REVERT: B  174 LYS cc_start: 0.8289 (tmmt) cc_final: 0.7838 (pttm)
REVERT: B  193 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7598 (tt)
REVERT: B  232 HIS cc_start: 0.7910 (OUTLIER) cc_final: 0.7533 (m-70)
REVERT: B  376 MET cc_start: 0.6225 (OUTLIER) cc_final: 0.6002 (ptp)
REVERT: B  427 LYS cc_start: 0.9110 (mptt) cc_final: 0.8509 (tmmt)
REVERT: B  446 LEU cc_start: 0.8588 (tp) cc_final: 0.8106 (tp)
REVERT: B  489 LYS cc_start: 0.8632 (mmmt) cc_final: 0.8411 (mmmt)
  outliers start: 31
  outliers final: 20
  residues processed: 151
  average time/residue: 0.0776
  time to fit residues: 15.5630
Evaluate side-chains
  158 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 132
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   91 ASP
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  193 ILE
Chi-restraints excluded: chain A residue  232 HIS
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  402 ASN
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain B residue  232 HIS
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  376 MET
Chi-restraints excluded: chain B residue  402 ASN
Chi-restraints excluded: chain B residue  433 THR
Chi-restraints excluded: chain B residue  486 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 51 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9980
   chunk 69 optimal weight:    6.9990
   chunk 68 optimal weight:    3.9990
   chunk 24 optimal weight:    6.9990
   chunk 63 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 80 optimal weight:    0.6980
   chunk 76 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0970
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.7178

-------------------------------------------------------------------------------
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 = 0.3588 r_free = 0.3588 target = 0.142812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.106933 restraints weight = 8977.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.109895 restraints weight = 5075.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.111858 restraints weight = 3647.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.112790 restraints weight = 3035.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.113548 restraints weight = 2763.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.3361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7174  Z= 0.121
  Angle     :  0.578  10.962   9776  Z= 0.289
  Chirality :  0.041   0.142   1126
  Planarity :  0.003   0.027   1188
  Dihedral  :  4.946  38.111   1004
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 14.19 %
    Favored  : 80.95 %
  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: -2.20 (0.27), residues: 896
  helix: -1.35 (0.20), residues: 630
  sheet:  None (None), residues: 0
  loop : -1.25 (0.40), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  22 
 TYR   0.010   0.001   TYR A 117 
 PHE   0.021   0.001   PHE B 179 
 TRP   0.010   0.001   TRP B  10 
 HIS   0.003   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7172)
  covalent geometry    : angle       0.57798 ( 9772)
  SS BOND              : bond        0.00004 (    2)
  SS BOND              : angle       1.14430 (    4)
  hydrogen bonds       : bond        0.03549 (  284)
  hydrogen bonds       : angle       4.36729 (  816)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 132
  time to evaluate  : 0.178 
Fit side-chains
REVERT: A    1 MET cc_start: 0.6310 (pmm) cc_final: 0.3609 (mmm)
REVERT: A   22 ARG cc_start: 0.6725 (ppt170) cc_final: 0.5548 (mtm110)
REVERT: A   83 TYR cc_start: 0.7850 (p90) cc_final: 0.7388 (p90)
REVERT: A   86 LEU cc_start: 0.8212 (mt) cc_final: 0.7954 (mt)
REVERT: A  119 SER cc_start: 0.8758 (t) cc_final: 0.8510 (m)
REVERT: A  232 HIS cc_start: 0.8053 (OUTLIER) cc_final: 0.7725 (m-70)
REVERT: A  407 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8366 (mp)
REVERT: A  425 ASN cc_start: 0.7462 (t0) cc_final: 0.6905 (p0)
REVERT: A  427 LYS cc_start: 0.8975 (mptt) cc_final: 0.8483 (tmmt)
REVERT: B    1 MET cc_start: 0.6617 (pmm) cc_final: 0.3933 (mmm)
REVERT: B   22 ARG cc_start: 0.6633 (ppt170) cc_final: 0.5616 (mtm110)
REVERT: B   80 LYS cc_start: 0.8104 (mmtm) cc_final: 0.7769 (mmtt)
REVERT: B   83 TYR cc_start: 0.7891 (p90) cc_final: 0.7537 (p90)
REVERT: B  119 SER cc_start: 0.8776 (t) cc_final: 0.8507 (m)
REVERT: B  174 LYS cc_start: 0.8294 (tmmt) cc_final: 0.7882 (pttm)
REVERT: B  232 HIS cc_start: 0.8057 (OUTLIER) cc_final: 0.7746 (m-70)
REVERT: B  376 MET cc_start: 0.6438 (OUTLIER) cc_final: 0.6209 (ptp)
REVERT: B  427 LYS cc_start: 0.9077 (mptt) cc_final: 0.8547 (tmmt)
REVERT: B  446 LEU cc_start: 0.8660 (tp) cc_final: 0.8252 (tp)
REVERT: B  489 LYS cc_start: 0.8455 (mmmt) cc_final: 0.8252 (mmmt)
  outliers start: 36
  outliers final: 21
  residues processed: 152
  average time/residue: 0.0754
  time to fit residues: 15.3274
Evaluate side-chains
  157 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 132
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   91 ASP
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  232 HIS
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  402 ASN
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  232 HIS
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  376 MET
Chi-restraints excluded: chain B residue  402 ASN
Chi-restraints excluded: chain B residue  433 THR
Chi-restraints excluded: chain B residue  486 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 36 optimal weight:    0.4980
   chunk 62 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0970
   chunk 33 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 70 optimal weight:    0.0970
   overall best weight:    0.5176

-------------------------------------------------------------------------------
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 = 0.3605 r_free = 0.3605 target = 0.144270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.108607 restraints weight = 8999.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.111582 restraints weight = 5109.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.113516 restraints weight = 3671.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.114473 restraints weight = 3063.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.115117 restraints weight = 2786.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.3504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7174  Z= 0.106
  Angle     :  0.565  11.448   9776  Z= 0.282
  Chirality :  0.041   0.148   1126
  Planarity :  0.003   0.025   1188
  Dihedral  :  4.831  38.485   1004
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 15.14 %
    Favored  : 80.68 %
  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: -2.08 (0.27), residues: 896
  helix: -1.29 (0.20), residues: 646
  sheet:  None (None), residues: 0
  loop : -1.09 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  17 
 TYR   0.009   0.001   TYR A 117 
 PHE   0.021   0.001   PHE A 179 
 TRP   0.009   0.001   TRP A 207 
 HIS   0.003   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 7172)
  covalent geometry    : angle       0.56496 ( 9772)
  SS BOND              : bond        0.00054 (    2)
  SS BOND              : angle       1.07186 (    4)
  hydrogen bonds       : bond        0.03345 (  284)
  hydrogen bonds       : angle       4.23528 (  816)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 142
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A    1 MET cc_start: 0.6320 (pmm) cc_final: 0.3478 (mmm)
REVERT: A   22 ARG cc_start: 0.6504 (ppt170) cc_final: 0.5254 (mtm110)
REVERT: A   47 LYS cc_start: 0.8970 (mtpp) cc_final: 0.8238 (mtmm)
REVERT: A   83 TYR cc_start: 0.7815 (p90) cc_final: 0.7364 (p90)
REVERT: A   86 LEU cc_start: 0.8145 (mt) cc_final: 0.7883 (mt)
REVERT: A  119 SER cc_start: 0.8772 (t) cc_final: 0.8448 (m)
REVERT: A  232 HIS cc_start: 0.8003 (OUTLIER) cc_final: 0.7718 (m-70)
REVERT: A  407 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8312 (mp)
REVERT: A  425 ASN cc_start: 0.7559 (t0) cc_final: 0.6911 (p0)
REVERT: A  427 LYS cc_start: 0.8995 (mptt) cc_final: 0.8446 (tmmt)
REVERT: B    1 MET cc_start: 0.6728 (pmm) cc_final: 0.3918 (mmm)
REVERT: B   22 ARG cc_start: 0.6505 (ppt170) cc_final: 0.5301 (mtm110)
REVERT: B   80 LYS cc_start: 0.8057 (mmtm) cc_final: 0.7687 (mmtt)
REVERT: B   83 TYR cc_start: 0.7946 (p90) cc_final: 0.7570 (p90)
REVERT: B  119 SER cc_start: 0.8760 (t) cc_final: 0.8425 (m)
REVERT: B  139 ASN cc_start: 0.8195 (p0) cc_final: 0.7828 (p0)
REVERT: B  193 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7623 (tt)
REVERT: B  232 HIS cc_start: 0.7998 (OUTLIER) cc_final: 0.7735 (m-70)
REVERT: B  376 MET cc_start: 0.6298 (OUTLIER) cc_final: 0.6089 (ptp)
REVERT: B  427 LYS cc_start: 0.9106 (mptt) cc_final: 0.8506 (tmmt)
REVERT: B  446 LEU cc_start: 0.8534 (tp) cc_final: 0.8094 (tp)
  outliers start: 31
  outliers final: 19
  residues processed: 156
  average time/residue: 0.0756
  time to fit residues: 15.7694
Evaluate side-chains
  159 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 135
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   91 ASP
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  193 ILE
Chi-restraints excluded: chain A residue  232 HIS
Chi-restraints excluded: chain A residue  402 ASN
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain B residue  232 HIS
Chi-restraints excluded: chain B residue  342 VAL
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  376 MET
Chi-restraints excluded: chain B residue  433 THR
Chi-restraints excluded: chain B residue  484 GLU
Chi-restraints excluded: chain B residue  486 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 37 optimal weight:    0.0170
   chunk 26 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   chunk 57 optimal weight:    0.0870
   chunk 87 optimal weight:    0.9990
   chunk 82 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 21 optimal weight:    0.4980
   chunk 58 optimal weight:    0.5980
   overall best weight:    0.3596

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

Flipped N/Q/H residues before XYZ refinement:
B 461 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.145909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.110086 restraints weight = 8868.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.113117 restraints weight = 4958.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.115103 restraints weight = 3555.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.116056 restraints weight = 2966.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.116773 restraints weight = 2705.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.3681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7174  Z= 0.100
  Angle     :  0.569  11.326   9776  Z= 0.285
  Chirality :  0.041   0.224   1126
  Planarity :  0.003   0.026   1188
  Dihedral  :  4.708  38.677   1004
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 16.49 %
    Favored  : 80.41 %
  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: -1.80 (0.28), residues: 896
  helix: -1.11 (0.20), residues: 652
  sheet:  None (None), residues: 0
  loop : -0.86 (0.42), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  13 
 TYR   0.008   0.001   TYR B 117 
 PHE   0.022   0.001   PHE B 179 
 TRP   0.009   0.001   TRP A 207 
 HIS   0.003   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 7172)
  covalent geometry    : angle       0.56661 ( 9772)
  SS BOND              : bond        0.00045 (    2)
  SS BOND              : angle       2.78681 (    4)
  hydrogen bonds       : bond        0.03194 (  284)
  hydrogen bonds       : angle       4.12929 (  816)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 143
  time to evaluate  : 0.212 
Fit side-chains
REVERT: A    1 MET cc_start: 0.6202 (pmm) cc_final: 0.3302 (mmm)
REVERT: A   22 ARG cc_start: 0.6298 (ppt170) cc_final: 0.5085 (mtm110)
REVERT: A   47 LYS cc_start: 0.8937 (mtpp) cc_final: 0.8210 (mtmm)
REVERT: A   83 TYR cc_start: 0.7844 (p90) cc_final: 0.7409 (p90)
REVERT: A   86 LEU cc_start: 0.8112 (mt) cc_final: 0.7850 (mt)
REVERT: A  119 SER cc_start: 0.8727 (t) cc_final: 0.8359 (m)
REVERT: A  232 HIS cc_start: 0.7920 (OUTLIER) cc_final: 0.7714 (m-70)
REVERT: A  413 SER cc_start: 0.9097 (t) cc_final: 0.8787 (p)
REVERT: A  425 ASN cc_start: 0.7585 (t0) cc_final: 0.6935 (p0)
REVERT: A  427 LYS cc_start: 0.8995 (mptt) cc_final: 0.8451 (tmmt)
REVERT: A  446 LEU cc_start: 0.8455 (tp) cc_final: 0.7962 (tp)
REVERT: B    1 MET cc_start: 0.6637 (pmm) cc_final: 0.3743 (mmm)
REVERT: B   22 ARG cc_start: 0.6330 (ppt170) cc_final: 0.5102 (mtm110)
REVERT: B   80 LYS cc_start: 0.8056 (mmtm) cc_final: 0.7698 (mmtt)
REVERT: B   83 TYR cc_start: 0.7853 (p90) cc_final: 0.7512 (p90)
REVERT: B  119 SER cc_start: 0.8730 (t) cc_final: 0.8375 (m)
REVERT: B  139 ASN cc_start: 0.8183 (p0) cc_final: 0.7810 (p0)
REVERT: B  193 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7548 (tt)
REVERT: B  232 HIS cc_start: 0.8087 (OUTLIER) cc_final: 0.7671 (m-70)
REVERT: B  425 ASN cc_start: 0.7689 (m-40) cc_final: 0.7323 (m-40)
REVERT: B  427 LYS cc_start: 0.9068 (mptt) cc_final: 0.8465 (tmmt)
REVERT: B  446 LEU cc_start: 0.8463 (tp) cc_final: 0.7968 (tp)
  outliers start: 23
  outliers final: 16
  residues processed: 151
  average time/residue: 0.0809
  time to fit residues: 16.2752
Evaluate side-chains
  156 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 137
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue   91 ASP
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  232 HIS
Chi-restraints excluded: chain A residue  402 ASN
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain B residue  232 HIS
Chi-restraints excluded: chain B residue  370 ILE
Chi-restraints excluded: chain B residue  376 MET
Chi-restraints excluded: chain B residue  484 GLU
Chi-restraints excluded: chain B residue  486 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 79 optimal weight:    0.0670
   chunk 70 optimal weight:    0.0050
   chunk 32 optimal weight:    1.9990
   chunk 84 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 61 optimal weight:    0.5980
   chunk 52 optimal weight:    0.0970
   chunk 73 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0470
   chunk 39 optimal weight:    3.9990
   overall best weight:    0.1628

-------------------------------------------------------------------------------
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 = 0.3659 r_free = 0.3659 target = 0.149244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.113209 restraints weight = 8818.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.116340 restraints weight = 4844.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.118221 restraints weight = 3474.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.119518 restraints weight = 2905.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.120171 restraints weight = 2624.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.3882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7174  Z= 0.096
  Angle     :  0.582  11.246   9776  Z= 0.287
  Chirality :  0.040   0.210   1126
  Planarity :  0.003   0.027   1188
  Dihedral  :  4.550  38.650   1004
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 18.24 %
    Favored  : 79.73 %
  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: -1.52 (0.28), residues: 896
  helix: -0.86 (0.20), residues: 648
  sheet:  None (None), residues: 0
  loop : -0.93 (0.41), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 111 
 TYR   0.007   0.001   TYR B 464 
 PHE   0.021   0.001   PHE A 179 
 TRP   0.008   0.001   TRP B  72 
 HIS   0.003   0.001   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00201 ( 7172)
  covalent geometry    : angle       0.57573 ( 9772)
  SS BOND              : bond        0.00320 (    2)
  SS BOND              : angle       4.09794 (    4)
  hydrogen bonds       : bond        0.02895 (  284)
  hydrogen bonds       : angle       3.99656 (  816)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 138
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A    1 MET cc_start: 0.6233 (pmm) cc_final: 0.3311 (mmm)
REVERT: A   22 ARG cc_start: 0.6239 (ppt170) cc_final: 0.5009 (mtm110)
REVERT: A   47 LYS cc_start: 0.8916 (mtpp) cc_final: 0.8215 (mtmm)
REVERT: A   83 TYR cc_start: 0.7846 (p90) cc_final: 0.7420 (p90)
REVERT: A   86 LEU cc_start: 0.8069 (mt) cc_final: 0.7834 (mt)
REVERT: A  119 SER cc_start: 0.8705 (t) cc_final: 0.8313 (m)
REVERT: A  413 SER cc_start: 0.9080 (t) cc_final: 0.8727 (p)
REVERT: A  425 ASN cc_start: 0.7584 (t0) cc_final: 0.6921 (p0)
REVERT: A  427 LYS cc_start: 0.8982 (mptt) cc_final: 0.8427 (tmmt)
REVERT: A  446 LEU cc_start: 0.8410 (tp) cc_final: 0.7902 (tp)
REVERT: B    1 MET cc_start: 0.6667 (pmm) cc_final: 0.3707 (mmm)
REVERT: B   22 ARG cc_start: 0.6203 (ppt170) cc_final: 0.4985 (mtm110)
REVERT: B   80 LYS cc_start: 0.7930 (mmtm) cc_final: 0.7604 (mmtt)
REVERT: B   83 TYR cc_start: 0.7809 (p90) cc_final: 0.7536 (p90)
REVERT: B  119 SER cc_start: 0.8689 (t) cc_final: 0.8322 (m)
REVERT: B  425 ASN cc_start: 0.7724 (m-40) cc_final: 0.7366 (m110)
REVERT: B  427 LYS cc_start: 0.8958 (mptt) cc_final: 0.8430 (tmmt)
REVERT: B  446 LEU cc_start: 0.8404 (tp) cc_final: 0.7908 (tp)
REVERT: B  483 LYS cc_start: 0.8118 (ttmm) cc_final: 0.7691 (ttmt)
  outliers start: 15
  outliers final: 10
  residues processed: 145
  average time/residue: 0.0776
  time to fit residues: 15.0558
Evaluate side-chains
  141 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ASP
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  402 ASN
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain B residue  376 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   chunk 84 optimal weight:    4.9990
   chunk 77 optimal weight:    4.9990
   chunk 87 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 86 optimal weight:    0.0670
   chunk 83 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0770
   overall best weight:    0.4876

-------------------------------------------------------------------------------
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 = 0.3637 r_free = 0.3637 target = 0.147438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.110191 restraints weight = 8927.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.113347 restraints weight = 5022.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.115205 restraints weight = 3629.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.116386 restraints weight = 3049.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.116386 restraints weight = 2782.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.3923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7174  Z= 0.106
  Angle     :  0.596  11.191   9776  Z= 0.293
  Chirality :  0.041   0.166   1126
  Planarity :  0.003   0.025   1188
  Dihedral  :  4.550  39.664   1004
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 18.38 %
    Favored  : 79.32 %
  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: -1.39 (0.28), residues: 896
  helix: -0.76 (0.20), residues: 646
  sheet:  None (None), residues: 0
  loop : -0.89 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  22 
 TYR   0.008   0.001   TYR A 117 
 PHE   0.007   0.001   PHE B 306 
 TRP   0.008   0.001   TRP B 207 
 HIS   0.003   0.001   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 7172)
  covalent geometry    : angle       0.59102 ( 9772)
  SS BOND              : bond        0.00043 (    2)
  SS BOND              : angle       3.88842 (    4)
  hydrogen bonds       : bond        0.03101 (  284)
  hydrogen bonds       : angle       4.06827 (  816)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1152.18 seconds
wall clock time: 20 minutes 27.85 seconds (1227.85 seconds total)