Starting phenix.real_space_refine
on Wed Jan 22 12:29:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yf5_39211/01_2025/8yf5_39211.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yf5_39211/01_2025/8yf5_39211.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yf5_39211/01_2025/8yf5_39211.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yf5_39211/01_2025/8yf5_39211.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yf5_39211/01_2025/8yf5_39211.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yf5_39211/01_2025/8yf5_39211.cif"
  }
  resolution = 3.78
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      69      5.16       5
     C   11848      2.51       5
     N    3142      2.21       5
     O    3417      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.07s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 18476
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 5640
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 685, 5640
          Classifications: {'peptide': 685}
          Link IDs: {'PTRANS': 45, 'TRANS': 639}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 3122
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 381, 3122
          Classifications: {'peptide': 381}
          Link IDs: {'PTRANS': 16, 'TRANS': 364}
    Chain: "C"
      Number of atoms: 5536
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 674, 5536
          Classifications: {'peptide': 674}
          Link IDs: {'PTRANS': 43, 'TRANS': 630}
          Chain breaks: 5
    Chain: "D"
      Number of atoms: 3114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 380, 3114
          Classifications: {'peptide': 380}
          Link IDs: {'PTRANS': 16, 'TRANS': 363}
    Chain: "E"
      Number of atoms: 1064
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 1064
          Classifications: {'peptide': 130}
          Link IDs: {'PTRANS': 3, 'TRANS': 126}
  Time building chain proxies: 10.82, per 1000 atoms: 0.59
  Number of scatterers: 18476
  At special positions: 0
  Unit cell: (152.388, 141.93, 125.496, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      69     16.00
     O    3417      8.00
     N    3142      7.00
     C   11848      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.76
  Conformation dependent library (CDL) restraints added in 2.3 seconds
  

  4444 Ramachandran restraints generated.
    2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4298

  Finding SS restraints...
    Secondary structure from input PDB file:
      99 helices and 14 sheets defined
      50.2% alpha, 10.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.02
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 14
      removed outlier: 3.698A  pdb=" N   TRP A   9 " --> pdb=" O   ALA A   5 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 32
      removed outlier: 3.634A  pdb=" N   GLY A  31 " --> pdb=" O   ASP A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 57
      No H-bonds generated for 'chain 'A' and resid 55 through 57'
    Processing helix  chain 'A' and resid 72 through 92
      removed outlier: 3.661A  pdb=" N   MET A  76 " --> pdb=" O   THR A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 129
      removed outlier: 3.624A  pdb=" N   MET A 110 " --> pdb=" O   PRO A 106 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   ASN A 111 " --> pdb=" O   ARG A 107 " (cutoff:3.500A)
      removed outlier: 4.938A  pdb=" N   GLN A 112 " --> pdb=" O   ALA A 108 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   GLN A 113 " --> pdb=" O   LYS A 109 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   SER A 115 " --> pdb=" O   ASN A 111 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   SER A 120 " --> pdb=" O   ARG A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 160
    Processing helix  chain 'A' and resid 164 through 185
      removed outlier: 3.670A  pdb=" N   HIS A 168 " --> pdb=" O   THR A 164 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ASP A 172 " --> pdb=" O   HIS A 168 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ARG A 175 " --> pdb=" O   ALA A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 189
      removed outlier: 3.589A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 186 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 186 through 189'
    Processing helix  chain 'A' and resid 203 through 217
      removed outlier: 3.782A  pdb=" N   ILE A 208 " --> pdb=" O   GLY A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 244
      removed outlier: 3.801A  pdb=" N   THR A 243 " --> pdb=" O   LEU A 239 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   HIS A 244 " --> pdb=" O   GLY A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 259
      removed outlier: 4.121A  pdb=" N   ASP A 259 " --> pdb=" O   VAL A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 302
    Processing helix  chain 'A' and resid 312 through 327
      removed outlier: 3.887A  pdb=" N   ASP A 318 " --> pdb=" O   GLU A 314 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   PHE A 326 " --> pdb=" O   PHE A 322 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   CYS A 327 " --> pdb=" O   ILE A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 356
    Processing helix  chain 'A' and resid 370 through 407
      removed outlier: 3.565A  pdb=" N   ARG A 376 " --> pdb=" O   PRO A 372 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LYS A 384 " --> pdb=" O   GLU A 380 " (cutoff:3.500A)
      removed outlier: 4.863A  pdb=" N   ASP A 386 " --> pdb=" O   ALA A 382 " (cutoff:3.500A)
      removed outlier: 4.813A  pdb=" N   TYR A 387 " --> pdb=" O   LYS A 383 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LYS A 391 " --> pdb=" O   TYR A 387 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ARG A 392 " --> pdb=" O   ILE A 388 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   TYR A 393 " --> pdb=" O   PHE A 389 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   GLU A 396 " --> pdb=" O   ARG A 392 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLN A 403 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LYS A 404 " --> pdb=" O   LEU A 400 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ARG A 405 " --> pdb=" O   GLU A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 552
      removed outlier: 4.273A  pdb=" N   TYR A 547 " --> pdb=" O   ARG A 543 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   GLU A 548 " --> pdb=" O   LYS A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 581
    Processing helix  chain 'A' and resid 599 through 603
    Processing helix  chain 'A' and resid 605 through 609
    Processing helix  chain 'A' and resid 620 through 629
    Processing helix  chain 'A' and resid 630 through 634
      removed outlier: 3.536A  pdb=" N   SER A 633 " --> pdb=" O   PRO A 630 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   SER A 634 " --> pdb=" O   ALA A 631 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 630 through 634'
    Processing helix  chain 'A' and resid 641 through 647
      removed outlier: 3.500A  pdb=" N   MET A 645 " --> pdb=" O   PHE A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 656
    Processing helix  chain 'A' and resid 669 through 673
    Processing helix  chain 'A' and resid 681 through 691
      removed outlier: 3.613A  pdb=" N   LYS A 687 " --> pdb=" O   ASN A 683 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   SER A 691 " --> pdb=" O   LYS A 687 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 692 through 696
    Processing helix  chain 'A' and resid 697 through 704
    Processing helix  chain 'A' and resid 719 through 728
      removed outlier: 3.810A  pdb=" N   LEU A 723 " --> pdb=" O   HIS A 719 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   VAL A 724 " --> pdb=" O   TYR A 720 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 812 through 819
    Processing helix  chain 'A' and resid 838 through 842
      removed outlier: 3.540A  pdb=" N   TYR A 841 " --> pdb=" O   PHE A 838 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 856 through 864
    Processing helix  chain 'B' and resid 48 through 54
      removed outlier: 3.839A  pdb=" N   ILE B  52 " --> pdb=" O   PRO B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 65
    Processing helix  chain 'B' and resid 69 through 75
    Processing helix  chain 'B' and resid 76 through 91
    Processing helix  chain 'B' and resid 102 through 110
    Processing helix  chain 'B' and resid 135 through 148
    Processing helix  chain 'B' and resid 151 through 167
      removed outlier: 3.547A  pdb=" N   ALA B 167 " --> pdb=" O   PHE B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 176
    Processing helix  chain 'B' and resid 177 through 183
    Processing helix  chain 'B' and resid 184 through 187
    Processing helix  chain 'B' and resid 225 through 229
      removed outlier: 4.259A  pdb=" N   ARG B 229 " --> pdb=" O   ASP B 225 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 225 through 229'
    Processing helix  chain 'B' and resid 241 through 261
    Processing helix  chain 'B' and resid 288 through 295
    Processing helix  chain 'B' and resid 306 through 326
      removed outlier: 3.815A  pdb=" N   VAL B 326 " --> pdb=" O   LEU B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 363
    Processing helix  chain 'B' and resid 364 through 380
    Processing helix  chain 'C' and resid 6 through 14
    Processing helix  chain 'C' and resid 54 through 59
    Processing helix  chain 'C' and resid 72 through 92
      removed outlier: 3.625A  pdb=" N   MET C  76 " --> pdb=" O   THR C  72 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   LEU C  78 " --> pdb=" O   ASP C  74 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ASP C  79 " --> pdb=" O   GLU C  75 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 106 through 128
      removed outlier: 3.852A  pdb=" N   ASN C 111 " --> pdb=" O   ARG C 107 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   GLN C 112 " --> pdb=" O   ALA C 108 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 156 through 161
      removed outlier: 4.024A  pdb=" N   ALA C 159 " --> pdb=" O   ASP C 156 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   ILE C 160 " --> pdb=" O   SER C 157 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   THR C 161 " --> pdb=" O   ASN C 158 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 156 through 161'
    Processing helix  chain 'C' and resid 164 through 184
      removed outlier: 3.506A  pdb=" N   ASP C 172 " --> pdb=" O   HIS C 168 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ARG C 175 " --> pdb=" O   ALA C 171 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 185 through 189
      removed outlier: 3.708A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 186 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 203 through 218
      removed outlier: 3.533A  pdb=" N   ARG C 216 " --> pdb=" O   VAL C 212 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   SER C 218 " --> pdb=" O   SER C 214 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 234 through 243
      removed outlier: 4.483A  pdb=" N   PHE C 238 " --> pdb=" O   ALA C 234 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   THR C 243 " --> pdb=" O   LEU C 239 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 291 through 302
    Processing helix  chain 'C' and resid 312 through 327
      removed outlier: 3.781A  pdb=" N   PHE C 325 " --> pdb=" O   VAL C 321 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   PHE C 326 " --> pdb=" O   PHE C 322 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   CYS C 327 " --> pdb=" O   ILE C 323 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 339 through 342
    Processing helix  chain 'C' and resid 343 through 356
    Processing helix  chain 'C' and resid 357 through 359
      No H-bonds generated for 'chain 'C' and resid 357 through 359'
    Processing helix  chain 'C' and resid 370 through 378
    Processing helix  chain 'C' and resid 381 through 383
      No H-bonds generated for 'chain 'C' and resid 381 through 383'
    Processing helix  chain 'C' and resid 384 through 406
      removed outlier: 3.642A  pdb=" N   LEU C 400 " --> pdb=" O   GLU C 396 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLN C 403 " --> pdb=" O   SER C 399 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 541 through 552
      removed outlier: 3.929A  pdb=" N   ARG C 545 " --> pdb=" O   GLY C 541 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 555 through 581
    Processing helix  chain 'C' and resid 599 through 603
      removed outlier: 3.597A  pdb=" N   PHE C 603 " --> pdb=" O   ALA C 600 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 620 through 629
    Processing helix  chain 'C' and resid 638 through 647
      removed outlier: 4.207A  pdb=" N   SER C 643 " --> pdb=" O   ASP C 639 " (cutoff:3.500A)
      removed outlier: 4.631A  pdb=" N   LEU C 644 " --> pdb=" O   VAL C 640 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   MET C 645 " --> pdb=" O   PHE C 641 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 652 through 656
    Processing helix  chain 'C' and resid 681 through 690
      removed outlier: 3.524A  pdb=" N   ALA C 688 " --> pdb=" O   ARG C 684 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 697 through 703
    Processing helix  chain 'C' and resid 718 through 728
      removed outlier: 4.448A  pdb=" N   THR C 722 " --> pdb=" O   SER C 718 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 810 through 819
      removed outlier: 3.751A  pdb=" N   ILE C 817 " --> pdb=" O   ASP C 813 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 856 through 867
      removed outlier: 3.629A  pdb=" N   ASP C 866 " --> pdb=" O   GLN C 862 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   GLU C 867 " --> pdb=" O   ILE C 863 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 48 through 54
      removed outlier: 3.955A  pdb=" N   ILE D  52 " --> pdb=" O   PRO D  48 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 61 through 65
    Processing helix  chain 'D' and resid 69 through 75
      removed outlier: 3.587A  pdb=" N   LYS D  75 " --> pdb=" O   VAL D  71 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 76 through 91
    Processing helix  chain 'D' and resid 102 through 111
    Processing helix  chain 'D' and resid 135 through 149
    Processing helix  chain 'D' and resid 150 through 167
      removed outlier: 4.040A  pdb=" N   LYS D 154 " --> pdb=" O   THR D 150 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 172 through 176
    Processing helix  chain 'D' and resid 177 through 183
    Processing helix  chain 'D' and resid 225 through 229
      removed outlier: 4.143A  pdb=" N   ARG D 229 " --> pdb=" O   ASP D 225 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 225 through 229'
    Processing helix  chain 'D' and resid 241 through 263
    Processing helix  chain 'D' and resid 287 through 295
      removed outlier: 4.523A  pdb=" N   LEU D 291 " --> pdb=" O   ASN D 287 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 306 through 326
      removed outlier: 3.817A  pdb=" N   SER D 310 " --> pdb=" O   ASN D 306 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   VAL D 326 " --> pdb=" O   LEU D 322 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 351 through 363
    Processing helix  chain 'D' and resid 364 through 380
      removed outlier: 3.886A  pdb=" N   GLY D 379 " --> pdb=" O   ARG D 375 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ASN D 380 " --> pdb=" O   ASN D 376 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 4 through 14
      removed outlier: 3.501A  pdb=" N   VAL E   8 " --> pdb=" O   SER E   4 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 18 through 32
      removed outlier: 3.563A  pdb=" N   ILE E  22 " --> pdb=" O   THR E  18 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 35 through 50
    Processing helix  chain 'E' and resid 53 through 71
    Processing helix  chain 'E' and resid 73 through 82
      removed outlier: 4.010A  pdb=" N   LEU E  77 " --> pdb=" O   LYS E  73 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   ASP E  78 " --> pdb=" O   THR E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 83 through 92
    Processing helix  chain 'E' and resid 93 through 95
      No H-bonds generated for 'chain 'E' and resid 93 through 95'
    Processing helix  chain 'E' and resid 96 through 113
    Processing helix  chain 'E' and resid 117 through 128
    Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20
      removed outlier: 6.551A  pdb=" N   ILE A 229 " --> pdb=" O   LEU A 251 " (cutoff:3.500A)
      removed outlier: 8.729A  pdb=" N   GLU A 253 " --> pdb=" O   ILE A 229 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   TYR A  51 " --> pdb=" O   TYR A 230 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   GLU A 709 " --> pdb=" O   PHE A 786 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 364 through 365
    Processing sheet with id=AA3, first strand: chain 'A' and resid 662 through 663
    Processing sheet with id=AA4, first strand: chain 'A' and resid 759 through 760
    Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 8
      removed outlier: 3.844A  pdb=" N   VAL B 345 " --> pdb=" O   SER B 335 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   SER B 335 " --> pdb=" O   VAL B 345 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   PHE B 119 " --> pdb=" O   TYR B 336 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   ILE B  99 " --> pdb=" O   ILE B 132 " (cutoff:3.500A)
      removed outlier: 8.822A  pdb=" N   PHE B 134 " --> pdb=" O   ILE B  99 " (cutoff:3.500A)
      removed outlier: 10.122A  pdb=" N   TRP B 101 " --> pdb=" O   PHE B 134 " (cutoff:3.500A)
      removed outlier: 5.945A  pdb=" N   ILE B  98 " --> pdb=" O   LEU B 209 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   GLY B 211 " --> pdb=" O   ILE B  98 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   THR B 100 " --> pdb=" O   GLY B 211 " (cutoff:3.500A)
      removed outlier: 9.256A  pdb=" N   ALA B 213 " --> pdb=" O   THR B 100 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   TYR B 195 " --> pdb=" O   VAL B 214 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   GLN B 194 " --> pdb=" O   ARG B  29 " (cutoff:3.500A)
      removed outlier: 5.957A  pdb=" N   ARG B 200 " --> pdb=" O   GLN B  23 " (cutoff:3.500A)
      removed outlier: 5.486A  pdb=" N   GLN B  23 " --> pdb=" O   ARG B 200 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 44 through 45
    Processing sheet with id=AA7, first strand: chain 'B' and resid 216 through 217
      removed outlier: 4.452A  pdb=" N   LYS B 266 " --> pdb=" O   TYR B 230 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   GLU B 232 " --> pdb=" O   LYS B 266 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   ILE B 267 " --> pdb=" O   GLU B 283 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   GLU B 283 " --> pdb=" O   ILE B 267 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   TYR B 269 " --> pdb=" O   VAL B 281 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   VAL B 281 " --> pdb=" O   TYR B 269 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   PHE B 271 " --> pdb=" O   ARG B 279 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 18 through 20
      removed outlier: 6.513A  pdb=" N   HIS C 227 " --> pdb=" O   LYS C 249 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   LEU C 251 " --> pdb=" O   HIS C 227 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   ILE C 229 " --> pdb=" O   LEU C 251 " (cutoff:3.500A)
      removed outlier: 8.758A  pdb=" N   GLU C 253 " --> pdb=" O   ILE C 229 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   ASP C  48 " --> pdb=" O   ARG C  94 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   VAL C 193 " --> pdb=" O   VAL C 712 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 364 through 365
    Processing sheet with id=AB1, first strand: chain 'C' and resid 662 through 663
    Processing sheet with id=AB2, first strand: chain 'C' and resid 759 through 760
    Processing sheet with id=AB3, first strand: chain 'D' and resid 5 through 8
      removed outlier: 3.732A  pdb=" N   VAL D 123 " --> pdb=" O   TRP D 332 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   PHE D 119 " --> pdb=" O   TYR D 336 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   ILE D  99 " --> pdb=" O   ILE D 132 " (cutoff:3.500A)
      removed outlier: 8.981A  pdb=" N   PHE D 134 " --> pdb=" O   ILE D  99 " (cutoff:3.500A)
      removed outlier: 10.446A  pdb=" N   TRP D 101 " --> pdb=" O   PHE D 134 " (cutoff:3.500A)
      removed outlier: 5.826A  pdb=" N   ILE D  98 " --> pdb=" O   LEU D 209 " (cutoff:3.500A)
      removed outlier: 7.539A  pdb=" N   GLY D 211 " --> pdb=" O   ILE D  98 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   THR D 100 " --> pdb=" O   GLY D 211 " (cutoff:3.500A)
      removed outlier: 9.134A  pdb=" N   ALA D 213 " --> pdb=" O   THR D 100 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   TYR D 195 " --> pdb=" O   VAL D 214 " (cutoff:3.500A)
      removed outlier: 5.830A  pdb=" N   ARG D 200 " --> pdb=" O   GLN D  23 " (cutoff:3.500A)
      removed outlier: 5.095A  pdb=" N   GLN D  23 " --> pdb=" O   ARG D 200 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 44 through 45
    Processing sheet with id=AB5, first strand: chain 'D' and resid 216 through 217
      removed outlier: 3.586A  pdb=" N   CYS D 216 " --> pdb=" O   ILE D 231 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   TYR D 230 " --> pdb=" O   LYS D 266 " (cutoff:3.500A)
      removed outlier: 8.126A  pdb=" N   ILE D 268 " --> pdb=" O   TYR D 230 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   GLU D 232 " --> pdb=" O   ILE D 268 " (cutoff:3.500A)
      removed outlier: 7.671A  pdb=" N   GLY D 270 " --> pdb=" O   GLU D 232 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   LYS D 234 " --> pdb=" O   GLY D 270 " (cutoff:3.500A)
      removed outlier: 7.611A  pdb=" N   ARG D 272 " --> pdb=" O   LYS D 234 " (cutoff:3.500A)
      removed outlier: 5.786A  pdb=" N   THR D 236 " --> pdb=" O   ARG D 272 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   ILE D 267 " --> pdb=" O   GLU D 283 " (cutoff:3.500A)
      removed outlier: 4.895A  pdb=" N   GLU D 283 " --> pdb=" O   ILE D 267 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   TYR D 269 " --> pdb=" O   VAL D 281 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   VAL D 281 " --> pdb=" O   TYR D 269 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   PHE D 271 " --> pdb=" O   ARG D 279 " (cutoff:3.500A)

    824 hydrogen bonds defined for protein.
    2328 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: 6.88

  Time building geometry restraints manager: 5.62 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3786
        1.33 -     1.45: 4473
        1.45 -     1.57: 10559
        1.57 -     1.69: 0
        1.69 -     1.81: 115
  Bond restraints: 18933
  Sorted by residual:
  bond pdb=" CA  CYS C 324 "
       pdb=" C   CYS C 324 "
    ideal  model  delta    sigma   weight residual
    1.523  1.497  0.026 1.80e-02 3.09e+03 2.08e+00
  bond pdb=" CD  GLN E  67 "
       pdb=" OE1 GLN E  67 "
    ideal  model  delta    sigma   weight residual
    1.231  1.206  0.025 1.90e-02 2.77e+03 1.73e+00
  bond pdb=" CA  ILE C  22 "
       pdb=" CB  ILE C  22 "
    ideal  model  delta    sigma   weight residual
    1.540  1.524  0.016 1.36e-02 5.41e+03 1.33e+00
  bond pdb=" C   LEU E  84 "
       pdb=" N   PRO E  85 "
    ideal  model  delta    sigma   weight residual
    1.335  1.351 -0.015 1.36e-02 5.41e+03 1.29e+00
  bond pdb=" C   TYR A  14 "
       pdb=" N   PRO A  15 "
    ideal  model  delta    sigma   weight residual
    1.336  1.323  0.013 1.20e-02 6.94e+03 1.15e+00
  ... (remaining 18928 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.50: 25061
        1.50 -     3.01: 412
        3.01 -     4.51: 87
        4.51 -     6.01: 33
        6.01 -     7.52: 6
  Bond angle restraints: 25599
  Sorted by residual:
  angle pdb=" N   VAL A 628 "
        pdb=" CA  VAL A 628 "
        pdb=" C   VAL A 628 "
      ideal   model   delta    sigma   weight residual
     113.53  109.46    4.07 9.80e-01 1.04e+00 1.72e+01
  angle pdb=" CA  ARG D 341 "
        pdb=" CB  ARG D 341 "
        pdb=" CG  ARG D 341 "
      ideal   model   delta    sigma   weight residual
     114.10  121.62   -7.52 2.00e+00 2.50e-01 1.41e+01
  angle pdb=" N   GLN E  67 "
        pdb=" CA  GLN E  67 "
        pdb=" CB  GLN E  67 "
      ideal   model   delta    sigma   weight residual
     110.40  116.28   -5.88 1.63e+00 3.76e-01 1.30e+01
  angle pdb=" C   GLN E  66 "
        pdb=" N   GLN E  67 "
        pdb=" CA  GLN E  67 "
      ideal   model   delta    sigma   weight residual
     121.14  115.23    5.91 1.75e+00 3.27e-01 1.14e+01
  angle pdb=" C   TYR E 125 "
        pdb=" N   GLN E 126 "
        pdb=" CA  GLN E 126 "
      ideal   model   delta    sigma   weight residual
     120.72  115.55    5.17 1.67e+00 3.59e-01 9.59e+00
  ... (remaining 25594 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.41: 10275
       17.41 -    34.81: 977
       34.81 -    52.22: 191
       52.22 -    69.63: 31
       69.63 -    87.04: 12
  Dihedral angle restraints: 11486
    sinusoidal: 4837
      harmonic: 6649
  Sorted by residual:
  dihedral pdb=" CA  VAL C 669 "
           pdb=" C   VAL C 669 "
           pdb=" N   ILE C 670 "
           pdb=" CA  ILE C 670 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.12  -17.88     0      5.00e+00 4.00e-02 1.28e+01
  dihedral pdb=" CA  MET E  95 "
           pdb=" C   MET E  95 "
           pdb=" N   ILE E  96 "
           pdb=" CA  ILE E  96 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.29  -17.71     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CA  ASP C  30 "
           pdb=" CB  ASP C  30 "
           pdb=" CG  ASP C  30 "
           pdb=" OD1 ASP C  30 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.28   59.28     1      2.00e+01 2.50e-03 1.17e+01
  ... (remaining 11483 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 2005
       0.042 -    0.084: 535
       0.084 -    0.126: 175
       0.126 -    0.168: 8
       0.168 -    0.210: 2
  Chirality restraints: 2725
  Sorted by residual:
  chirality pdb=" CB  ILE E 115 "
            pdb=" CA  ILE E 115 "
            pdb=" CG1 ILE E 115 "
            pdb=" CG2 ILE E 115 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CA  TYR E 125 "
            pdb=" N   TYR E 125 "
            pdb=" C   TYR E 125 "
            pdb=" CB  TYR E 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.62e-01
  chirality pdb=" CA  ARG D 341 "
            pdb=" N   ARG D 341 "
            pdb=" C   ARG D 341 "
            pdb=" CB  ARG D 341 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.64e-01
  ... (remaining 2722 not shown)

  Planarity restraints: 3289
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP E 110 "    0.031 2.00e-02 2.50e+03   2.98e-02 2.21e+01
        pdb=" CG  TRP E 110 "   -0.081 2.00e-02 2.50e+03
        pdb=" CD1 TRP E 110 "    0.036 2.00e-02 2.50e+03
        pdb=" CD2 TRP E 110 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP E 110 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP E 110 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP E 110 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ2 TRP E 110 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP E 110 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP E 110 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 637 "   -0.030 5.00e-02 4.00e+02   4.62e-02 3.41e+00
        pdb=" N   PRO A 638 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A 638 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 638 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A  67 "    0.023 5.00e-02 4.00e+02   3.54e-02 2.01e+00
        pdb=" N   PRO A  68 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A  68 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A  68 "    0.020 5.00e-02 4.00e+02
  ... (remaining 3286 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 335
        2.66 -     3.22: 18288
        3.22 -     3.78: 29637
        3.78 -     4.34: 39142
        4.34 -     4.90: 62432
  Nonbonded interactions: 149834
  Sorted by model distance:
  nonbonded pdb=" O   MET C 626 "
            pdb=" OH  TYR C 656 "
     model   vdw
     2.098 3.040
  nonbonded pdb=" OH  TYR A 850 "
            pdb=" OH  TYR B  45 "
     model   vdw
     2.156 3.040
  nonbonded pdb=" OH  TYR C 850 "
            pdb=" OH  TYR D  45 "
     model   vdw
     2.169 3.040
  nonbonded pdb=" OH  TYR C 596 "
            pdb=" OD2 ASP C 663 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OH  TYR A 596 "
            pdb=" OD2 ASP A 663 "
     model   vdw
     2.209 3.040
  ... (remaining 149829 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 5 through 63 or resid 69 through 129 or resid 156 through  \ 
257 or resid 283 through 407 or resid 532 through 824 or resid 834 through 864)) \ 

  selection = (chain 'C' and resid 5 through 864)
}
ncs_group {
  reference = (chain 'B' and resid 1 through 380)
  selection = chain 'D'
}

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:             0.400
  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:             0.020
  Extract box with map and model:          0.730
  Check model and map are aligned:         0.140
  Set scattering table:                    0.180
  Process input model:                     42.130
  Find NCS groups from input model:        0.620
  Set up NCS constraints:                  0.080
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
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      :  0.003   0.028  18933  Z= 0.211
  Angle     :  0.530   7.517  25599  Z= 0.269
  Chirality :  0.041   0.210   2725
  Planarity :  0.003   0.050   3289
  Dihedral  : 13.978  87.035   7188
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.19), residues: 2222
  helix:  1.49 (0.18), residues: 937
  sheet:  0.08 (0.32), residues: 270
  loop :  0.41 (0.21), residues: 1015

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.081   0.001   TRP E 110 
 HIS   0.003   0.001   HIS C 717 
 PHE   0.013   0.001   PHE B 152 
 TYR   0.018   0.001   TYR B 269 
 ARG   0.007   0.000   ARG E  69 

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

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

  4444 Ramachandran restraints generated.
    2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4444 Ramachandran restraints generated.
    2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 2.044 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  566 MET cc_start: 0.8822 (tmm) cc_final: 0.8552 (tmm)
REVERT: A  626 MET cc_start: 0.8757 (ptt) cc_final: 0.8008 (ppp)
REVERT: A  838 PHE cc_start: 0.7323 (m-80) cc_final: 0.7049 (m-80)
REVERT: B  189 CYS cc_start: 0.9363 (m) cc_final: 0.9106 (m)
REVERT: C   76 MET cc_start: 0.9090 (ptt) cc_final: 0.8452 (ppp)
REVERT: C  167 MET cc_start: 0.8213 (mmp) cc_final: 0.7651 (mmm)
REVERT: C  360 LYS cc_start: 0.8573 (ptmt) cc_final: 0.8178 (tppt)
REVERT: C  645 MET cc_start: 0.8399 (tmm) cc_final: 0.7239 (tmm)
REVERT: C  783 MET cc_start: 0.7987 (mtp) cc_final: 0.7556 (mtm)
REVERT: D    1 MET cc_start: 0.6673 (ppp) cc_final: 0.5640 (ppp)
REVERT: D   17 MET cc_start: 0.7757 (tmm) cc_final: 0.7386 (tmm)
REVERT: D   53 ASP cc_start: 0.8889 (m-30) cc_final: 0.8586 (m-30)
REVERT: E   72 ARG cc_start: 0.7671 (mtp85) cc_final: 0.6627 (ptt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.3210
  time to fit residues: 73.1084
Evaluate side-chains
  119 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 2.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 189 optimal weight:    1.9990
   chunk 169 optimal weight:    4.9990
   chunk 94 optimal weight:    0.9980
   chunk 57 optimal weight:   10.0000
   chunk 114 optimal weight:    5.9990
   chunk 90 optimal weight:    6.9990
   chunk 175 optimal weight:    9.9990
   chunk 67 optimal weight:    0.9990
   chunk 106 optimal weight:    8.9990
   chunk 130 optimal weight:    0.0050
   chunk 203 optimal weight:    8.9990
   overall best weight:    1.8000

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

Flipped N/Q/H residues before XYZ refinement:
A 672 GLN
C 402 ASN
C 565 ASN
D 191 ASN
** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.079384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.054359 restraints weight = 72942.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.056198 restraints weight = 39215.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.057243 restraints weight = 28157.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.1096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  18933  Z= 0.210
  Angle     :  0.565   7.267  25599  Z= 0.291
  Chirality :  0.043   0.208   2725
  Planarity :  0.004   0.050   3289
  Dihedral  :  3.830  18.214   2479
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  7.37 %
    Favored  : 92.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.18), residues: 2222
  helix:  1.46 (0.17), residues: 978
  sheet:  0.05 (0.32), residues: 269
  loop :  0.24 (0.21), residues: 975

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.001   TRP E 110 
 HIS   0.005   0.001   HIS E 122 
 PHE   0.020   0.001   PHE C   7 
 TYR   0.013   0.001   TYR B 269 
 ARG   0.006   0.000   ARG E  69 

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

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

  4444 Ramachandran restraints generated.
    2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4444 Ramachandran restraints generated.
    2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 138
  time to evaluate  : 2.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.8813 (pmm) cc_final: 0.8269 (pmm)
REVERT: A  566 MET cc_start: 0.8069 (tmm) cc_final: 0.7679 (tmm)
REVERT: A  838 PHE cc_start: 0.7281 (m-80) cc_final: 0.6964 (m-80)
REVERT: B   53 ASP cc_start: 0.8154 (m-30) cc_final: 0.7945 (m-30)
REVERT: B  179 LYS cc_start: 0.9264 (mmmm) cc_final: 0.9059 (mmmm)
REVERT: B  189 CYS cc_start: 0.9394 (m) cc_final: 0.9157 (m)
REVERT: C   76 MET cc_start: 0.8935 (ptt) cc_final: 0.8333 (ppp)
REVERT: C  167 MET cc_start: 0.8069 (mmp) cc_final: 0.7832 (mmm)
REVERT: C  360 LYS cc_start: 0.8710 (ptmt) cc_final: 0.8238 (tppt)
REVERT: C  645 MET cc_start: 0.7833 (tmm) cc_final: 0.6887 (tmm)
REVERT: C  783 MET cc_start: 0.7838 (mtp) cc_final: 0.7479 (mtm)
REVERT: D   17 MET cc_start: 0.7749 (tmm) cc_final: 0.7388 (tmm)
REVERT: D   53 ASP cc_start: 0.8904 (m-30) cc_final: 0.8556 (m-30)
REVERT: E   69 ARG cc_start: 0.8216 (ttm-80) cc_final: 0.7651 (mmm-85)
REVERT: E   72 ARG cc_start: 0.7848 (mtp85) cc_final: 0.6677 (ptt-90)
REVERT: E   80 PHE cc_start: 0.9081 (m-80) cc_final: 0.8740 (m-80)
  outliers start: 10
  outliers final: 7
  residues processed: 143
  average time/residue: 0.3096
  time to fit residues: 71.6364
Evaluate side-chains
  128 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 121
  time to evaluate  : 3.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  672 GLN
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain E residue   20 ILE
Chi-restraints excluded: chain E residue   67 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 155 optimal weight:    7.9990
   chunk 198 optimal weight:   10.0000
   chunk 81 optimal weight:    9.9990
   chunk 175 optimal weight:    9.9990
   chunk 146 optimal weight:    0.2980
   chunk 27 optimal weight:    0.7980
   chunk 159 optimal weight:    3.9990
   chunk 183 optimal weight:    7.9990
   chunk 148 optimal weight:    6.9990
   chunk 36 optimal weight:    0.6980
   chunk 191 optimal weight:    0.0570
   overall best weight:    1.1700

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

Flipped N/Q/H residues before XYZ refinement:
C 636 ASN
D 376 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.080060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.055058 restraints weight = 72484.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.056921 restraints weight = 39153.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.057989 restraints weight = 28170.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.1422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  18933  Z= 0.161
  Angle     :  0.521   7.370  25599  Z= 0.265
  Chirality :  0.042   0.221   2725
  Planarity :  0.004   0.046   3289
  Dihedral  :  3.727  18.076   2479
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  9.78 %
    Favored  : 89.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.18), residues: 2222
  helix:  1.60 (0.17), residues: 978
  sheet:  0.09 (0.32), residues: 276
  loop :  0.26 (0.21), residues: 968

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP E 110 
 HIS   0.003   0.001   HIS A 221 
 PHE   0.016   0.001   PHE C   7 
 TYR   0.013   0.001   TYR C 841 
 ARG   0.005   0.000   ARG E  69 

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

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

  4444 Ramachandran restraints generated.
    2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4444 Ramachandran restraints generated.
    2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 135
  time to evaluate  : 2.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.8820 (pmm) cc_final: 0.8223 (pmm)
REVERT: A  113 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.8798 (pm20)
REVERT: A  380 GLU cc_start: 0.8555 (tp30) cc_final: 0.8287 (tp30)
REVERT: A  566 MET cc_start: 0.7889 (tmm) cc_final: 0.7438 (tmm)
REVERT: A  838 PHE cc_start: 0.7193 (m-80) cc_final: 0.6854 (m-80)
REVERT: B   53 ASP cc_start: 0.8196 (m-30) cc_final: 0.7909 (m-30)
REVERT: B  189 CYS cc_start: 0.9386 (m) cc_final: 0.9174 (m)
REVERT: C   76 MET cc_start: 0.8921 (ptt) cc_final: 0.8350 (ppp)
REVERT: C  167 MET cc_start: 0.7962 (mmp) cc_final: 0.7729 (mmm)
REVERT: C  354 GLN cc_start: 0.8896 (tm-30) cc_final: 0.8671 (tm-30)
REVERT: C  360 LYS cc_start: 0.8701 (ptmt) cc_final: 0.8188 (tppt)
REVERT: C  645 MET cc_start: 0.7224 (tmm) cc_final: 0.6347 (tmm)
REVERT: C  783 MET cc_start: 0.7786 (mtp) cc_final: 0.7459 (mtm)
REVERT: C  797 MET cc_start: 0.8957 (ptp) cc_final: 0.8555 (ptp)
REVERT: D   17 MET cc_start: 0.7841 (tmm) cc_final: 0.7499 (tmm)
REVERT: D   53 ASP cc_start: 0.8864 (m-30) cc_final: 0.8569 (m-30)
REVERT: E   69 ARG cc_start: 0.7973 (ttm-80) cc_final: 0.7718 (ttm-80)
REVERT: E   72 ARG cc_start: 0.7712 (mtp85) cc_final: 0.6526 (ptt-90)
REVERT: E   80 PHE cc_start: 0.9068 (m-80) cc_final: 0.8711 (m-80)
  outliers start: 14
  outliers final: 9
  residues processed: 144
  average time/residue: 0.3012
  time to fit residues: 69.9217
Evaluate side-chains
  137 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 127
  time to evaluate  : 2.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 GLN
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  401 GLU
Chi-restraints excluded: chain C residue  669 VAL
Chi-restraints excluded: chain E residue   20 ILE
Chi-restraints excluded: chain E residue   50 THR
Chi-restraints excluded: chain E residue  100 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 11 optimal weight:    7.9990
   chunk 1 optimal weight:    0.0470
   chunk 220 optimal weight:    6.9990
   chunk 171 optimal weight:    0.3980
   chunk 207 optimal weight:    7.9990
   chunk 161 optimal weight:    6.9990
   chunk 100 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 20 optimal weight:    7.9990
   chunk 59 optimal weight:    4.9990
   chunk 212 optimal weight:    5.9990
   overall best weight:    3.0884

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

Flipped N/Q/H residues before XYZ refinement:
** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 301 GLN
D 356 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.078320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.053327 restraints weight = 73242.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.055083 restraints weight = 39910.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.056115 restraints weight = 28924.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.1547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  18933  Z= 0.291
  Angle     :  0.564   7.569  25599  Z= 0.286
  Chirality :  0.043   0.170   2725
  Planarity :  0.004   0.045   3289
  Dihedral  :  3.893  19.081   2479
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 11.11 %
    Favored  : 87.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.18), residues: 2222
  helix:  1.63 (0.17), residues: 976
  sheet: -0.07 (0.31), residues: 276
  loop :  0.23 (0.21), residues: 970

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP E 110 
 HIS   0.005   0.001   HIS C 334 
 PHE   0.015   0.001   PHE A 248 
 TYR   0.016   0.001   TYR C 841 
 ARG   0.005   0.000   ARG E  69 

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

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

  4444 Ramachandran restraints generated.
    2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4444 Ramachandran restraints generated.
    2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 2.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.8908 (pmm) cc_final: 0.8516 (pmm)
REVERT: A  113 GLN cc_start: 0.9271 (OUTLIER) cc_final: 0.8903 (pm20)
REVERT: A  205 GLU cc_start: 0.7963 (pm20) cc_final: 0.7726 (pm20)
REVERT: A  380 GLU cc_start: 0.8635 (tp30) cc_final: 0.8365 (tp30)
REVERT: A  566 MET cc_start: 0.8002 (tmm) cc_final: 0.7555 (tmm)
REVERT: A  624 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8426 (tm-30)
REVERT: A  838 PHE cc_start: 0.7231 (m-80) cc_final: 0.6847 (m-80)
REVERT: B   53 ASP cc_start: 0.8299 (m-30) cc_final: 0.7971 (m-30)
REVERT: C  110 MET cc_start: 0.8299 (mmp) cc_final: 0.7604 (mmp)
REVERT: C  167 MET cc_start: 0.8124 (mmp) cc_final: 0.7860 (mmm)
REVERT: C  354 GLN cc_start: 0.8981 (tm-30) cc_final: 0.8739 (tm-30)
REVERT: C  360 LYS cc_start: 0.8700 (ptmt) cc_final: 0.8197 (tppt)
REVERT: C  783 MET cc_start: 0.7868 (mtp) cc_final: 0.7574 (mtm)
REVERT: C  797 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8372 (ptp)
REVERT: D   17 MET cc_start: 0.7950 (tmm) cc_final: 0.7746 (tmm)
REVERT: D   53 ASP cc_start: 0.8856 (m-30) cc_final: 0.8492 (m-30)
REVERT: E   69 ARG cc_start: 0.8027 (ttm-80) cc_final: 0.7773 (ttm-80)
REVERT: E   72 ARG cc_start: 0.7738 (mtp85) cc_final: 0.6525 (ptt-90)
REVERT: E   80 PHE cc_start: 0.9082 (m-80) cc_final: 0.8815 (m-80)
REVERT: E   95 MET cc_start: 0.6288 (ppp) cc_final: 0.5848 (ppp)
  outliers start: 22
  outliers final: 13
  residues processed: 146
  average time/residue: 0.3048
  time to fit residues: 70.8431
Evaluate side-chains
  137 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 2.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 GLN
Chi-restraints excluded: chain A residue  326 PHE
Chi-restraints excluded: chain A residue  577 VAL
Chi-restraints excluded: chain A residue  652 ILE
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  401 GLU
Chi-restraints excluded: chain C residue  669 VAL
Chi-restraints excluded: chain C residue  797 MET
Chi-restraints excluded: chain D residue  198 ILE
Chi-restraints excluded: chain E residue   20 ILE
Chi-restraints excluded: chain E residue   50 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 85 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9990
   chunk 197 optimal weight:   10.0000
   chunk 210 optimal weight:    4.9990
   chunk 116 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 81 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 119 optimal weight:    7.9990
   chunk 58 optimal weight:    6.9990
   chunk 84 optimal weight:    1.9990
   overall best weight:    2.0988

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

Flipped N/Q/H residues before XYZ refinement:
A 672 GLN
** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.078926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.053900 restraints weight = 73270.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.055706 restraints weight = 39879.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.056736 restraints weight = 28678.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.1692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  18933  Z= 0.211
  Angle     :  0.536   8.655  25599  Z= 0.270
  Chirality :  0.042   0.279   2725
  Planarity :  0.004   0.044   3289
  Dihedral  :  3.822  18.085   2479
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 11.89 %
    Favored  : 86.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.18), residues: 2222
  helix:  1.68 (0.17), residues: 976
  sheet: -0.09 (0.31), residues: 278
  loop :  0.26 (0.21), residues: 968

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP E 110 
 HIS   0.004   0.001   HIS A 247 
 PHE   0.014   0.001   PHE C 655 
 TYR   0.017   0.001   TYR C 841 
 ARG   0.004   0.000   ARG E  69 

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

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

  4444 Ramachandran restraints generated.
    2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4444 Ramachandran restraints generated.
    2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 2.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.8918 (pmm) cc_final: 0.8555 (pmm)
REVERT: A  113 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8918 (pm20)
REVERT: A  205 GLU cc_start: 0.7978 (pm20) cc_final: 0.7746 (pm20)
REVERT: A  380 GLU cc_start: 0.8626 (tp30) cc_final: 0.8313 (tp30)
REVERT: A  566 MET cc_start: 0.7880 (tmm) cc_final: 0.7418 (tmm)
REVERT: A  624 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8180 (tm-30)
REVERT: A  645 MET cc_start: 0.7720 (tmm) cc_final: 0.6715 (tmm)
REVERT: A  838 PHE cc_start: 0.7199 (m-80) cc_final: 0.6806 (m-80)
REVERT: B   53 ASP cc_start: 0.8275 (m-30) cc_final: 0.7911 (m-30)
REVERT: C   76 MET cc_start: 0.8973 (ptt) cc_final: 0.8296 (ppp)
REVERT: C  167 MET cc_start: 0.8155 (mmp) cc_final: 0.7926 (mmm)
REVERT: C  354 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8742 (tm-30)
REVERT: C  356 LEU cc_start: 0.9746 (OUTLIER) cc_final: 0.9483 (mt)
REVERT: C  360 LYS cc_start: 0.8697 (ptmt) cc_final: 0.8192 (tppt)
REVERT: C  783 MET cc_start: 0.7877 (mtp) cc_final: 0.7601 (mtm)
REVERT: C  797 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8470 (ptp)
REVERT: D   53 ASP cc_start: 0.8819 (m-30) cc_final: 0.8500 (m-30)
REVERT: E   69 ARG cc_start: 0.7871 (ttm-80) cc_final: 0.7636 (ttm-80)
REVERT: E   72 ARG cc_start: 0.7766 (mtp85) cc_final: 0.6526 (ptt-90)
REVERT: E   80 PHE cc_start: 0.9081 (m-80) cc_final: 0.8849 (m-80)
REVERT: E  100 GLN cc_start: 0.6911 (OUTLIER) cc_final: 0.6208 (mp10)
  outliers start: 25
  outliers final: 14
  residues processed: 148
  average time/residue: 0.3201
  time to fit residues: 77.2102
Evaluate side-chains
  141 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 2.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 HIS
Chi-restraints excluded: chain A residue  113 GLN
Chi-restraints excluded: chain A residue  326 PHE
Chi-restraints excluded: chain A residue  652 ILE
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  356 LEU
Chi-restraints excluded: chain C residue  401 GLU
Chi-restraints excluded: chain C residue  669 VAL
Chi-restraints excluded: chain C residue  797 MET
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  198 ILE
Chi-restraints excluded: chain D residue  252 LEU
Chi-restraints excluded: chain D residue  262 LEU
Chi-restraints excluded: chain E residue   20 ILE
Chi-restraints excluded: chain E residue  100 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 69 optimal weight:   20.0000
   chunk 199 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9980
   chunk 115 optimal weight:    6.9990
   chunk 159 optimal weight:    5.9990
   chunk 203 optimal weight:    2.9990
   chunk 95 optimal weight:    8.9990
   chunk 74 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   chunk 121 optimal weight:    0.9990
   chunk 130 optimal weight:    6.9990
   overall best weight:    3.1988

-------------------------------------------------------------------------------
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 = 0.3523 r_free = 0.3523 target = 0.077902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.052936 restraints weight = 73975.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.054671 restraints weight = 40339.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.055698 restraints weight = 29258.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.1810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  18933  Z= 0.296
  Angle     :  0.581   8.606  25599  Z= 0.292
  Chirality :  0.043   0.255   2725
  Planarity :  0.004   0.044   3289
  Dihedral  :  3.951  18.544   2479
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 12.97 %
    Favored  : 85.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.18), residues: 2222
  helix:  1.66 (0.17), residues: 978
  sheet: -0.25 (0.31), residues: 286
  loop :  0.20 (0.21), residues: 958

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP E 110 
 HIS   0.004   0.001   HIS C 334 
 PHE   0.013   0.001   PHE A 248 
 TYR   0.020   0.001   TYR C 841 
 ARG   0.004   0.000   ARG E  69 

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

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

  4444 Ramachandran restraints generated.
    2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4444 Ramachandran restraints generated.
    2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 124
  time to evaluate  : 2.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.8935 (pmm) cc_final: 0.8582 (pmm)
REVERT: A  113 GLN cc_start: 0.9257 (OUTLIER) cc_final: 0.8872 (pm20)
REVERT: A  205 GLU cc_start: 0.8011 (pm20) cc_final: 0.7755 (pm20)
REVERT: A  380 GLU cc_start: 0.8689 (tp30) cc_final: 0.8321 (tp30)
REVERT: A  566 MET cc_start: 0.8036 (tmm) cc_final: 0.7611 (tmm)
REVERT: A  645 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7162 (tmm)
REVERT: A  838 PHE cc_start: 0.7259 (m-80) cc_final: 0.6837 (m-80)
REVERT: B   53 ASP cc_start: 0.8365 (m-30) cc_final: 0.8000 (m-30)
REVERT: B  252 LEU cc_start: 0.9641 (OUTLIER) cc_final: 0.9339 (mm)
REVERT: C   76 MET cc_start: 0.9021 (ptt) cc_final: 0.8349 (ppp)
REVERT: C  167 MET cc_start: 0.8109 (mmp) cc_final: 0.7594 (mmm)
REVERT: C  354 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8813 (tm-30)
REVERT: C  356 LEU cc_start: 0.9747 (OUTLIER) cc_final: 0.9476 (mt)
REVERT: C  360 LYS cc_start: 0.8667 (ptmt) cc_final: 0.8158 (tppt)
REVERT: D   53 ASP cc_start: 0.8843 (m-30) cc_final: 0.8557 (m-30)
REVERT: D  164 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8664 (pp20)
REVERT: E   69 ARG cc_start: 0.7931 (ttm-80) cc_final: 0.7703 (ttm-80)
REVERT: E   72 ARG cc_start: 0.7728 (mtp85) cc_final: 0.6542 (ptt-90)
REVERT: E   80 PHE cc_start: 0.9101 (m-80) cc_final: 0.8838 (m-80)
REVERT: E  100 GLN cc_start: 0.6845 (OUTLIER) cc_final: 0.6260 (mp10)
  outliers start: 35
  outliers final: 19
  residues processed: 151
  average time/residue: 0.3094
  time to fit residues: 75.8770
Evaluate side-chains
  146 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 122
  time to evaluate  : 2.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 HIS
Chi-restraints excluded: chain A residue  113 GLN
Chi-restraints excluded: chain A residue  326 PHE
Chi-restraints excluded: chain A residue  548 GLU
Chi-restraints excluded: chain A residue  645 MET
Chi-restraints excluded: chain A residue  652 ILE
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  269 TYR
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  356 LEU
Chi-restraints excluded: chain C residue  401 GLU
Chi-restraints excluded: chain C residue  669 VAL
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  198 ILE
Chi-restraints excluded: chain D residue  252 LEU
Chi-restraints excluded: chain D residue  262 LEU
Chi-restraints excluded: chain D residue  269 TYR
Chi-restraints excluded: chain E residue   20 ILE
Chi-restraints excluded: chain E residue  100 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 198 optimal weight:    8.9990
   chunk 203 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 81 optimal weight:    9.9990
   chunk 13 optimal weight:    0.8980
   chunk 201 optimal weight:   10.0000
   chunk 9 optimal weight:    5.9990
   chunk 56 optimal weight:    4.9990
   chunk 221 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    2.5788

-------------------------------------------------------------------------------
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 = 0.3530 r_free = 0.3530 target = 0.078226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.053287 restraints weight = 73207.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.055052 restraints weight = 39921.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.056073 restraints weight = 28869.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.1887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  18933  Z= 0.248
  Angle     :  0.569  12.048  25599  Z= 0.283
  Chirality :  0.043   0.268   2725
  Planarity :  0.004   0.045   3289
  Dihedral  :  3.916  18.764   2479
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 13.86 %
    Favored  : 84.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.18), residues: 2222
  helix:  1.63 (0.17), residues: 982
  sheet: -0.25 (0.31), residues: 286
  loop :  0.21 (0.21), residues: 954

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP E 110 
 HIS   0.004   0.001   HIS C 719 
 PHE   0.012   0.001   PHE D 158 
 TYR   0.021   0.001   TYR C 841 
 ARG   0.003   0.000   ARG E  69 

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

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

  4444 Ramachandran restraints generated.
    2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4444 Ramachandran restraints generated.
    2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 128
  time to evaluate  : 2.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.8882 (pmm) cc_final: 0.8520 (pmm)
REVERT: A  113 GLN cc_start: 0.9286 (OUTLIER) cc_final: 0.8954 (pm20)
REVERT: A  205 GLU cc_start: 0.8013 (pm20) cc_final: 0.7759 (pm20)
REVERT: A  380 GLU cc_start: 0.8704 (tp30) cc_final: 0.8316 (tp30)
REVERT: A  566 MET cc_start: 0.7903 (tmm) cc_final: 0.7364 (tmm)
REVERT: A  645 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7268 (tmm)
REVERT: A  838 PHE cc_start: 0.7239 (m-80) cc_final: 0.6789 (m-80)
REVERT: B   53 ASP cc_start: 0.8326 (m-30) cc_final: 0.7967 (m-30)
REVERT: B  252 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9365 (mm)
REVERT: C   76 MET cc_start: 0.9007 (ptt) cc_final: 0.8345 (ppp)
REVERT: C  110 MET cc_start: 0.8447 (mmp) cc_final: 0.8198 (mmp)
REVERT: C  167 MET cc_start: 0.8141 (mmp) cc_final: 0.7619 (mmm)
REVERT: C  356 LEU cc_start: 0.9735 (OUTLIER) cc_final: 0.9478 (mt)
REVERT: C  360 LYS cc_start: 0.8664 (ptmt) cc_final: 0.8157 (tppt)
REVERT: C  625 LEU cc_start: 0.8574 (mt) cc_final: 0.8276 (mt)
REVERT: D   53 ASP cc_start: 0.8834 (m-30) cc_final: 0.8552 (m-30)
REVERT: D  164 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8661 (pp20)
REVERT: E   72 ARG cc_start: 0.7881 (mtp85) cc_final: 0.6679 (ptt-90)
REVERT: E   80 PHE cc_start: 0.9102 (m-80) cc_final: 0.8838 (m-80)
REVERT: E  100 GLN cc_start: 0.6859 (OUTLIER) cc_final: 0.6226 (mp10)
REVERT: E  110 TRP cc_start: 0.8940 (m-10) cc_final: 0.8525 (m-10)
  outliers start: 27
  outliers final: 20
  residues processed: 150
  average time/residue: 0.2797
  time to fit residues: 68.1922
Evaluate side-chains
  150 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 125
  time to evaluate  : 2.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 HIS
Chi-restraints excluded: chain A residue  113 GLN
Chi-restraints excluded: chain A residue  326 PHE
Chi-restraints excluded: chain A residue  548 GLU
Chi-restraints excluded: chain A residue  577 VAL
Chi-restraints excluded: chain A residue  645 MET
Chi-restraints excluded: chain A residue  652 ILE
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  269 TYR
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  356 LEU
Chi-restraints excluded: chain C residue  401 GLU
Chi-restraints excluded: chain C residue  669 VAL
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  123 VAL
Chi-restraints excluded: chain D residue  198 ILE
Chi-restraints excluded: chain D residue  252 LEU
Chi-restraints excluded: chain D residue  262 LEU
Chi-restraints excluded: chain D residue  269 TYR
Chi-restraints excluded: chain E residue   20 ILE
Chi-restraints excluded: chain E residue  100 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 47 optimal weight:    9.9990
   chunk 18 optimal weight:    1.9990
   chunk 176 optimal weight:    3.9990
   chunk 212 optimal weight:    5.9990
   chunk 160 optimal weight:    2.9990
   chunk 95 optimal weight:    7.9990
   chunk 7 optimal weight:    8.9990
   chunk 189 optimal weight:    2.9990
   chunk 221 optimal weight:    5.9990
   chunk 170 optimal weight:    0.9990
   chunk 205 optimal weight:   10.0000
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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 = 0.3528 r_free = 0.3528 target = 0.078145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.053233 restraints weight = 73253.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.054979 restraints weight = 39821.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.056021 restraints weight = 28781.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.1971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  18933  Z= 0.251
  Angle     :  0.578  12.103  25599  Z= 0.286
  Chirality :  0.043   0.272   2725
  Planarity :  0.004   0.043   3289
  Dihedral  :  3.914  19.622   2479
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 14.05 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.19), residues: 2222
  helix:  1.67 (0.17), residues: 984
  sheet: -0.18 (0.31), residues: 280
  loop :  0.19 (0.21), residues: 958

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 352 
 HIS   0.004   0.001   HIS C 719 
 PHE   0.011   0.001   PHE D 158 
 TYR   0.023   0.001   TYR C 841 
 ARG   0.004   0.000   ARG E  69 

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

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

  4444 Ramachandran restraints generated.
    2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4444 Ramachandran restraints generated.
    2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 127
  time to evaluate  : 2.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.8885 (pmm) cc_final: 0.8629 (pmm)
REVERT: A  113 GLN cc_start: 0.9260 (OUTLIER) cc_final: 0.8888 (pm20)
REVERT: A  205 GLU cc_start: 0.8024 (pm20) cc_final: 0.7776 (pm20)
REVERT: A  209 MET cc_start: 0.8768 (tpp) cc_final: 0.8501 (tpp)
REVERT: A  380 GLU cc_start: 0.8677 (tp30) cc_final: 0.8289 (tp30)
REVERT: A  566 MET cc_start: 0.7930 (tmm) cc_final: 0.7397 (tmm)
REVERT: A  645 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7220 (tmm)
REVERT: A  838 PHE cc_start: 0.7238 (m-80) cc_final: 0.6773 (m-80)
REVERT: B   53 ASP cc_start: 0.8399 (m-30) cc_final: 0.8048 (m-30)
REVERT: B  252 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9338 (mm)
REVERT: C   76 MET cc_start: 0.9010 (ptt) cc_final: 0.8345 (ppp)
REVERT: C  167 MET cc_start: 0.8312 (mmp) cc_final: 0.8019 (mmm)
REVERT: C  324 CYS cc_start: 0.8432 (m) cc_final: 0.7821 (m)
REVERT: C  360 LYS cc_start: 0.8680 (ptmt) cc_final: 0.8167 (tppt)
REVERT: C  797 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8687 (ptp)
REVERT: D    1 MET cc_start: 0.6613 (ppp) cc_final: 0.6045 (ppp)
REVERT: D   53 ASP cc_start: 0.8831 (m-30) cc_final: 0.8550 (m-30)
REVERT: D  164 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8659 (pp20)
REVERT: E   72 ARG cc_start: 0.7879 (mtp85) cc_final: 0.6681 (ptt-90)
REVERT: E   80 PHE cc_start: 0.9091 (m-80) cc_final: 0.8846 (m-80)
REVERT: E  100 GLN cc_start: 0.6857 (OUTLIER) cc_final: 0.6206 (mp10)
  outliers start: 31
  outliers final: 21
  residues processed: 153
  average time/residue: 0.2824
  time to fit residues: 70.6546
Evaluate side-chains
  148 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 122
  time to evaluate  : 2.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 HIS
Chi-restraints excluded: chain A residue  113 GLN
Chi-restraints excluded: chain A residue  326 PHE
Chi-restraints excluded: chain A residue  548 GLU
Chi-restraints excluded: chain A residue  577 VAL
Chi-restraints excluded: chain A residue  645 MET
Chi-restraints excluded: chain A residue  652 ILE
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  269 TYR
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  401 GLU
Chi-restraints excluded: chain C residue  669 VAL
Chi-restraints excluded: chain C residue  797 MET
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  123 VAL
Chi-restraints excluded: chain D residue  198 ILE
Chi-restraints excluded: chain D residue  252 LEU
Chi-restraints excluded: chain D residue  262 LEU
Chi-restraints excluded: chain D residue  269 TYR
Chi-restraints excluded: chain E residue   20 ILE
Chi-restraints excluded: chain E residue  100 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 95 optimal weight:    7.9990
   chunk 92 optimal weight:    7.9990
   chunk 164 optimal weight:    2.9990
   chunk 137 optimal weight:    2.9990
   chunk 105 optimal weight:    8.9990
   chunk 90 optimal weight:    0.5980
   chunk 118 optimal weight:    0.0060
   chunk 76 optimal weight:    0.9990
   chunk 79 optimal weight:    9.9990
   chunk 47 optimal weight:    9.9990
   overall best weight:    1.1202

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

Flipped N/Q/H residues before XYZ refinement:
** E  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  62 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.079452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.054581 restraints weight = 73316.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.056365 restraints weight = 39231.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.057435 restraints weight = 28186.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.2063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  18933  Z= 0.159
  Angle     :  0.558  12.605  25599  Z= 0.274
  Chirality :  0.043   0.283   2725
  Planarity :  0.003   0.043   3289
  Dihedral  :  3.761  19.002   2479
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 14.55 %
    Favored  : 84.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.18), residues: 2222
  helix:  1.72 (0.17), residues: 977
  sheet: -0.04 (0.31), residues: 280
  loop :  0.26 (0.21), residues: 965

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 352 
 HIS   0.003   0.001   HIS A 221 
 PHE   0.014   0.001   PHE A 551 
 TYR   0.020   0.001   TYR C 841 
 ARG   0.004   0.000   ARG E  69 

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

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

  4444 Ramachandran restraints generated.
    2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4444 Ramachandran restraints generated.
    2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 132
  time to evaluate  : 2.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8603 (pmm)
REVERT: A  113 GLN cc_start: 0.9277 (OUTLIER) cc_final: 0.8920 (pm20)
REVERT: A  205 GLU cc_start: 0.8035 (pm20) cc_final: 0.7832 (pm20)
REVERT: A  318 ASP cc_start: 0.8601 (m-30) cc_final: 0.8378 (m-30)
REVERT: A  380 GLU cc_start: 0.8685 (tp30) cc_final: 0.8376 (tp30)
REVERT: A  566 MET cc_start: 0.7728 (tmm) cc_final: 0.7181 (tmm)
REVERT: A  645 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7336 (tmm)
REVERT: A  838 PHE cc_start: 0.7145 (m-80) cc_final: 0.6701 (m-80)
REVERT: B   53 ASP cc_start: 0.8354 (m-30) cc_final: 0.8009 (m-30)
REVERT: B  252 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9296 (mm)
REVERT: C   76 MET cc_start: 0.8999 (ptt) cc_final: 0.8373 (ppp)
REVERT: C  110 MET cc_start: 0.8269 (mmp) cc_final: 0.7850 (mmp)
REVERT: C  167 MET cc_start: 0.8327 (mmp) cc_final: 0.8022 (mmm)
REVERT: C  324 CYS cc_start: 0.8281 (m) cc_final: 0.7688 (m)
REVERT: C  360 LYS cc_start: 0.8713 (ptmt) cc_final: 0.8229 (tppt)
REVERT: C  625 LEU cc_start: 0.8877 (mt) cc_final: 0.8440 (mt)
REVERT: C  797 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8674 (ptp)
REVERT: D    1 MET cc_start: 0.6837 (ppp) cc_final: 0.6540 (ppp)
REVERT: D   53 ASP cc_start: 0.8786 (m-30) cc_final: 0.8526 (m-30)
REVERT: E   72 ARG cc_start: 0.7873 (mtp85) cc_final: 0.6643 (ptt-90)
REVERT: E   80 PHE cc_start: 0.9100 (m-80) cc_final: 0.8823 (m-80)
REVERT: E  100 GLN cc_start: 0.6865 (OUTLIER) cc_final: 0.6305 (mp10)
  outliers start: 26
  outliers final: 17
  residues processed: 151
  average time/residue: 0.2765
  time to fit residues: 67.9625
Evaluate side-chains
  151 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 2.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 HIS
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain A residue  113 GLN
Chi-restraints excluded: chain A residue  326 PHE
Chi-restraints excluded: chain A residue  548 GLU
Chi-restraints excluded: chain A residue  645 MET
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  269 TYR
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  401 GLU
Chi-restraints excluded: chain C residue  669 VAL
Chi-restraints excluded: chain C residue  797 MET
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  252 LEU
Chi-restraints excluded: chain D residue  269 TYR
Chi-restraints excluded: chain E residue   20 ILE
Chi-restraints excluded: chain E residue   62 ASN
Chi-restraints excluded: chain E residue   95 MET
Chi-restraints excluded: chain E residue  100 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 182 optimal weight:    4.9990
   chunk 57 optimal weight:   10.0000
   chunk 115 optimal weight:    4.9990
   chunk 196 optimal weight:    3.9990
   chunk 110 optimal weight:    3.9990
   chunk 10 optimal weight:    0.4980
   chunk 5 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 221 optimal weight:   20.0000
   chunk 48 optimal weight:    0.0060
   chunk 46 optimal weight:    0.0370
   overall best weight:    0.9078

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

Flipped N/Q/H residues before XYZ refinement:
** E  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  62 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.079863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.054943 restraints weight = 73362.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.056775 restraints weight = 39183.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.057862 restraints weight = 28085.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  18933  Z= 0.150
  Angle     :  0.566  12.603  25599  Z= 0.276
  Chirality :  0.043   0.284   2725
  Planarity :  0.003   0.043   3289
  Dihedral  :  3.716  19.598   2479
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 14.74 %
    Favored  : 83.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.19), residues: 2222
  helix:  1.72 (0.17), residues: 983
  sheet:  0.06 (0.31), residues: 285
  loop :  0.25 (0.21), residues: 954

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 352 
 HIS   0.003   0.001   HIS A 221 
 PHE   0.011   0.001   PHE A 551 
 TYR   0.020   0.001   TYR C 841 
 ARG   0.003   0.000   ARG E  69 

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

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

  4444 Ramachandran restraints generated.
    2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4444 Ramachandran restraints generated.
    2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 134
  time to evaluate  : 2.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8659 (pmm)
REVERT: A  113 GLN cc_start: 0.9247 (OUTLIER) cc_final: 0.8887 (pm20)
REVERT: A  318 ASP cc_start: 0.8505 (m-30) cc_final: 0.8270 (m-30)
REVERT: A  380 GLU cc_start: 0.8670 (tp30) cc_final: 0.8262 (tp30)
REVERT: A  566 MET cc_start: 0.7709 (tmm) cc_final: 0.7172 (tmm)
REVERT: A  645 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7160 (tmm)
REVERT: A  838 PHE cc_start: 0.7142 (m-80) cc_final: 0.6706 (m-80)
REVERT: B   53 ASP cc_start: 0.8344 (m-30) cc_final: 0.8001 (m-30)
REVERT: B  252 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9293 (mm)
REVERT: C   76 MET cc_start: 0.8990 (ptt) cc_final: 0.8366 (ppp)
REVERT: C  110 MET cc_start: 0.8256 (mmp) cc_final: 0.7823 (mmp)
REVERT: C  167 MET cc_start: 0.8335 (mmp) cc_final: 0.8027 (mmm)
REVERT: C  324 CYS cc_start: 0.8204 (m) cc_final: 0.7628 (m)
REVERT: C  360 LYS cc_start: 0.8755 (ptmt) cc_final: 0.8241 (tppt)
REVERT: C  625 LEU cc_start: 0.8881 (mt) cc_final: 0.8405 (mt)
REVERT: D   53 ASP cc_start: 0.8768 (m-30) cc_final: 0.8513 (m-30)
REVERT: D  164 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8594 (pp20)
REVERT: E   69 ARG cc_start: 0.7964 (ttm170) cc_final: 0.7721 (ttm170)
REVERT: E   72 ARG cc_start: 0.7863 (mtp85) cc_final: 0.6647 (ptt-90)
REVERT: E   80 PHE cc_start: 0.9102 (m-80) cc_final: 0.8855 (m-80)
REVERT: E  100 GLN cc_start: 0.6844 (OUTLIER) cc_final: 0.6337 (mp10)
REVERT: E  113 ARG cc_start: 0.8164 (mtt180) cc_final: 0.7918 (tpp-160)
  outliers start: 27
  outliers final: 17
  residues processed: 152
  average time/residue: 0.2908
  time to fit residues: 71.9628
Evaluate side-chains
  151 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 129
  time to evaluate  : 2.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 HIS
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain A residue  113 GLN
Chi-restraints excluded: chain A residue  548 GLU
Chi-restraints excluded: chain A residue  645 MET
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  269 TYR
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  401 GLU
Chi-restraints excluded: chain C residue  669 VAL
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue  252 LEU
Chi-restraints excluded: chain D residue  269 TYR
Chi-restraints excluded: chain E residue   20 ILE
Chi-restraints excluded: chain E residue   62 ASN
Chi-restraints excluded: chain E residue   63 GLU
Chi-restraints excluded: chain E residue   95 MET
Chi-restraints excluded: chain E residue  100 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 219 optimal weight:    7.9990
   chunk 142 optimal weight:    0.9990
   chunk 84 optimal weight:    5.9990
   chunk 64 optimal weight:    0.0770
   chunk 126 optimal weight:    2.9990
   chunk 192 optimal weight:   10.0000
   chunk 27 optimal weight:    0.7980
   chunk 99 optimal weight:    1.9990
   chunk 159 optimal weight:    3.9990
   chunk 212 optimal weight:   10.0000
   chunk 73 optimal weight:    5.9990
   overall best weight:    1.3744

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

Flipped N/Q/H residues before XYZ refinement:
** E  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  62 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.079674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.054805 restraints weight = 73297.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.056613 restraints weight = 39212.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.057668 restraints weight = 28182.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  18933  Z= 0.174
  Angle     :  0.577  12.682  25599  Z= 0.281
  Chirality :  0.043   0.281   2725
  Planarity :  0.003   0.043   3289
  Dihedral  :  3.717  20.715   2479
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 14.94 %
    Favored  : 83.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.18), residues: 2222
  helix:  1.74 (0.17), residues: 982
  sheet:  0.01 (0.31), residues: 287
  loop :  0.25 (0.21), residues: 953

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 352 
 HIS   0.003   0.001   HIS A 221 
 PHE   0.010   0.001   PHE A 551 
 TYR   0.020   0.001   TYR C 841 
 ARG   0.002   0.000   ARG E  69 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5340.51 seconds
wall clock time: 101 minutes 15.19 seconds (6075.19 seconds total)