Starting phenix.real_space_refine
on Thu Mar  5 00:31:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lxd_23570/03_2026/7lxd_23570.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lxd_23570/03_2026/7lxd_23570.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7lxd_23570/03_2026/7lxd_23570.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lxd_23570/03_2026/7lxd_23570.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lxd_23570/03_2026/7lxd_23570.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lxd_23570/03_2026/7lxd_23570.cif"
  }
  resolution = 4.11
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Fe      4      7.16       5
     S      83      5.16       5
     C   11249      2.51       5
     N    2898      2.21       5
     O    3222      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 111 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 17456
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 9725
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1190, 9725
          Classifications: {'peptide': 1190}
          Link IDs: {'PTRANS': 56, 'TRANS': 1133}
          Chain breaks: 10
    Chain: "D"
      Number of atoms: 1364
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 163, 1364
          Classifications: {'peptide': 163}
          Link IDs: {'PTRANS': 9, 'TRANS': 153}
          Chain breaks: 2
    Chain: "E"
      Number of atoms: 1718
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 205, 1718
          Classifications: {'peptide': 205}
          Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 196}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 3668
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 459, 3668
          Classifications: {'peptide': 459}
          Link IDs: {'CIS': 1, 'PTRANS': 28, 'TRANS': 429}
          Chain breaks: 3
    Chain: "G"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 973
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 5, 'TRANS': 112}
    Chain: "A"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 8
          Unusual residues: {'SF4': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   9591  SG  CYS A1473      44.489  79.651  84.983  1.00123.06           S
  ATOM   9403  SG  CYS A1449      39.309  82.759  85.540  1.00111.91           S
  ATOM   9379  SG  CYS A1446      43.965  84.368  80.827  1.00106.48           S
  ATOM   9551  SG  CYS A1468      45.400  84.939  86.732  1.00115.48           S

  Time building chain proxies: 3.60, per 1000 atoms: 0.21
  Number of scatterers: 17456
  At special positions: 0
  Unit cell: (86.478, 143.136, 168.483, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      4     26.01
     S      83     16.00
     O    3222      8.00
     N    2898      7.00
     C   11249      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: 1.72
  Conformation dependent library (CDL) restraints added in 781.1 milliseconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" SF4 A1601 "
        pdb="FE4  SF4 A1601 " - pdb=" SG  CYS A1468 "
        pdb="FE2  SF4 A1601 " - pdb=" SG  CYS A1449 "
        pdb="FE3  SF4 A1601 " - pdb=" SG  CYS A1446 "
        pdb="FE1  SF4 A1601 " - pdb=" SG  CYS A1473 "
      Number of angles added : 12


  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4102

  Finding SS restraints...
    Secondary structure from input PDB file:
      70 helices and 22 sheets defined
      37.6% alpha, 6.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 91 through 96
      removed outlier: 3.937A  pdb=" N   THR A  95 " --> pdb=" O   THR A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 114
    Processing helix  chain 'A' and resid 168 through 179
    Processing helix  chain 'A' and resid 189 through 193
    Processing helix  chain 'A' and resid 194 through 203
      removed outlier: 3.922A  pdb=" N   PHE A 203 " --> pdb=" O   TRP A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 233
      removed outlier: 3.638A  pdb=" N   LEU A 232 " --> pdb=" O   ASP A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 242
      removed outlier: 3.639A  pdb=" N   GLN A 239 " --> pdb=" O   ASN A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 288
    Processing helix  chain 'A' and resid 345 through 360
      removed outlier: 3.576A  pdb=" N   PHE A 349 " --> pdb=" O   SER A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 378
      removed outlier: 3.788A  pdb=" N   ILE A 374 " --> pdb=" O   PHE A 370 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ASP A 375 " --> pdb=" O   GLU A 371 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ASN A 377 " --> pdb=" O   PHE A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 390
      removed outlier: 3.794A  pdb=" N   LEU A 390 " --> pdb=" O   PRO A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 541
      removed outlier: 3.547A  pdb=" N   GLY A 541 " --> pdb=" O   LEU A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 561
    Processing helix  chain 'A' and resid 612 through 623
      removed outlier: 3.616A  pdb=" N   VAL A 616 " --> pdb=" O   THR A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 724
      removed outlier: 3.766A  pdb=" N   SER A 724 " --> pdb=" O   SER A 721 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 721 through 724'
    Processing helix  chain 'A' and resid 725 through 734
      removed outlier: 3.689A  pdb=" N   ILE A 730 " --> pdb=" O   PHE A 726 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   HIS A 732 " --> pdb=" O   THR A 728 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 745 through 759
    Processing helix  chain 'A' and resid 773 through 784
      removed outlier: 3.572A  pdb=" N   ILE A 777 " --> pdb=" O   SER A 773 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 789 through 794
    Processing helix  chain 'A' and resid 836 through 840
      removed outlier: 3.501A  pdb=" N   THR A 840 " --> pdb=" O   THR A 837 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 843 through 848
      removed outlier: 3.581A  pdb=" N   ILE A 848 " --> pdb=" O   ALA A 844 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 857 through 864
    Processing helix  chain 'A' and resid 870 through 895
      removed outlier: 4.213A  pdb=" N   LEU A 874 " --> pdb=" O   SER A 870 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 901 through 909
    Processing helix  chain 'A' and resid 911 through 918
      removed outlier: 4.117A  pdb=" N   VAL A 915 " --> pdb=" O   ASP A 911 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   TYR A 916 " --> pdb=" O   PHE A 912 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 922 through 935
    Processing helix  chain 'A' and resid 943 through 948
    Processing helix  chain 'A' and resid 979 through 988
    Processing helix  chain 'A' and resid 990 through 994
      removed outlier: 3.873A  pdb=" N   THR A 993 " --> pdb=" O   CYS A 990 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   MET A 994 " --> pdb=" O   TYR A 991 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 990 through 994'
    Processing helix  chain 'A' and resid 1018 through 1023
    Processing helix  chain 'A' and resid 1038 through 1043
      removed outlier: 3.780A  pdb=" N   ARG A1042 " --> pdb=" O   LYS A1038 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1044 through 1067
    Processing helix  chain 'A' and resid 1074 through 1090
    Processing helix  chain 'A' and resid 1106 through 1130
    Processing helix  chain 'A' and resid 1157 through 1173
      removed outlier: 4.046A  pdb=" N   HIS A1163 " --> pdb=" O   PHE A1159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1224 through 1241
      removed outlier: 3.942A  pdb=" N   GLN A1228 " --> pdb=" O   ILE A1224 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   THR A1241 " --> pdb=" O   LEU A1237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1244 through 1260
    Processing helix  chain 'A' and resid 1335 through 1339
    Processing helix  chain 'A' and resid 1344 through 1358
      removed outlier: 4.025A  pdb=" N   ASN A1348 " --> pdb=" O   GLU A1344 " (cutoff:3.500A)
      Proline residue:  A1353  - end of helix
      removed outlier: 3.501A  pdb=" N   ARG A1357 " --> pdb=" O   PRO A1353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1358 through 1363
      removed outlier: 3.846A  pdb=" N   ILE A1362 " --> pdb=" O   LEU A1358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1365 through 1376
      removed outlier: 4.262A  pdb=" N   LYS A1375 " --> pdb=" O   GLN A1371 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   SER A1376 " --> pdb=" O   GLU A1372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1424 through 1450
    Processing helix  chain 'A' and resid 1451 through 1453
      No H-bonds generated for 'chain 'A' and resid 1451 through 1453'
    Processing helix  chain 'A' and resid 1460 through 1467
      removed outlier: 3.738A  pdb=" N   ILE A1464 " --> pdb=" O   GLU A1460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1475 through 1486
    Processing helix  chain 'D' and resid 5 through 24
    Processing helix  chain 'D' and resid 51 through 68
    Processing helix  chain 'D' and resid 69 through 72
    Processing helix  chain 'D' and resid 110 through 129
      removed outlier: 3.995A  pdb=" N   ARG D 118 " --> pdb=" O   PHE D 114 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   SER D 119 " --> pdb=" O   ASP D 115 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 3 through 24
      removed outlier: 3.667A  pdb=" N   LYS E   7 " --> pdb=" O   ARG E   3 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 66
    Processing helix  chain 'E' and resid 98 through 103
      removed outlier: 3.851A  pdb=" N   ASP E 102 " --> pdb=" O   LEU E  98 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 109 through 130
    Processing helix  chain 'E' and resid 152 through 157
      removed outlier: 3.862A  pdb=" N   LEU E 156 " --> pdb=" O   GLY E 153 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 164 through 176
    Processing helix  chain 'F' and resid 1 through 9
    Processing helix  chain 'F' and resid 52 through 70
      removed outlier: 3.748A  pdb=" N   ILE F  56 " --> pdb=" O   GLN F  52 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLN F  58 " --> pdb=" O   TYR F  54 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   LYS F  70 " --> pdb=" O   GLU F  66 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 92 through 97
      removed outlier: 3.732A  pdb=" N   GLN F  97 " --> pdb=" O   VAL F  93 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 129 through 143
      removed outlier: 3.633A  pdb=" N   THR F 133 " --> pdb=" O   ALA F 129 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   TYR F 136 " --> pdb=" O   LEU F 132 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   THR F 137 " --> pdb=" O   THR F 133 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   LYS F 139 " --> pdb=" O   SER F 135 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   GLU F 140 " --> pdb=" O   TYR F 136 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 160 through 165
      removed outlier: 3.632A  pdb=" N   SER F 164 " --> pdb=" O   ASP F 160 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 226 through 231
      removed outlier: 3.940A  pdb=" N   LEU F 230 " --> pdb=" O   SER F 226 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 248 through 254
      removed outlier: 3.959A  pdb=" N   SER F 252 " --> pdb=" O   ILE F 248 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 267 through 271
      removed outlier: 3.617A  pdb=" N   VAL F 271 " --> pdb=" O   ILE F 268 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 272 through 291
      removed outlier: 3.581A  pdb=" N   SER F 279 " --> pdb=" O   GLU F 275 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 321 through 331
      removed outlier: 4.010A  pdb=" N   SER F 326 " --> pdb=" O   LYS F 322 " (cutoff:3.500A)
      removed outlier: 5.144A  pdb=" N   TYR F 327 " --> pdb=" O   SER F 323 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   PHE F 328 " --> pdb=" O   LEU F 324 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ASN F 329 " --> pdb=" O   GLU F 325 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 357 through 365
      removed outlier: 4.581A  pdb=" N   ILE F 363 " --> pdb=" O   ASN F 359 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 392 through 406
      removed outlier: 4.384A  pdb=" N   ASP F 397 " --> pdb=" O   GLU F 393 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   LEU F 398 " --> pdb=" O   HIS F 394 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   MET F 399 " --> pdb=" O   ARG F 395 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   GLU F 400 " --> pdb=" O   LEU F 396 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 3 through 15
      removed outlier: 4.246A  pdb=" N   PHE G   8 " --> pdb=" O   LYS G   4 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 22 through 30
      removed outlier: 3.821A  pdb=" N   ILE G  26 " --> pdb=" O   PHE G  22 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 32 through 46
    Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 35
      removed outlier: 3.895A  pdb=" N   ASP A  31 " --> pdb=" O   ARG A  60 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 65
      removed outlier: 3.550A  pdb=" N   LEU A  65 " --> pdb=" O   HIS A  69 " (cutoff:3.500A)
      removed outlier: 5.077A  pdb=" N   HIS A  69 " --> pdb=" O   LEU A  65 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82
    Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 143
    Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147
      removed outlier: 6.817A  pdb=" N   ILE A 146 " --> pdb=" O   ILE A 938 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 581 through 582
      removed outlier: 6.630A  pdb=" N   ILE A 581 " --> pdb=" O   GLN D  38 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 87 through 92
      removed outlier: 6.636A  pdb=" N   ILE E  79 " --> pdb=" O   ILE E  88 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   LYS E  90 " --> pdb=" O   ILE E  77 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   ILE E  77 " --> pdb=" O   LYS E  90 " (cutoff:3.500A)
      removed outlier: 5.341A  pdb=" N   VAL E  92 " --> pdb=" O   PHE E  75 " (cutoff:3.500A)
      removed outlier: 7.317A  pdb=" N   PHE E  75 " --> pdb=" O   VAL E  92 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   VAL E 144 " --> pdb=" O   SER E  76 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ILE E  80 " --> pdb=" O   THR E 140 " (cutoff:3.500A)
      removed outlier: 5.349A  pdb=" N   ALA E 143 " --> pdb=" O   TYR A 606 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   TYR A 606 " --> pdb=" O   ALA E 143 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   SER A 602 " --> pdb=" O   ALA E 147 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 669 through 670
    Processing sheet with id=AA9, first strand: chain 'A' and resid 694 through 696
      removed outlier: 3.742A  pdb=" N   TRP A 696 " --> pdb=" O   GLY A 713 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLY A 713 " --> pdb=" O   TRP A 696 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 971 through 973
      removed outlier: 3.831A  pdb=" N   VAL A1148 " --> pdb=" O   ILE A 972 " (cutoff:3.500A)
      removed outlier: 5.692A  pdb=" N   TYR A1149 " --> pdb=" O   VAL A1138 " (cutoff:3.500A)
      removed outlier: 5.657A  pdb=" N   VAL A1138 " --> pdb=" O   TYR A1149 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1027 through 1029
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1199 through 1200
    Processing sheet with id=AB4, first strand: chain 'D' and resid 75 through 80
    Processing sheet with id=AB5, first strand: chain 'D' and resid 89 through 90
    Processing sheet with id=AB6, first strand: chain 'E' and resid 32 through 37
      removed outlier: 6.705A  pdb=" N   TYR E  37 " --> pdb=" O   GLN E  44 " (cutoff:3.500A)
      removed outlier: 11.269A  pdb=" N   GLN E  44 " --> pdb=" O   TYR E  37 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 198 through 200
    Processing sheet with id=AB8, first strand: chain 'E' and resid 205 through 206
      removed outlier: 3.534A  pdb=" N   ILE E 212 " --> pdb=" O   SER E 205 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'F' and resid 171 through 175
      removed outlier: 4.448A  pdb=" N   VAL F 171 " --> pdb=" O   ILE F 108 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ILE F 108 " --> pdb=" O   VAL F 171 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ILE F 175 " --> pdb=" O   CYS F 104 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   CYS F 104 " --> pdb=" O   ILE F 175 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   ILE F 146 " --> pdb=" O   LEU F 157 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   LEU F 156 " --> pdb=" O   PHE F 185 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'F' and resid 257 through 258
      removed outlier: 6.447A  pdb=" N   LEU F 257 " --> pdb=" O   ASP F 297 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC1
    Processing sheet with id=AC2, first strand: chain 'F' and resid 344 through 346
      removed outlier: 7.233A  pdb=" N   ASP F 351 " --> pdb=" O   VAL F 435 " (cutoff:3.500A)
      removed outlier: 8.404A  pdb=" N   ILE F 437 " --> pdb=" O   ASP F 351 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   LEU F 353 " --> pdb=" O   ILE F 437 " (cutoff:3.500A)
      removed outlier: 8.445A  pdb=" N   ALA F 439 " --> pdb=" O   LEU F 353 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   TYR F 436 " --> pdb=" O   ILE F 459 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   VAL F 461 " --> pdb=" O   TYR F 436 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   VAL F 438 " --> pdb=" O   VAL F 461 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'F' and resid 470 through 472
    Processing sheet with id=AC4, first strand: chain 'G' and resid 56 through 58

    537 hydrogen bonds defined for protein.
    1530 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: 3.51

  Time building geometry restraints manager: 2.25 seconds

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

  Histogram of bond lengths:
        1.21 -     1.43: 7460
        1.43 -     1.64: 10270
        1.64 -     1.86: 113
        1.86 -     2.07: 0
        2.07 -     2.29: 12
  Bond restraints: 17855
  Sorted by residual:
  bond pdb=" CA  LYS A1214 "
       pdb=" C   LYS A1214 "
    ideal  model  delta    sigma   weight residual
    1.523  1.473  0.050 1.24e-02 6.50e+03 1.64e+01
  bond pdb=" C   PRO A1353 "
       pdb=" N   PRO A1354 "
    ideal  model  delta    sigma   weight residual
    1.336  1.378 -0.042 1.20e-02 6.94e+03 1.20e+01
  bond pdb=" C   HIS A1186 "
       pdb=" N   PRO A1187 "
    ideal  model  delta    sigma   weight residual
    1.334  1.410 -0.076 2.34e-02 1.83e+03 1.06e+01
  bond pdb=" C   ASN F 199 "
       pdb=" N   PRO F 200 "
    ideal  model  delta    sigma   weight residual
    1.332  1.359 -0.027 1.12e-02 7.97e+03 5.94e+00
  bond pdb=" N   THR A1154 "
       pdb=" CA  THR A1154 "
    ideal  model  delta    sigma   weight residual
    1.460  1.491 -0.031 1.45e-02 4.76e+03 4.54e+00
  ... (remaining 17850 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.16: 23728
        4.16 -     8.33: 373
        8.33 -    12.49: 51
       12.49 -    16.66: 7
       16.66 -    20.82: 3
  Bond angle restraints: 24162
  Sorted by residual:
  angle pdb=" CG1 ILE A 709 "
        pdb=" CB  ILE A 709 "
        pdb=" CG2 ILE A 709 "
      ideal   model   delta    sigma   weight residual
     110.70   91.53   19.17 3.00e+00 1.11e-01 4.08e+01
  angle pdb=" C   GLY A1215 "
        pdb=" N   ILE A1216 "
        pdb=" CA  ILE A1216 "
      ideal   model   delta    sigma   weight residual
     120.49  128.78   -8.29 1.38e+00 5.25e-01 3.61e+01
  angle pdb=" CA  LEU F 478 "
        pdb=" CB  LEU F 478 "
        pdb=" CG  LEU F 478 "
      ideal   model   delta    sigma   weight residual
     116.30  137.12  -20.82 3.50e+00 8.16e-02 3.54e+01
  angle pdb=" N   GLU G  11 "
        pdb=" CA  GLU G  11 "
        pdb=" CB  GLU G  11 "
      ideal   model   delta    sigma   weight residual
     110.07  118.67   -8.60 1.45e+00 4.76e-01 3.52e+01
  angle pdb=" C   GLY A1094 "
        pdb=" N   TYR A1095 "
        pdb=" CA  TYR A1095 "
      ideal   model   delta    sigma   weight residual
     121.54  132.07  -10.53 1.91e+00 2.74e-01 3.04e+01
  ... (remaining 24157 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.43: 9425
       17.43 -    34.86: 1131
       34.86 -    52.29: 208
       52.29 -    69.71: 30
       69.71 -    87.14: 16
  Dihedral angle restraints: 10810
    sinusoidal: 4493
      harmonic: 6317
  Sorted by residual:
  dihedral pdb=" CA  ARG F  25 "
           pdb=" C   ARG F  25 "
           pdb=" N   VAL F  26 "
           pdb=" CA  VAL F  26 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  105.34   74.66     0      5.00e+00 4.00e-02 2.23e+02
  dihedral pdb=" CA  ASP F 414 "
           pdb=" C   ASP F 414 "
           pdb=" N   THR F 415 "
           pdb=" CA  THR F 415 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  122.17   57.83     0      5.00e+00 4.00e-02 1.34e+02
  dihedral pdb=" CA  TYR A1196 "
           pdb=" C   TYR A1196 "
           pdb=" N   VAL A1197 "
           pdb=" CA  VAL A1197 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -124.51  -55.49     0      5.00e+00 4.00e-02 1.23e+02
  ... (remaining 10807 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.104: 2345
       0.104 -    0.209: 302
       0.209 -    0.313: 32
       0.313 -    0.418: 9
       0.418 -    0.522: 3
  Chirality restraints: 2691
  Sorted by residual:
  chirality pdb=" CB  ILE E 108 "
            pdb=" CA  ILE E 108 "
            pdb=" CG1 ILE E 108 "
            pdb=" CG2 ILE E 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.12    0.52 2.00e-01 2.50e+01 6.81e+00
  chirality pdb=" CG  LEU D 202 "
            pdb=" CB  LEU D 202 "
            pdb=" CD1 LEU D 202 "
            pdb=" CD2 LEU D 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.14   -0.45 2.00e-01 2.50e+01 5.11e+00
  chirality pdb=" CB  VAL F 438 "
            pdb=" CA  VAL F 438 "
            pdb=" CG1 VAL F 438 "
            pdb=" CG2 VAL F 438 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.21   -0.42 2.00e-01 2.50e+01 4.41e+00
  ... (remaining 2688 not shown)

  Planarity restraints: 3064
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 961 "   -0.068 5.00e-02 4.00e+02   1.03e-01 1.69e+01
        pdb=" N   PRO A 962 "    0.178 5.00e-02 4.00e+02
        pdb=" CA  PRO A 962 "   -0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO A 962 "   -0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A1213 "    0.019 2.00e-02 2.50e+03   3.90e-02 1.52e+01
        pdb=" C   ALA A1213 "   -0.067 2.00e-02 2.50e+03
        pdb=" O   ALA A1213 "    0.026 2.00e-02 2.50e+03
        pdb=" N   LYS A1214 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A1173 "   -0.063 5.00e-02 4.00e+02   9.35e-02 1.40e+01
        pdb=" N   PRO A1174 "    0.162 5.00e-02 4.00e+02
        pdb=" CA  PRO A1174 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO A1174 "   -0.051 5.00e-02 4.00e+02
  ... (remaining 3061 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 4256
        2.80 -     3.33: 16853
        3.33 -     3.85: 30622
        3.85 -     4.38: 34537
        4.38 -     4.90: 56527
  Nonbonded interactions: 142795
  Sorted by model distance:
  nonbonded pdb=" O   ILE A  78 "
            pdb=" OH  TYR A 195 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O   ASP A 139 "
            pdb=" OG  SER A 162 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OH  TYR A 149 "
            pdb=" O   LEU A1008 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   SER A1047 "
            pdb=" OG1 THR A1051 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" OG1 THR A 668 "
            pdb=" O   ASP A 760 "
     model   vdw
     2.284 3.040
  ... (remaining 142790 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.940
  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:          0.270
  Check model and map are aligned:         0.070
  Set scattering table:                    0.060
  Process input model:                     20.110
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6422
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      :  0.006   0.087  17859  Z= 0.283
  Angle     :  1.351  28.323  24174  Z= 0.694
  Chirality :  0.074   0.522   2691
  Planarity :  0.009   0.103   3064
  Dihedral  : 15.453  87.143   6708
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.05 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 1.94 %
    Twisted General : 0.65 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.73 (0.16), residues: 2093
  helix: -1.88 (0.17), residues: 685
  sheet: -2.88 (0.34), residues: 179
  loop : -2.88 (0.15), residues: 1229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG E 160 
 TYR   0.035   0.003   TYR A1201 
 PHE   0.039   0.003   PHE A1199 
 TRP   0.024   0.003   TRP A 155 
 HIS   0.008   0.001   HIS A 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00577 (17855)
  covalent geometry    : angle       1.30300 (24162)
  hydrogen bonds       : bond        0.16187 (  537)
  hydrogen bonds       : angle       8.48931 ( 1530)
  metal coordination   : bond        0.00758 (    4)
  metal coordination   : angle      16.03973 (   12)

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

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

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  350 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 350
  time to evaluate  : 0.699 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.6726 (ptp) cc_final: 0.6490 (ptt)
REVERT: A   84 ILE cc_start: 0.5036 (pt) cc_final: 0.4779 (pt)
REVERT: A  240 LEU cc_start: 0.9085 (mm) cc_final: 0.8250 (tt)
REVERT: A  530 TYR cc_start: 0.5956 (t80) cc_final: 0.5578 (t80)
REVERT: A  532 ASP cc_start: 0.7476 (p0) cc_final: 0.6717 (t0)
REVERT: A  618 LYS cc_start: 0.8848 (mmtt) cc_final: 0.8639 (mmmm)
REVERT: A  872 THR cc_start: 0.8702 (p) cc_final: 0.8249 (t)
REVERT: A  912 PHE cc_start: 0.8018 (t80) cc_final: 0.7764 (t80)
REVERT: A 1043 LYS cc_start: 0.7598 (ttpt) cc_final: 0.7158 (tptt)
REVERT: A 1076 ARG cc_start: 0.8843 (ptt90) cc_final: 0.8316 (ptt-90)
REVERT: A 1080 ASN cc_start: 0.7803 (p0) cc_final: 0.7494 (p0)
REVERT: A 1156 ILE cc_start: 0.8530 (tt) cc_final: 0.8312 (tp)
REVERT: A 1232 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7611 (tm-30)
REVERT: A 1251 LEU cc_start: 0.8937 (mm) cc_final: 0.8553 (mt)
REVERT: D   64 ASP cc_start: 0.8090 (m-30) cc_final: 0.7477 (m-30)
REVERT: D  124 LEU cc_start: 0.9382 (tp) cc_final: 0.9171 (tp)
REVERT: D  126 MET cc_start: 0.6281 (tpp) cc_final: 0.5956 (mmp)
REVERT: D  142 GLU cc_start: 0.6927 (tm-30) cc_final: 0.6253 (tm-30)
REVERT: E   66 LEU cc_start: 0.9071 (mt) cc_final: 0.8711 (pp)
REVERT: F  226 SER cc_start: 0.5230 (m) cc_final: 0.5015 (m)
REVERT: F  277 MET cc_start: 0.8185 (mpp) cc_final: 0.7481 (mpp)
REVERT: F  288 HIS cc_start: 0.6171 (t-90) cc_final: 0.5936 (t70)
REVERT: G   46 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8021 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 350
  average time/residue: 0.1685
  time to fit residues: 85.1133
Evaluate side-chains
  211 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 211
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 194 optimal weight:    0.0040
   chunk 107 optimal weight:    0.0030
   chunk 10 optimal weight:    0.2980
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    3.9990
   chunk 200 optimal weight:    5.9990
   chunk 77 optimal weight:    0.2980
   chunk 122 optimal weight:    8.9990
   overall best weight:    0.3202

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

Flipped N/Q/H residues before XYZ refinement:
A 224 ASN
A 731 GLN
** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 890 GLN
** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1259 GLN
** A1266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1368 ASN
A1371 GLN
D  41 ASN
** E  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  71 HIS
E 100 HIS
F  15 GLN
F 245 ASN
F 262 ASN
F 312 GLN
** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 440 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.106528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.094612 restraints weight = 80761.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.096816 restraints weight = 53568.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.098411 restraints weight = 38747.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.099577 restraints weight = 29847.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.100425 restraints weight = 23995.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.4190
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4190
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4190 r_free = 0.4190    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4190 r_free = 0.4190    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.4190
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6326
moved from start:          0.2077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  17859  Z= 0.131
  Angle     :  0.756  21.066  24174  Z= 0.375
  Chirality :  0.047   0.168   2691
  Planarity :  0.006   0.077   3064
  Dihedral  :  7.235  50.224   2308
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 13.89
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  9.27 %
    Favored  : 90.68 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  6.02 %
    Favored  : 93.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.97 %
    Twisted General : 0.20 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.92 (0.17), residues: 2093
  helix: -0.89 (0.18), residues: 685
  sheet: -2.66 (0.35), residues: 169
  loop : -2.56 (0.16), residues: 1239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 884 
 TYR   0.020   0.002   TYR A1346 
 PHE   0.028   0.001   PHE F   8 
 TRP   0.019   0.002   TRP A1134 
 HIS   0.004   0.001   HIS E  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (17855)
  covalent geometry    : angle       0.71837 (24162)
  hydrogen bonds       : bond        0.04161 (  537)
  hydrogen bonds       : angle       6.13698 ( 1530)
  metal coordination   : bond        0.00621 (    4)
  metal coordination   : angle      10.61005 (   12)

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

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

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 284
  time to evaluate  : 0.717 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLN cc_start: 0.6999 (mp-120) cc_final: 0.6304 (mp10)
REVERT: A   84 ILE cc_start: 0.4660 (pt) cc_final: 0.4448 (pt)
REVERT: A  240 LEU cc_start: 0.8928 (mm) cc_final: 0.8294 (tp)
REVERT: A  369 ASN cc_start: 0.5716 (m-40) cc_final: 0.5490 (m-40)
REVERT: A  530 TYR cc_start: 0.5625 (t80) cc_final: 0.5157 (t80)
REVERT: A  618 LYS cc_start: 0.8895 (mmtt) cc_final: 0.8488 (mmmm)
REVERT: A  774 TRP cc_start: 0.7877 (m100) cc_final: 0.7452 (m100)
REVERT: A  911 ASP cc_start: 0.5897 (p0) cc_final: 0.5519 (p0)
REVERT: A  912 PHE cc_start: 0.8039 (t80) cc_final: 0.7715 (t80)
REVERT: A 1018 ASN cc_start: 0.7563 (t0) cc_final: 0.7316 (t0)
REVERT: A 1043 LYS cc_start: 0.7892 (ttpt) cc_final: 0.7257 (pttm)
REVERT: A 1076 ARG cc_start: 0.8721 (ptt90) cc_final: 0.7670 (mtt180)
REVERT: A 1232 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7627 (tm-30)
REVERT: A 1251 LEU cc_start: 0.8798 (mm) cc_final: 0.8545 (mt)
REVERT: D   33 ASP cc_start: 0.8692 (p0) cc_final: 0.8411 (p0)
REVERT: D  124 LEU cc_start: 0.9290 (tp) cc_final: 0.9047 (tp)
REVERT: D  126 MET cc_start: 0.6627 (tpp) cc_final: 0.6246 (mmp)
REVERT: D  142 GLU cc_start: 0.6730 (tm-30) cc_final: 0.6163 (tm-30)
REVERT: D  196 LYS cc_start: 0.1828 (tptt) cc_final: 0.1456 (tptt)
REVERT: E   66 LEU cc_start: 0.9122 (mt) cc_final: 0.8509 (pp)
REVERT: E  126 MET cc_start: 0.7392 (ttp) cc_final: 0.6759 (ttp)
REVERT: E  158 ARG cc_start: 0.4788 (mpt180) cc_final: 0.2945 (mpt90)
REVERT: F  257 LEU cc_start: 0.8002 (tp) cc_final: 0.7736 (tp)
REVERT: G   46 GLN cc_start: 0.8286 (mm-40) cc_final: 0.7642 (pp30)
  outliers start: 7
  outliers final: 0
  residues processed: 290
  average time/residue: 0.1542
  time to fit residues: 66.7922
Evaluate side-chains
  188 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 211
   random chunks:
   chunk 84 optimal weight:   20.0000
   chunk 187 optimal weight:    0.0970
   chunk 30 optimal weight:    6.9990
   chunk 170 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0060
   chunk 46 optimal weight:    3.9990
   chunk 154 optimal weight:    9.9990
   chunk 147 optimal weight:    0.9980
   chunk 192 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   overall best weight:    1.4198

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

Flipped N/Q/H residues before XYZ refinement:
A  44 HIS
** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 531 GLN
A 560 ASN
A 617 GLN
A 677 ASN
A 731 GLN
** A 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1266 GLN
A1338 ASN
A1371 GLN
D  41 ASN
E   2 ASN
** E  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  15 GLN
** F 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 312 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.104147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.092055 restraints weight = 82467.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.094197 restraints weight = 55095.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.095732 restraints weight = 40237.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.096861 restraints weight = 31216.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.097705 restraints weight = 25308.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.4145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6430
moved from start:          0.2798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  17859  Z= 0.139
  Angle     :  0.735  18.736  24174  Z= 0.367
  Chirality :  0.047   0.189   2691
  Planarity :  0.006   0.074   3064
  Dihedral  :  6.816  50.046   2308
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 16.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.08 %
    Favored  : 90.92 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  5.92 %
    Favored  : 94.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.77 (0.17), residues: 2093
  helix: -0.64 (0.18), residues: 710
  sheet: -2.75 (0.34), residues: 178
  loop : -2.55 (0.17), residues: 1205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 278 
 TYR   0.027   0.002   TYR D  91 
 PHE   0.028   0.002   PHE F   8 
 TRP   0.012   0.001   TRP D   8 
 HIS   0.006   0.001   HIS E 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (17855)
  covalent geometry    : angle       0.70127 (24162)
  hydrogen bonds       : bond        0.03713 (  537)
  hydrogen bonds       : angle       5.70759 ( 1530)
  metal coordination   : bond        0.00518 (    4)
  metal coordination   : angle       9.85860 (   12)

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

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

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 267
  time to evaluate  : 0.690 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLN cc_start: 0.7257 (mp-120) cc_final: 0.6736 (mp10)
REVERT: A   84 ILE cc_start: 0.4524 (pt) cc_final: 0.4288 (pt)
REVERT: A  240 LEU cc_start: 0.8886 (mm) cc_final: 0.8396 (tp)
REVERT: A  244 ARG cc_start: 0.6803 (ppt170) cc_final: 0.6575 (mmm160)
REVERT: A  530 TYR cc_start: 0.5794 (t80) cc_final: 0.5259 (t80)
REVERT: A  618 LYS cc_start: 0.8934 (mmtt) cc_final: 0.8578 (mmmm)
REVERT: A  911 ASP cc_start: 0.6027 (p0) cc_final: 0.5532 (p0)
REVERT: A  912 PHE cc_start: 0.8070 (t80) cc_final: 0.7806 (t80)
REVERT: A 1043 LYS cc_start: 0.7914 (ttpt) cc_final: 0.7469 (ptmt)
REVERT: A 1049 MET cc_start: 0.7870 (mtm) cc_final: 0.7625 (mtp)
REVERT: A 1064 MET cc_start: 0.7812 (ptt) cc_final: 0.7526 (ptm)
REVERT: A 1076 ARG cc_start: 0.8860 (ptt90) cc_final: 0.7812 (tpp-160)
REVERT: A 1080 ASN cc_start: 0.8226 (p0) cc_final: 0.7900 (p0)
REVERT: A 1191 ILE cc_start: 0.6431 (tt) cc_final: 0.6147 (tt)
REVERT: A 1208 LEU cc_start: 0.8214 (tp) cc_final: 0.7948 (tp)
REVERT: A 1232 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7750 (tm-30)
REVERT: D  126 MET cc_start: 0.6567 (tpp) cc_final: 0.6190 (mmp)
REVERT: D  142 GLU cc_start: 0.6593 (tm-30) cc_final: 0.5624 (tm-30)
REVERT: D  196 LYS cc_start: 0.1528 (tptt) cc_final: 0.1092 (tptt)
REVERT: E   16 TYR cc_start: 0.7583 (t80) cc_final: 0.7037 (t80)
REVERT: E   66 LEU cc_start: 0.9209 (mt) cc_final: 0.8584 (pp)
REVERT: F  112 MET cc_start: 0.3624 (mpp) cc_final: 0.2189 (mpp)
REVERT: F  257 LEU cc_start: 0.7670 (tp) cc_final: 0.7369 (tp)
REVERT: F  277 MET cc_start: 0.8084 (mpp) cc_final: 0.7852 (mpp)
REVERT: F  399 MET cc_start: 0.7953 (ttt) cc_final: 0.7738 (ptp)
REVERT: G   46 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7700 (pp30)
REVERT: G  115 LEU cc_start: 0.7092 (mp) cc_final: 0.6866 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 268
  average time/residue: 0.1468
  time to fit residues: 59.1544
Evaluate side-chains
  188 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 211
   random chunks:
   chunk 193 optimal weight:    0.4980
   chunk 184 optimal weight:    6.9990
   chunk 127 optimal weight:    2.9990
   chunk 180 optimal weight:    6.9990
   chunk 124 optimal weight:    5.9990
   chunk 202 optimal weight:    7.9990
   chunk 126 optimal weight:    3.9990
   chunk 100 optimal weight:    4.9990
   chunk 143 optimal weight:    7.9990
   chunk 39 optimal weight:   10.0000
   chunk 12 optimal weight:    4.9990
   overall best weight:    3.4988

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

Flipped N/Q/H residues before XYZ refinement:
A 198 GLN
A 263 ASN
** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 822 HIS
** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 913 HIS
** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1240 GLN
A1371 GLN
D  18 ASN
D  41 ASN
** D  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 213 HIS
F  21 GLN
** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 245 ASN
** F 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.098026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.086284 restraints weight = 81568.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.088258 restraints weight = 54898.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.089685 restraints weight = 40351.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.090727 restraints weight = 31509.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.091401 restraints weight = 25784.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.4018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6678
moved from start:          0.3789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  17859  Z= 0.222
  Angle     :  0.840  21.460  24174  Z= 0.424
  Chirality :  0.051   0.221   2691
  Planarity :  0.006   0.061   3064
  Dihedral  :  6.989  54.330   2308
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 25.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.08 %
    Favored  : 88.92 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  6.62 %
    Favored  : 93.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.87 (0.17), residues: 2093
  helix: -0.70 (0.18), residues: 710
  sheet: -2.77 (0.35), residues: 179
  loop : -2.63 (0.17), residues: 1204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F  12 
 TYR   0.023   0.002   TYR A1477 
 PHE   0.044   0.003   PHE F 464 
 TRP   0.021   0.002   TRP F 405 
 HIS   0.014   0.002   HIS F 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 (17855)
  covalent geometry    : angle       0.80185 (24162)
  hydrogen bonds       : bond        0.04268 (  537)
  hydrogen bonds       : angle       5.98869 ( 1530)
  metal coordination   : bond        0.00710 (    4)
  metal coordination   : angle      11.30231 (   12)

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

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

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 248
  time to evaluate  : 0.745 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLN cc_start: 0.6849 (mp-120) cc_final: 0.6506 (mp10)
REVERT: A   84 ILE cc_start: 0.5364 (pt) cc_final: 0.4931 (pt)
REVERT: A  239 GLN cc_start: 0.7689 (mp10) cc_final: 0.7273 (tp-100)
REVERT: A  243 ASP cc_start: 0.7831 (p0) cc_final: 0.7264 (p0)
REVERT: A  352 PHE cc_start: 0.8169 (t80) cc_final: 0.7816 (t80)
REVERT: A  355 LYS cc_start: 0.8248 (mtpt) cc_final: 0.7949 (ttpp)
REVERT: A  579 THR cc_start: 0.7555 (m) cc_final: 0.7249 (p)
REVERT: A  614 ASP cc_start: 0.7222 (m-30) cc_final: 0.7013 (m-30)
REVERT: A  911 ASP cc_start: 0.6471 (p0) cc_final: 0.6143 (p0)
REVERT: A 1005 GLU cc_start: 0.7250 (tm-30) cc_final: 0.6841 (tm-30)
REVERT: A 1043 LYS cc_start: 0.7516 (ttpt) cc_final: 0.6977 (tppt)
REVERT: A 1076 ARG cc_start: 0.8795 (ptt90) cc_final: 0.7863 (tpp-160)
REVERT: A 1146 LEU cc_start: 0.6711 (tp) cc_final: 0.6358 (tp)
REVERT: A 1229 LYS cc_start: 0.8365 (tptt) cc_final: 0.8051 (mmmt)
REVERT: A 1251 LEU cc_start: 0.8933 (mm) cc_final: 0.8713 (mt)
REVERT: D   64 ASP cc_start: 0.8068 (m-30) cc_final: 0.7517 (t70)
REVERT: D  126 MET cc_start: 0.6518 (tpp) cc_final: 0.5967 (mmt)
REVERT: E   22 PHE cc_start: 0.7841 (t80) cc_final: 0.7547 (t80)
REVERT: E   69 LEU cc_start: 0.6024 (tp) cc_final: 0.5819 (tp)
REVERT: E   95 PHE cc_start: 0.7329 (m-10) cc_final: 0.6955 (m-10)
REVERT: F   21 GLN cc_start: 0.6612 (OUTLIER) cc_final: 0.5786 (pm20)
REVERT: F  151 GLU cc_start: 0.6545 (mm-30) cc_final: 0.6260 (tm-30)
REVERT: F  277 MET cc_start: 0.7930 (mpp) cc_final: 0.7697 (mpp)
REVERT: F  403 MET cc_start: 0.8748 (ppp) cc_final: 0.8379 (ppp)
REVERT: G   46 GLN cc_start: 0.8290 (mm-40) cc_final: 0.7804 (pp30)
  outliers start: 4
  outliers final: 0
  residues processed: 252
  average time/residue: 0.1447
  time to fit residues: 54.4642
Evaluate side-chains
  171 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 170
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 211
   random chunks:
   chunk 70 optimal weight:    5.9990
   chunk 179 optimal weight:    2.9990
   chunk 134 optimal weight:    8.9990
   chunk 94 optimal weight:    2.9990
   chunk 96 optimal weight:    5.9990
   chunk 171 optimal weight:    2.9990
   chunk 187 optimal weight:    0.9980
   chunk 66 optimal weight:    7.9990
   chunk 1 optimal weight:    7.9990
   chunk 62 optimal weight:    6.9990
   chunk 90 optimal weight:    0.9980
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1172 ASN
A1338 ASN
** E  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 127 HIS
E 146 ASN
E 213 HIS
** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 312 GLN
F 337 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.099088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.086886 restraints weight = 79793.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.089054 restraints weight = 52224.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.090581 restraints weight = 37642.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.091712 restraints weight = 28991.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.092457 restraints weight = 23452.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.4041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6716
moved from start:          0.4031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  17859  Z= 0.167
  Angle     :  0.782  19.347  24174  Z= 0.388
  Chirality :  0.049   0.241   2691
  Planarity :  0.006   0.074   3064
  Dihedral  :  6.859  51.151   2308
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 22.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.18 %
    Favored  : 89.82 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  4.20 %
    Favored  : 95.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.77 (0.17), residues: 2093
  helix: -0.60 (0.19), residues: 707
  sheet: -2.77 (0.35), residues: 186
  loop : -2.57 (0.17), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  50 
 TYR   0.019   0.002   TYR G   7 
 PHE   0.036   0.002   PHE F 464 
 TRP   0.015   0.002   TRP D   8 
 HIS   0.005   0.001   HIS A1463 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 (17855)
  covalent geometry    : angle       0.74525 (24162)
  hydrogen bonds       : bond        0.03847 (  537)
  hydrogen bonds       : angle       5.86977 ( 1530)
  metal coordination   : bond        0.00312 (    4)
  metal coordination   : angle      10.58991 (   12)

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

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

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 243
  time to evaluate  : 0.714 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLN cc_start: 0.7084 (mp-120) cc_final: 0.6809 (mp10)
REVERT: A   53 PHE cc_start: 0.5831 (m-80) cc_final: 0.5306 (m-80)
REVERT: A   84 ILE cc_start: 0.5488 (pt) cc_final: 0.5080 (pt)
REVERT: A  614 ASP cc_start: 0.7665 (m-30) cc_final: 0.7407 (m-30)
REVERT: A  740 MET cc_start: 0.6406 (mpp) cc_final: 0.6194 (mpp)
REVERT: A  911 ASP cc_start: 0.6294 (p0) cc_final: 0.5753 (p0)
REVERT: A 1005 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6775 (tm-30)
REVERT: A 1043 LYS cc_start: 0.7530 (ttpt) cc_final: 0.7087 (tppt)
REVERT: A 1062 LYS cc_start: 0.8775 (mptt) cc_final: 0.8472 (mptt)
REVERT: A 1064 MET cc_start: 0.8252 (ptt) cc_final: 0.7927 (ptm)
REVERT: A 1076 ARG cc_start: 0.9093 (ptt90) cc_final: 0.8771 (ttp-170)
REVERT: A 1146 LEU cc_start: 0.7183 (tp) cc_final: 0.6893 (tp)
REVERT: A 1251 LEU cc_start: 0.8920 (mm) cc_final: 0.8602 (mm)
REVERT: D   64 ASP cc_start: 0.7839 (m-30) cc_final: 0.7287 (t70)
REVERT: D  124 LEU cc_start: 0.9380 (tp) cc_final: 0.9175 (tp)
REVERT: D  126 MET cc_start: 0.6685 (tpp) cc_final: 0.6137 (mmt)
REVERT: E   16 TYR cc_start: 0.8053 (t80) cc_final: 0.7701 (t80)
REVERT: E   22 PHE cc_start: 0.8105 (t80) cc_final: 0.7900 (t80)
REVERT: E   66 LEU cc_start: 0.9235 (mt) cc_final: 0.8710 (pp)
REVERT: E  158 ARG cc_start: 0.5895 (mpt180) cc_final: 0.5389 (mmt-90)
REVERT: E  206 ASP cc_start: 0.7647 (m-30) cc_final: 0.7058 (m-30)
REVERT: F  403 MET cc_start: 0.8751 (ppp) cc_final: 0.8304 (ppp)
REVERT: G   46 GLN cc_start: 0.8365 (mm-40) cc_final: 0.7806 (pp30)
REVERT: G  107 LEU cc_start: 0.8495 (tp) cc_final: 0.8121 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 244
  average time/residue: 0.1402
  time to fit residues: 51.6035
Evaluate side-chains
  172 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 211
   random chunks:
   chunk 183 optimal weight:    2.9990
   chunk 9 optimal weight:    8.9990
   chunk 132 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   chunk 84 optimal weight:   20.0000
   chunk 73 optimal weight:    0.7980
   chunk 117 optimal weight:    9.9990
   chunk 162 optimal weight:    3.9990
   chunk 196 optimal weight:    1.9990
   chunk 186 optimal weight:    6.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 239 GLN
** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1172 ASN
A1338 ASN
** E  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 213 HIS
** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 434 HIS ** 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 = 0.4165 r_free = 0.4165 target = 0.098309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.086839 restraints weight = 79140.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.088800 restraints weight = 52910.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.090220 restraints weight = 38704.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.091229 restraints weight = 30013.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.091987 restraints weight = 24500.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.4035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6653
moved from start:          0.4352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  17859  Z= 0.174
  Angle     :  0.778  18.800  24174  Z= 0.388
  Chirality :  0.049   0.229   2691
  Planarity :  0.006   0.071   3064
  Dihedral  :  6.741  48.073   2308
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 22.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.37 %
    Favored  : 88.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.68 (0.18), residues: 2093
  helix: -0.51 (0.19), residues: 717
  sheet: -2.79 (0.33), residues: 199
  loop : -2.51 (0.17), residues: 1177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  50 
 TYR   0.018   0.002   TYR D  16 
 PHE   0.034   0.002   PHE F 464 
 TRP   0.025   0.002   TRP A1134 
 HIS   0.006   0.001   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 (17855)
  covalent geometry    : angle       0.74319 (24162)
  hydrogen bonds       : bond        0.03802 (  537)
  hydrogen bonds       : angle       5.81407 ( 1530)
  metal coordination   : bond        0.00442 (    4)
  metal coordination   : angle      10.40643 (   12)

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

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

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 0.685 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 PHE cc_start: 0.5747 (m-80) cc_final: 0.5257 (m-80)
REVERT: A   84 ILE cc_start: 0.5797 (pt) cc_final: 0.5406 (pt)
REVERT: A  355 LYS cc_start: 0.8284 (mtpt) cc_final: 0.7969 (ttpp)
REVERT: A  614 ASP cc_start: 0.7413 (m-30) cc_final: 0.7177 (m-30)
REVERT: A  863 ASN cc_start: 0.9038 (t0) cc_final: 0.8837 (t0)
REVERT: A  903 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7040 (mt-10)
REVERT: A  911 ASP cc_start: 0.6407 (p0) cc_final: 0.5835 (p0)
REVERT: A 1005 GLU cc_start: 0.7238 (tm-30) cc_final: 0.6898 (tm-30)
REVERT: A 1043 LYS cc_start: 0.7462 (ttpt) cc_final: 0.6975 (tppt)
REVERT: A 1062 LYS cc_start: 0.8798 (mptt) cc_final: 0.8440 (mptt)
REVERT: A 1080 ASN cc_start: 0.8389 (p0) cc_final: 0.7328 (p0)
REVERT: A 1229 LYS cc_start: 0.8315 (tptt) cc_final: 0.8051 (mmmt)
REVERT: A 1251 LEU cc_start: 0.8793 (mm) cc_final: 0.8360 (mm)
REVERT: D  126 MET cc_start: 0.6496 (tpp) cc_final: 0.6037 (mmt)
REVERT: E   16 TYR cc_start: 0.7878 (t80) cc_final: 0.7421 (t80)
REVERT: E   34 TYR cc_start: 0.6686 (m-80) cc_final: 0.6295 (m-10)
REVERT: E   66 LEU cc_start: 0.9234 (mt) cc_final: 0.8784 (pp)
REVERT: E  158 ARG cc_start: 0.5770 (mpt180) cc_final: 0.5327 (mmt-90)
REVERT: E  206 ASP cc_start: 0.7690 (m-30) cc_final: 0.7128 (m-30)
REVERT: F  403 MET cc_start: 0.8582 (ppp) cc_final: 0.8113 (ppp)
REVERT: G   46 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7689 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 230
  average time/residue: 0.1393
  time to fit residues: 48.7599
Evaluate side-chains
  179 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 211
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 50 optimal weight:    7.9990
   chunk 15 optimal weight:    4.9990
   chunk 191 optimal weight:    0.8980
   chunk 137 optimal weight:    0.9980
   chunk 97 optimal weight:    6.9990
   chunk 135 optimal weight:    0.8980
   chunk 33 optimal weight:    9.9990
   chunk 24 optimal weight:    8.9990
   chunk 104 optimal weight:   10.0000
   chunk 180 optimal weight:    7.9990
   overall best weight:    1.7382

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

Flipped N/Q/H residues before XYZ refinement:
** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1172 ASN
A1338 ASN
** E  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  49 ASN
E 213 HIS
** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 434 HIS ** 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 = 0.4181 r_free = 0.4181 target = 0.099105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.086901 restraints weight = 80775.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.089067 restraints weight = 52740.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.090582 restraints weight = 37967.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.091689 restraints weight = 29277.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.092481 restraints weight = 23695.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.4042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6708
moved from start:          0.4498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  17859  Z= 0.153
  Angle     :  0.761  18.121  24174  Z= 0.380
  Chirality :  0.048   0.177   2691
  Planarity :  0.005   0.066   3064
  Dihedral  :  6.639  45.649   2308
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 21.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.65 %
    Favored  : 89.35 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  2.07 %
    Favored  : 97.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.66 (0.17), residues: 2093
  helix: -0.53 (0.18), residues: 708
  sheet: -2.60 (0.34), residues: 192
  loop : -2.49 (0.17), residues: 1193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 237 
 TYR   0.018   0.002   TYR A1346 
 PHE   0.034   0.002   PHE F 464 
 TRP   0.035   0.002   TRP A 394 
 HIS   0.005   0.001   HIS E  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (17855)
  covalent geometry    : angle       0.72715 (24162)
  hydrogen bonds       : bond        0.03631 (  537)
  hydrogen bonds       : angle       5.75817 ( 1530)
  metal coordination   : bond        0.00339 (    4)
  metal coordination   : angle      10.03880 (   12)

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

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

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 239
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 PHE cc_start: 0.5821 (m-80) cc_final: 0.5312 (m-80)
REVERT: A   84 ILE cc_start: 0.5870 (pt) cc_final: 0.5495 (pt)
REVERT: A  614 ASP cc_start: 0.7647 (m-30) cc_final: 0.7397 (m-30)
REVERT: A  863 ASN cc_start: 0.9158 (t0) cc_final: 0.8945 (t0)
REVERT: A  903 GLU cc_start: 0.7817 (mt-10) cc_final: 0.6951 (mt-10)
REVERT: A 1043 LYS cc_start: 0.7513 (ttpt) cc_final: 0.7033 (tppt)
REVERT: A 1062 LYS cc_start: 0.8808 (mptt) cc_final: 0.8452 (mptt)
REVERT: A 1080 ASN cc_start: 0.8255 (p0) cc_final: 0.7277 (p0)
REVERT: A 1147 PHE cc_start: 0.7002 (m-80) cc_final: 0.6786 (m-80)
REVERT: A 1186 HIS cc_start: 0.6517 (m-70) cc_final: 0.6292 (m90)
REVERT: A 1229 LYS cc_start: 0.8459 (tptt) cc_final: 0.8146 (mmmt)
REVERT: A 1251 LEU cc_start: 0.8806 (mm) cc_final: 0.8403 (mm)
REVERT: D   64 ASP cc_start: 0.7994 (m-30) cc_final: 0.7274 (t70)
REVERT: D  124 LEU cc_start: 0.9339 (tp) cc_final: 0.9119 (tp)
REVERT: D  126 MET cc_start: 0.6594 (tpp) cc_final: 0.6130 (mmt)
REVERT: E   16 TYR cc_start: 0.7974 (t80) cc_final: 0.7488 (t80)
REVERT: E   34 TYR cc_start: 0.6744 (m-80) cc_final: 0.6169 (m-80)
REVERT: E   66 LEU cc_start: 0.9142 (mt) cc_final: 0.8696 (pp)
REVERT: E  158 ARG cc_start: 0.5950 (mpt180) cc_final: 0.5579 (mmt-90)
REVERT: E  206 ASP cc_start: 0.7871 (m-30) cc_final: 0.7315 (m-30)
REVERT: F  403 MET cc_start: 0.8688 (ppp) cc_final: 0.8277 (ppp)
REVERT: G   46 GLN cc_start: 0.8247 (mm-40) cc_final: 0.7763 (pp30)
REVERT: G   69 HIS cc_start: 0.7433 (m-70) cc_final: 0.6830 (m170)
  outliers start: 1
  outliers final: 0
  residues processed: 239
  average time/residue: 0.1402
  time to fit residues: 50.9670
Evaluate side-chains
  175 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 211
   random chunks:
   chunk 169 optimal weight:    5.9990
   chunk 45 optimal weight:    0.0050
   chunk 205 optimal weight:    0.7980
   chunk 167 optimal weight:   20.0000
   chunk 140 optimal weight:    2.9990
   chunk 110 optimal weight:    0.0870
   chunk 208 optimal weight:   10.0000
   chunk 130 optimal weight:   10.0000
   chunk 42 optimal weight:    8.9990
   chunk 49 optimal weight:    9.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    1.3776

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

Flipped N/Q/H residues before XYZ refinement:
** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1172 ASN
A1338 ASN
** E  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 213 HIS
** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 199 ASN
** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 312 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.099771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.087886 restraints weight = 79104.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.089990 restraints weight = 52308.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.091494 restraints weight = 37703.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.092515 restraints weight = 29005.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.093309 restraints weight = 23691.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.4066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6619
moved from start:          0.4582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  17859  Z= 0.142
  Angle     :  0.762  17.796  24174  Z= 0.379
  Chirality :  0.049   0.190   2691
  Planarity :  0.005   0.093   3064
  Dihedral  :  6.493  39.286   2308
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 20.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.04 %
    Favored  : 88.96 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  1.87 %
    Favored  : 98.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.61 (0.17), residues: 2093
  helix: -0.51 (0.19), residues: 708
  sheet: -2.58 (0.35), residues: 192
  loop : -2.45 (0.17), residues: 1193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F 237 
 TYR   0.025   0.002   TYR D  91 
 PHE   0.034   0.001   PHE F 464 
 TRP   0.026   0.002   TRP A 394 
 HIS   0.004   0.001   HIS A1463 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (17855)
  covalent geometry    : angle       0.73163 (24162)
  hydrogen bonds       : bond        0.03589 (  537)
  hydrogen bonds       : angle       5.68096 ( 1530)
  metal coordination   : bond        0.00277 (    4)
  metal coordination   : angle       9.55208 (   12)

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

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

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 239
  time to evaluate  : 0.651 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 ILE cc_start: 0.5203 (pt) cc_final: 0.4822 (pt)
REVERT: A  373 PHE cc_start: 0.7199 (t80) cc_final: 0.6899 (t80)
REVERT: A  593 TYR cc_start: 0.7729 (p90) cc_final: 0.7313 (p90)
REVERT: A  614 ASP cc_start: 0.7503 (m-30) cc_final: 0.7272 (m-30)
REVERT: A  863 ASN cc_start: 0.9128 (t0) cc_final: 0.8902 (t0)
REVERT: A  903 GLU cc_start: 0.7698 (mt-10) cc_final: 0.6878 (mt-10)
REVERT: A 1043 LYS cc_start: 0.7494 (ttpt) cc_final: 0.6998 (tppt)
REVERT: A 1064 MET cc_start: 0.7899 (ptt) cc_final: 0.7602 (ptm)
REVERT: A 1076 ARG cc_start: 0.9005 (ptt-90) cc_final: 0.8725 (ptt-90)
REVERT: A 1080 ASN cc_start: 0.8235 (p0) cc_final: 0.7142 (p0)
REVERT: A 1142 ASP cc_start: 0.7773 (t0) cc_final: 0.7478 (t0)
REVERT: A 1147 PHE cc_start: 0.6907 (m-80) cc_final: 0.6500 (m-80)
REVERT: A 1186 HIS cc_start: 0.6405 (m-70) cc_final: 0.6181 (m90)
REVERT: A 1234 CYS cc_start: 0.8649 (t) cc_final: 0.7835 (m)
REVERT: A 1251 LEU cc_start: 0.8833 (mm) cc_final: 0.8452 (mm)
REVERT: A 1324 ARG cc_start: 0.8002 (tpt-90) cc_final: 0.7721 (tpt-90)
REVERT: D  124 LEU cc_start: 0.9310 (tp) cc_final: 0.9078 (tp)
REVERT: D  126 MET cc_start: 0.6553 (tpp) cc_final: 0.6131 (mmt)
REVERT: E   16 TYR cc_start: 0.7798 (t80) cc_final: 0.7438 (t80)
REVERT: E   66 LEU cc_start: 0.9030 (mt) cc_final: 0.8626 (pp)
REVERT: E  158 ARG cc_start: 0.5605 (mpt180) cc_final: 0.4075 (mmt-90)
REVERT: E  206 ASP cc_start: 0.7834 (m-30) cc_final: 0.7295 (m-30)
REVERT: F  403 MET cc_start: 0.8607 (ppp) cc_final: 0.8176 (ppp)
REVERT: G   46 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7608 (pp30)
  outliers start: 1
  outliers final: 0
  residues processed: 240
  average time/residue: 0.1401
  time to fit residues: 51.2079
Evaluate side-chains
  176 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 211
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 62 optimal weight:   10.0000
   chunk 161 optimal weight:    7.9990
   chunk 133 optimal weight:    0.0060
   chunk 78 optimal weight:    9.9990
   chunk 152 optimal weight:    9.9990
   chunk 86 optimal weight:   10.0000
   chunk 30 optimal weight:    5.9990
   chunk 174 optimal weight:    7.9990
   chunk 80 optimal weight:    8.9990
   chunk 200 optimal weight:    4.9990
   overall best weight:    4.8004

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

Flipped N/Q/H residues before XYZ refinement:
** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 732 HIS
** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  49 ASN
E 213 HIS
** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  69 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.094087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.082394 restraints weight = 80804.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.084359 restraints weight = 54042.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.085764 restraints weight = 39474.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.086782 restraints weight = 30831.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.087539 restraints weight = 25289.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6854
moved from start:          0.5386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.078  17859  Z= 0.284
  Angle     :  0.936  20.011  24174  Z= 0.473
  Chirality :  0.054   0.355   2691
  Planarity :  0.007   0.093   3064
  Dihedral  :  7.206  40.333   2308
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 31.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.61 %
    Favored  : 87.39 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  1.16 %
    Favored  : 98.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.02 (0.17), residues: 2093
  helix: -0.99 (0.18), residues: 720
  sheet: -2.80 (0.34), residues: 201
  loop : -2.61 (0.17), residues: 1172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG D  74 
 TYR   0.036   0.003   TYR D  91 
 PHE   0.052   0.003   PHE F 464 
 TRP   0.026   0.003   TRP A 394 
 HIS   0.014   0.002   HIS A1186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00624 (17855)
  covalent geometry    : angle       0.89596 (24162)
  hydrogen bonds       : bond        0.04439 (  537)
  hydrogen bonds       : angle       6.34843 ( 1530)
  metal coordination   : bond        0.00935 (    4)
  metal coordination   : angle      12.13447 (   12)

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

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

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 221
  time to evaluate  : 0.563 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 ILE cc_start: 0.5537 (pt) cc_final: 0.5188 (pt)
REVERT: A  355 LYS cc_start: 0.8331 (mtpt) cc_final: 0.8106 (ttpp)
REVERT: A  373 PHE cc_start: 0.7772 (t80) cc_final: 0.7388 (t80)
REVERT: A  711 TYR cc_start: 0.6101 (t80) cc_final: 0.5746 (t80)
REVERT: A  863 ASN cc_start: 0.9194 (t0) cc_final: 0.8966 (t0)
REVERT: A  903 GLU cc_start: 0.7335 (mt-10) cc_final: 0.6555 (mt-10)
REVERT: A 1043 LYS cc_start: 0.7554 (ttpt) cc_final: 0.6961 (tppt)
REVERT: A 1062 LYS cc_start: 0.8939 (mptt) cc_final: 0.8643 (mptt)
REVERT: A 1064 MET cc_start: 0.8079 (ptt) cc_final: 0.7787 (ptm)
REVERT: A 1076 ARG cc_start: 0.8987 (ptt-90) cc_final: 0.8661 (ptt-90)
REVERT: A 1173 ASN cc_start: 0.8557 (t0) cc_final: 0.8015 (m110)
REVERT: A 1229 LYS cc_start: 0.8448 (tptt) cc_final: 0.8095 (mmmt)
REVERT: A 1234 CYS cc_start: 0.8744 (t) cc_final: 0.7995 (m)
REVERT: A 1250 TYR cc_start: 0.7986 (t80) cc_final: 0.7319 (t80)
REVERT: A 1251 LEU cc_start: 0.8938 (mm) cc_final: 0.8457 (mm)
REVERT: A 1324 ARG cc_start: 0.7995 (tpt-90) cc_final: 0.7595 (tpt-90)
REVERT: A 1326 ARG cc_start: 0.7757 (mmt90) cc_final: 0.7241 (mmt-90)
REVERT: D  124 LEU cc_start: 0.9299 (tp) cc_final: 0.9050 (tp)
REVERT: D  126 MET cc_start: 0.6858 (tpp) cc_final: 0.6506 (mmt)
REVERT: E  158 ARG cc_start: 0.6582 (mpt180) cc_final: 0.6133 (mmt-90)
REVERT: E  159 ASN cc_start: 0.7613 (t0) cc_final: 0.7394 (t0)
REVERT: E  203 VAL cc_start: 0.6577 (t) cc_final: 0.6359 (t)
REVERT: E  206 ASP cc_start: 0.7644 (m-30) cc_final: 0.7164 (m-30)
REVERT: F  403 MET cc_start: 0.8602 (ppp) cc_final: 0.8293 (ppp)
REVERT: G   46 GLN cc_start: 0.8427 (mm-40) cc_final: 0.7831 (pp30)
REVERT: G  107 LEU cc_start: 0.8856 (tp) cc_final: 0.8628 (tt)
  outliers start: 1
  outliers final: 0
  residues processed: 222
  average time/residue: 0.1362
  time to fit residues: 46.1833
Evaluate side-chains
  163 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 211
   random chunks:
   chunk 127 optimal weight:    0.9990
   chunk 73 optimal weight:    3.9990
   chunk 83 optimal weight:   10.0000
   chunk 175 optimal weight:    0.8980
   chunk 140 optimal weight:    4.9990
   chunk 9 optimal weight:    6.9990
   chunk 7 optimal weight:   10.0000
   chunk 19 optimal weight:    6.9990
   chunk 75 optimal weight:    0.9980
   chunk 111 optimal weight:    4.9990
   chunk 129 optimal weight:    0.2980
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 337 HIS
** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1371 GLN
E  18 ASN
E  38 GLN
E  49 ASN
E 213 HIS
F  99 ASN
** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 224 ASN
** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 312 GLN
** F 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  69 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.096879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.085311 restraints weight = 78825.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.087345 restraints weight = 51779.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.088792 restraints weight = 37382.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.089838 restraints weight = 28853.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.090595 restraints weight = 23438.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.4028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6681
moved from start:          0.5256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  17859  Z= 0.160
  Angle     :  0.824  22.392  24174  Z= 0.408
  Chirality :  0.050   0.223   2691
  Planarity :  0.006   0.085   3064
  Dihedral  :  6.858  38.732   2308
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 23.42
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  : 11.08 %
    Favored  : 88.87 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.46 %
    Favored  : 99.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.88 (0.17), residues: 2093
  helix: -0.81 (0.18), residues: 710
  sheet: -2.71 (0.34), residues: 195
  loop : -2.56 (0.17), residues: 1188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG F  75 
 TYR   0.024   0.002   TYR D  16 
 PHE   0.039   0.002   PHE F 464 
 TRP   0.034   0.003   TRP F  76 
 HIS   0.008   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (17855)
  covalent geometry    : angle       0.78215 (24162)
  hydrogen bonds       : bond        0.03885 (  537)
  hydrogen bonds       : angle       6.03936 ( 1530)
  metal coordination   : bond        0.00319 (    4)
  metal coordination   : angle      11.69031 (   12)

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

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

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4186 Ramachandran restraints generated.
    2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 232
  time to evaluate  : 0.635 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 ILE cc_start: 0.5741 (pt) cc_final: 0.5345 (pt)
REVERT: A  355 LYS cc_start: 0.8245 (mtpt) cc_final: 0.7969 (ttpp)
REVERT: A  373 PHE cc_start: 0.7680 (t80) cc_final: 0.7309 (t80)
REVERT: A  711 TYR cc_start: 0.5570 (t80) cc_final: 0.5224 (t80)
REVERT: A  863 ASN cc_start: 0.9098 (t0) cc_final: 0.8840 (t0)
REVERT: A  903 GLU cc_start: 0.7663 (mt-10) cc_final: 0.6700 (mt-10)
REVERT: A 1043 LYS cc_start: 0.7366 (ttpt) cc_final: 0.6882 (tppt)
REVERT: A 1062 LYS cc_start: 0.8890 (mptt) cc_final: 0.8550 (mptt)
REVERT: A 1064 MET cc_start: 0.7823 (ptt) cc_final: 0.7583 (ptm)
REVERT: A 1080 ASN cc_start: 0.8035 (p0) cc_final: 0.7099 (p0)
REVERT: A 1229 LYS cc_start: 0.8399 (tptt) cc_final: 0.8104 (mmmt)
REVERT: A 1234 CYS cc_start: 0.8544 (t) cc_final: 0.7812 (m)
REVERT: A 1251 LEU cc_start: 0.8953 (mm) cc_final: 0.8747 (mm)
REVERT: A 1324 ARG cc_start: 0.7956 (tpt-90) cc_final: 0.7640 (tpt-90)
REVERT: A 1326 ARG cc_start: 0.7578 (mmt90) cc_final: 0.7098 (mmt-90)
REVERT: D  124 LEU cc_start: 0.9239 (tp) cc_final: 0.8909 (tp)
REVERT: D  126 MET cc_start: 0.6664 (tpp) cc_final: 0.6247 (mmt)
REVERT: E    3 ARG cc_start: 0.7827 (tmm160) cc_final: 0.7500 (ttp80)
REVERT: E   22 PHE cc_start: 0.7598 (t80) cc_final: 0.7367 (t80)
REVERT: E   66 LEU cc_start: 0.9177 (mt) cc_final: 0.8635 (pp)
REVERT: E  158 ARG cc_start: 0.6063 (mpt180) cc_final: 0.5848 (mmt-90)
REVERT: E  159 ASN cc_start: 0.7321 (t0) cc_final: 0.7080 (t0)
REVERT: E  203 VAL cc_start: 0.6540 (t) cc_final: 0.6336 (t)
REVERT: E  206 ASP cc_start: 0.7415 (m-30) cc_final: 0.6929 (m-30)
REVERT: F  277 MET cc_start: 0.7325 (mtm) cc_final: 0.7077 (mpp)
REVERT: F  403 MET cc_start: 0.8532 (ppp) cc_final: 0.8099 (ppp)
REVERT: G   46 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7604 (pp30)
REVERT: G  107 LEU cc_start: 0.8533 (tp) cc_final: 0.8315 (tt)
  outliers start: 4
  outliers final: 0
  residues processed: 234
  average time/residue: 0.1374
  time to fit residues: 49.6874
Evaluate side-chains
  172 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 211
   random chunks:
   chunk 118 optimal weight:    5.9990
   chunk 83 optimal weight:    7.9990
   chunk 52 optimal weight:    0.9990
   chunk 43 optimal weight:    8.9990
   chunk 86 optimal weight:    8.9990
   chunk 101 optimal weight:    0.8980
   chunk 19 optimal weight:   10.0000
   chunk 205 optimal weight:   10.0000
   chunk 66 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 337 HIS
A 369 ASN
** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1371 GLN
E  38 GLN
E  49 ASN
E 100 HIS
E 213 HIS
** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 312 GLN
** F 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.099139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.087570 restraints weight = 79476.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.089614 restraints weight = 52360.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.091051 restraints weight = 37799.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.092109 restraints weight = 29171.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.092906 restraints weight = 23654.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.4051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6615
moved from start:          0.5225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  17859  Z= 0.144
  Angle     :  0.786  19.380  24174  Z= 0.389
  Chirality :  0.049   0.193   2691
  Planarity :  0.005   0.082   3064
  Dihedral  :  6.594  33.919   2308
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 21.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.47 %
    Favored  : 88.53 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.35 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.77 (0.17), residues: 2093
  helix: -0.70 (0.18), residues: 708
  sheet: -2.76 (0.34), residues: 194
  loop : -2.48 (0.17), residues: 1191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG F  75 
 TYR   0.056   0.002   TYR D  91 
 PHE   0.033   0.002   PHE F 464 
 TRP   0.034   0.002   TRP F  76 
 HIS   0.007   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (17855)
  covalent geometry    : angle       0.75398 (24162)
  hydrogen bonds       : bond        0.03728 (  537)
  hydrogen bonds       : angle       5.83938 ( 1530)
  metal coordination   : bond        0.00219 (    4)
  metal coordination   : angle       9.94893 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2608.86 seconds
wall clock time: 46 minutes 34.23 seconds (2794.23 seconds total)