Starting phenix.real_space_refine
on Thu Mar  5 01:29:05 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6v85_21095/03_2026/6v85_21095.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6v85_21095/03_2026/6v85_21095.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.38
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6v85_21095/03_2026/6v85_21095.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6v85_21095/03_2026/6v85_21095.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6v85_21095/03_2026/6v85_21095.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6v85_21095/03_2026/6v85_21095.map"
  }
  resolution = 4.38
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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
     Zn      2      6.06       5
     S      97      5.16       5
     C   11421      2.51       5
     N    3050      2.21       5
     O    3308      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s

  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: 17878
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 15200
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1901, 15200
          Classifications: {'peptide': 1901}
          Link IDs: {'PTRANS': 84, 'TRANS': 1816}
          Chain breaks: 28
    Chain: "F"
      Number of atoms: 374
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 374
          Classifications: {'peptide': 47}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 45}
    Chain: "B"
      Number of atoms: 569
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 72, 545
          Classifications: {'peptide': 72}
          Link IDs: {'TRANS': 71}
      Conformer: "B"
        Number of residues, atoms: 72, 545
          Classifications: {'peptide': 72}
          Link IDs: {'TRANS': 71}
          bond proxies already assigned to first conformer: 517
    Chain: "C"
      Number of atoms: 582
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 74, 559
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 1, 'TRANS': 72}
      Conformer: "B"
        Number of residues, atoms: 74, 559
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 1, 'TRANS': 72}
          bond proxies already assigned to first conformer: 532
    Chain: "D"
      Number of atoms: 569
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 72, 545
          Classifications: {'peptide': 72}
          Link IDs: {'TRANS': 71}
      Conformer: "B"
        Number of residues, atoms: 72, 545
          Classifications: {'peptide': 72}
          Link IDs: {'TRANS': 71}
          bond proxies already assigned to first conformer: 517
    Chain: "E"
      Number of atoms: 582
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 74, 559
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 1, 'TRANS': 72}
      Conformer: "B"
        Number of residues, atoms: 74, 559
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 1, 'TRANS': 72}
          bond proxies already assigned to first conformer: 532
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   8264  SG  CYS A1136     113.479  58.500 106.151  1.00 75.09           S
  ATOM  10033  SG  CYS A1373     114.339  55.329 104.362  1.00105.67           S

  Residues with excluded nonbonded symmetry interactions: 10
    residue:
      pdb=" N  ASER B 211 " occ=0.48
      ... (10 atoms not shown)
      pdb=" OG BSER B 211 " occ=0.52
    residue:
      pdb=" N   GLU B 221 " occ=0.84
      ... (7 atoms not shown)
      pdb=" OE2 GLU B 221 " occ=0.84
    residue:
      pdb=" N  AASN B 228 " occ=0.42
      ... (14 atoms not shown)
      pdb=" ND2BASN B 228 " occ=0.58
    residue:
      pdb=" N  AASN C 220 " occ=0.37
      ... (14 atoms not shown)
      pdb=" ND2BASN C 220 " occ=0.63
    residue:
      pdb=" N  ASER C 231 " occ=0.60
      ... (10 atoms not shown)
      pdb=" OG BSER C 231 " occ=0.40
    residue:
      pdb=" N  ASER D 211 " occ=0.48
      ... (10 atoms not shown)
      pdb=" OG BSER D 211 " occ=0.52
    residue:
      pdb=" N   GLU D 221 " occ=0.84
      ... (7 atoms not shown)
      pdb=" OE2 GLU D 221 " occ=0.84
    residue:
      pdb=" N  AASN D 228 " occ=0.42
      ... (14 atoms not shown)
      pdb=" ND2BASN D 228 " occ=0.58
    residue:
      pdb=" N  AASN E 220 " occ=0.37
      ... (14 atoms not shown)
      pdb=" ND2BASN E 220 " occ=0.63
    residue:
      pdb=" N  ASER E 231 " occ=0.60
      ... (10 atoms not shown)
      pdb=" OG BSER E 231 " occ=0.40
  Time building chain proxies: 3.63, per 1000 atoms: 0.20
  Number of scatterers: 17878
  At special positions: 0
  Unit cell: (184.8, 143.36, 140, 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)
     Zn      2     29.99
     S      97     16.00
     O    3308      8.00
     N    3050      7.00
     C   11421      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: 1.30
  Conformation dependent library (CDL) restraints added in 826.8 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A3001 "
        pdb="ZN    ZN A3001 " - pdb=" NE2 HIS A1368 "
      pdb="  ZN A3002 "
        pdb="ZN    ZN A3002 " - pdb=" SG  CYS A1136 "
        pdb="ZN    ZN A3002 " - pdb=" SG  CYS A1373 "


  4408 Ramachandran restraints generated.
    2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4294

  Finding SS restraints...
    Secondary structure from input PDB file:
      94 helices and 7 sheets defined
      62.7% alpha, 2.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 30
      removed outlier: 3.658A  pdb=" N   TYR A  24 " --> pdb=" O   LYS A  20 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   GLY A  30 " --> pdb=" O   TYR A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 54
    Processing helix  chain 'A' and resid 58 through 74
    Processing helix  chain 'A' and resid 93 through 98
    Processing helix  chain 'A' and resid 107 through 140
      removed outlier: 3.668A  pdb=" N   LYS A 111 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
      removed outlier: 5.325A  pdb=" N   ALA A 126 " --> pdb=" O   SER A 122 " (cutoff:3.500A)
      removed outlier: 5.342A  pdb=" N   GLY A 127 " --> pdb=" O   VAL A 123 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   THR A 128 " --> pdb=" O   ILE A 124 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   SER A 129 " --> pdb=" O   ASN A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 169
    Processing helix  chain 'A' and resid 174 through 197
    Processing helix  chain 'A' and resid 235 through 257
      removed outlier: 3.590A  pdb=" N   VAL A 257 " --> pdb=" O   SER A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 283
      removed outlier: 3.969A  pdb=" N   LYS A 265 " --> pdb=" O   LEU A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 302
      removed outlier: 4.061A  pdb=" N   ASN A 288 " --> pdb=" O   ASP A 284 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   SER A 295 " --> pdb=" O   ALA A 291 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   VAL A 297 " --> pdb=" O   LEU A 293 " (cutoff:3.500A)
      removed outlier: 4.695A  pdb=" N   TYR A 298 " --> pdb=" O   GLU A 294 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ALA A 299 " --> pdb=" O   SER A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 328
      removed outlier: 3.982A  pdb=" N   ALA A 316 " --> pdb=" O   GLY A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 346
    Processing helix  chain 'A' and resid 352 through 364
    Processing helix  chain 'A' and resid 372 through 383
      removed outlier: 3.791A  pdb=" N   ALA A 376 " --> pdb=" O   THR A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 415
    Processing helix  chain 'A' and resid 427 through 437
      removed outlier: 3.596A  pdb=" N   LEU A 431 " --> pdb=" O   ALA A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 448
      removed outlier: 3.944A  pdb=" N   LYS A 448 " --> pdb=" O   GLU A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 475
    Processing helix  chain 'A' and resid 485 through 490
    Processing helix  chain 'A' and resid 513 through 520
    Processing helix  chain 'A' and resid 527 through 534
      removed outlier: 3.515A  pdb=" N   GLN A 531 " --> pdb=" O   ASN A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 583
    Processing helix  chain 'A' and resid 584 through 587
    Processing helix  chain 'A' and resid 597 through 611
    Processing helix  chain 'A' and resid 665 through 671
      removed outlier: 3.664A  pdb=" N   GLN A 670 " --> pdb=" O   TYR A 667 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   TRP A 671 " --> pdb=" O   CYS A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 675
    Processing helix  chain 'A' and resid 676 through 687
    Processing helix  chain 'A' and resid 694 through 702
      removed outlier: 3.954A  pdb=" N   LEU A 698 " --> pdb=" O   GLU A 694 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ARG A 702 " --> pdb=" O   LEU A 698 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 743 through 761
      removed outlier: 4.143A  pdb=" N   TRP A 747 " --> pdb=" O   CYS A 743 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 788 through 815
    Processing helix  chain 'A' and resid 846 through 851
    Processing helix  chain 'A' and resid 863 through 881
      removed outlier: 3.667A  pdb=" N   ASN A 881 " --> pdb=" O   ARG A 877 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 884 through 905
      removed outlier: 3.502A  pdb=" N   CYS A 888 " --> pdb=" O   GLU A 884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 915 through 923
      removed outlier: 3.575A  pdb=" N   ASN A 923 " --> pdb=" O   GLU A 919 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 923 through 932
      removed outlier: 4.352A  pdb=" N   VAL A 927 " --> pdb=" O   ASN A 923 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 934 through 938
    Processing helix  chain 'A' and resid 945 through 950
    Processing helix  chain 'A' and resid 955 through 971
    Processing helix  chain 'A' and resid 976 through 983
    Processing helix  chain 'A' and resid 990 through 997
      removed outlier: 3.663A  pdb=" N   ASP A 997 " --> pdb=" O   THR A 993 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1008 through 1023
      removed outlier: 3.896A  pdb=" N   ALA A1012 " --> pdb=" O   PRO A1008 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1028 through 1034
    Processing helix  chain 'A' and resid 1035 through 1036
      No H-bonds generated for 'chain 'A' and resid 1035 through 1036'
    Processing helix  chain 'A' and resid 1037 through 1051
    Processing helix  chain 'A' and resid 1056 through 1067
    Processing helix  chain 'A' and resid 1067 through 1078
      removed outlier: 3.545A  pdb=" N   ARG A1071 " --> pdb=" O   THR A1067 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1082 through 1091
    Processing helix  chain 'A' and resid 1097 through 1105
    Processing helix  chain 'A' and resid 1105 through 1117
    Processing helix  chain 'A' and resid 1124 through 1132
      removed outlier: 3.659A  pdb=" N   LYS A1129 " --> pdb=" O   PRO A1125 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   THR A1132 " --> pdb=" O   LEU A1128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1136 through 1154
      Proline residue:  A1151  - end of helix
    Processing helix  chain 'A' and resid 1165 through 1170
    Processing helix  chain 'A' and resid 1237 through 1250
      removed outlier: 3.770A  pdb=" N   ALA A1241 " --> pdb=" O   SER A1237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1256 through 1271
    Processing helix  chain 'A' and resid 1333 through 1352
    Processing helix  chain 'A' and resid 1438 through 1452
    Processing helix  chain 'A' and resid 1485 through 1502
    Processing helix  chain 'A' and resid 1510 through 1523
      removed outlier: 3.776A  pdb=" N   ILE A1514 " --> pdb=" O   GLY A1510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1525 through 1537
      removed outlier: 4.448A  pdb=" N   ALA A1529 " --> pdb=" O   ILE A1525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1540 through 1549
      removed outlier: 3.834A  pdb=" N   ARG A1544 " --> pdb=" O   PRO A1540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1566 through 1586
      removed outlier: 4.009A  pdb=" N   VAL A1570 " --> pdb=" O   ILE A1566 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ASN A1586 " --> pdb=" O   ASN A1582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1605 through 1624
    Processing helix  chain 'A' and resid 1636 through 1649
    Processing helix  chain 'A' and resid 1650 through 1652
      No H-bonds generated for 'chain 'A' and resid 1650 through 1652'
    Processing helix  chain 'A' and resid 1658 through 1665
      removed outlier: 3.840A  pdb=" N   ASN A1662 " --> pdb=" O   GLU A1658 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   MET A1664 " --> pdb=" O   LEU A1660 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   TYR A1665 " --> pdb=" O   SER A1661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1678 through 1690
    Processing helix  chain 'A' and resid 1697 through 1701
    Processing helix  chain 'A' and resid 1768 through 1775
      removed outlier: 4.090A  pdb=" N   HIS A1771 " --> pdb=" O   ALA A1768 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   THR A1773 " --> pdb=" O   SER A1770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1783 through 1796
    Processing helix  chain 'A' and resid 1814 through 1822
      removed outlier: 4.138A  pdb=" N   ILE A1818 " --> pdb=" O   SER A1814 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   GLU A1819 " --> pdb=" O   MET A1815 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1848 through 1862
      removed outlier: 4.160A  pdb=" N   ILE A1852 " --> pdb=" O   PRO A1848 " (cutoff:3.500A)
      Proline residue:  A1856  - end of helix
      removed outlier: 4.497A  pdb=" N   ALA A1862 " --> pdb=" O   LYS A1858 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1890 through 1899
    Processing helix  chain 'A' and resid 1923 through 1935
    Processing helix  chain 'A' and resid 1952 through 1964
    Processing helix  chain 'A' and resid 2001 through 2012
    Processing helix  chain 'A' and resid 2021 through 2045
      removed outlier: 4.077A  pdb=" N   GLN A2025 " --> pdb=" O   GLU A2021 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2053 through 2061
      removed outlier: 3.929A  pdb=" N   ILE A2060 " --> pdb=" O   ASP A2056 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2083 through 2104
    Processing helix  chain 'A' and resid 2126 through 2144
    Processing helix  chain 'A' and resid 2145 through 2147
      No H-bonds generated for 'chain 'A' and resid 2145 through 2147'
    Processing helix  chain 'A' and resid 2149 through 2161
      removed outlier: 3.716A  pdb=" N   ARG A2153 " --> pdb=" O   PRO A2149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2170 through 2175
      removed outlier: 3.655A  pdb=" N   SER A2173 " --> pdb=" O   ILE A2170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2187 through 2191
    Processing helix  chain 'A' and resid 2194 through 2200
    Processing helix  chain 'A' and resid 2208 through 2226
      removed outlier: 3.554A  pdb=" N   HIS A2226 " --> pdb=" O   VAL A2222 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 347 through 358
    Processing helix  chain 'F' and resid 360 through 374
      removed outlier: 3.620A  pdb=" N   GLN F 373 " --> pdb=" O   LEU F 369 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 376 through 390
    Processing helix  chain 'B' and resid 201 through 204
    Processing helix  chain 'B' and resid 205 through 270
      removed outlier: 4.550A  pdb=" N   SER B 248 " --> pdb=" O   LEU B 244 " (cutoff:3.500A)
      removed outlier: 4.810A  pdb=" N   LEU B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   ILE B 250 " --> pdb=" O   SER B 246 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   GLN B 251 " --> pdb=" O   GLN B 247 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 201 through 271
      removed outlier: 3.513A  pdb=" N   LEU C 205 " --> pdb=" O   GLN C 201 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU C 208 " --> pdb=" O   ASP C 204 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ASN C 218 " --> pdb=" O   SER C 214 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   SER C 248 " --> pdb=" O   LEU C 244 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   LEU C 249 " --> pdb=" O   SER C 245 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   GLN C 251 " --> pdb=" O   GLN C 247 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 201 through 204
    Processing helix  chain 'D' and resid 205 through 270
      removed outlier: 4.551A  pdb=" N   SER D 248 " --> pdb=" O   LEU D 244 " (cutoff:3.500A)
      removed outlier: 4.808A  pdb=" N   LEU D 249 " --> pdb=" O   SER D 245 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ILE D 250 " --> pdb=" O   SER D 246 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   GLN D 251 " --> pdb=" O   GLN D 247 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 201 through 270
      removed outlier: 3.511A  pdb=" N   LEU E 205 " --> pdb=" O   GLN E 201 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ASN E 218 " --> pdb=" O   SER E 214 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   SER E 248 " --> pdb=" O   LEU E 244 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   LEU E 249 " --> pdb=" O   SER E 245 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   GLN E 251 " --> pdb=" O   GLN E 247 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 204 through 207
      removed outlier: 4.015A  pdb=" N   ILE A 214 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 765 through 771
      removed outlier: 3.799A  pdb=" N   ARG A 765 " --> pdb=" O   THR A 780 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   SER A 658 " --> pdb=" O   VAL A 779 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 704 through 705
    Processing sheet with id=AA4, first strand: chain 'A' and resid 829 through 832
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1173 through 1176
      removed outlier: 3.817A  pdb=" N   THR A1192 " --> pdb=" O   LEU A1367 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   TRP A1193 " --> pdb=" O   SER A1318 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   SER A1318 " --> pdb=" O   TRP A1193 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1593 through 1594
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1828 through 1829
      removed outlier: 7.207A  pdb=" N   LEU A1805 " --> pdb=" O   HIS A1909 " (cutoff:3.500A)
      removed outlier: 9.149A  pdb=" N   ASP A1911 " --> pdb=" O   LEU A1805 " (cutoff:3.500A)
      removed outlier: 6.135A  pdb=" N   VAL A1908 " --> pdb=" O   ILE A1945 " (cutoff:3.500A)
      removed outlier: 7.960A  pdb=" N   LYS A1947 " --> pdb=" O   VAL A1908 " (cutoff:3.500A)
      removed outlier: 7.320A  pdb=" N   VAL A1910 " --> pdb=" O   LYS A1947 " (cutoff:3.500A)

    1028 hydrogen bonds defined for protein.
    2986 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.99

  Time building geometry restraints manager: 1.78 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 5548
        1.34 -     1.46: 3121
        1.46 -     1.58: 9384
        1.58 -     1.70: 0
        1.70 -     1.82: 154
  Bond restraints: 18207
  Sorted by residual:
  bond pdb=" N   TRP A1738 "
       pdb=" CA  TRP A1738 "
    ideal  model  delta    sigma   weight residual
    1.457  1.503 -0.045 1.29e-02 6.01e+03 1.23e+01
  bond pdb=" N   ILE A1739 "
       pdb=" CA  ILE A1739 "
    ideal  model  delta    sigma   weight residual
    1.459  1.499 -0.040 1.25e-02 6.40e+03 1.00e+01
  bond pdb=" N   GLU A1134 "
       pdb=" CA  GLU A1134 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.29e-02 6.01e+03 9.55e+00
  bond pdb=" N   ILE A1740 "
       pdb=" CA  ILE A1740 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 1.25e-02 6.40e+03 9.53e+00
  bond pdb=" N   ILE A1970 "
       pdb=" CA  ILE A1970 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.24e-02 6.50e+03 9.13e+00
  ... (remaining 18202 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.18: 23828
        2.18 -     4.37: 755
        4.37 -     6.55: 87
        6.55 -     8.74: 18
        8.74 -    10.92: 3
  Bond angle restraints: 24691
  Sorted by residual:
  angle pdb=" C   CYS A1374 "
        pdb=" N   VAL A1375 "
        pdb=" CA  VAL A1375 "
      ideal   model   delta    sigma   weight residual
     122.97  129.97   -7.00 9.80e-01 1.04e+00 5.10e+01
  angle pdb=" O   VAL A1375 "
        pdb=" C   VAL A1375 "
        pdb=" N   ARG A1376 "
      ideal   model   delta    sigma   weight residual
     121.85  126.95   -5.10 7.60e-01 1.73e+00 4.51e+01
  angle pdb=" N   VAL A2045 "
        pdb=" CA  VAL A2045 "
        pdb=" C   VAL A2045 "
      ideal   model   delta    sigma   weight residual
     112.98  106.33    6.65 1.25e+00 6.40e-01 2.83e+01
  angle pdb=" N   VAL A1375 "
        pdb=" CA  VAL A1375 "
        pdb=" C   VAL A1375 "
      ideal   model   delta    sigma   weight residual
     111.48  106.53    4.95 9.40e-01 1.13e+00 2.77e+01
  angle pdb=" CA  ILE A1138 "
        pdb=" C   ILE A1138 "
        pdb=" O   ILE A1138 "
      ideal   model   delta    sigma   weight residual
     121.27  116.56    4.71 1.04e+00 9.25e-01 2.05e+01
  ... (remaining 24686 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 9862
       18.00 -    35.99: 1017
       35.99 -    53.99: 155
       53.99 -    71.99: 13
       71.99 -    89.99: 16
  Dihedral angle restraints: 11063
    sinusoidal: 4457
      harmonic: 6606
  Sorted by residual:
  dihedral pdb=" CA  LEU A1563 "
           pdb=" C   LEU A1563 "
           pdb=" N   ASP A1564 "
           pdb=" CA  ASP A1564 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.67  -29.33     0      5.00e+00 4.00e-02 3.44e+01
  dihedral pdb=" CA  TYR A 260 "
           pdb=" C   TYR A 260 "
           pdb=" N   LEU A 261 "
           pdb=" CA  LEU A 261 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.31  -24.69     0      5.00e+00 4.00e-02 2.44e+01
  dihedral pdb=" CA  LEU A2148 "
           pdb=" C   LEU A2148 "
           pdb=" N   PRO A2149 "
           pdb=" CA  PRO A2149 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.58   24.42     0      5.00e+00 4.00e-02 2.38e+01
  ... (remaining 11060 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 2554
       0.076 -    0.152: 320
       0.152 -    0.229: 27
       0.229 -    0.305: 6
       0.305 -    0.381: 3
  Chirality restraints: 2910
  Sorted by residual:
  chirality pdb=" CB  ILE A1740 "
            pdb=" CA  ILE A1740 "
            pdb=" CG1 ILE A1740 "
            pdb=" CG2 ILE A1740 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.26    0.38 2.00e-01 2.50e+01 3.63e+00
  chirality pdb=" CA  HIS A 415 "
            pdb=" N   HIS A 415 "
            pdb=" C   HIS A 415 "
            pdb=" CB  HIS A 415 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.90e+00
  chirality pdb=" CA  ASN A1743 "
            pdb=" N   ASN A1743 "
            pdb=" C   ASN A1743 "
            pdb=" CB  ASN A1743 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.77e+00
  ... (remaining 2907 not shown)

  Planarity restraints: 3105
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A1367 "    0.020 2.00e-02 2.50e+03   3.98e-02 1.58e+01
        pdb=" C   LEU A1367 "   -0.069 2.00e-02 2.50e+03
        pdb=" O   LEU A1367 "    0.026 2.00e-02 2.50e+03
        pdb=" N   HIS A1368 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A  98 "   -0.047 5.00e-02 4.00e+02   7.05e-02 7.95e+00
        pdb=" N   PRO A  99 "    0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO A  99 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A  99 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A1950 "   -0.023 2.00e-02 2.50e+03   1.70e-02 7.23e+00
        pdb=" CG  TRP A1950 "    0.047 2.00e-02 2.50e+03
        pdb=" CD1 TRP A1950 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TRP A1950 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A1950 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A1950 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP A1950 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A1950 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A1950 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A1950 "    0.000 2.00e-02 2.50e+03
  ... (remaining 3102 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 347
        2.64 -     3.21: 18676
        3.21 -     3.77: 27486
        3.77 -     4.34: 35375
        4.34 -     4.90: 55536
  Nonbonded interactions: 137420
  Sorted by model distance:
  nonbonded pdb=" O   ASN A1743 "
            pdb=" ND2 ASN A1743 "
     model   vdw
     2.077 3.120
  nonbonded pdb=" NE1 TRP A1193 "
            pdb=" OG  SER A1318 "
     model   vdw
     2.091 3.120
  nonbonded pdb=" O   MET A2006 "
            pdb=" OG1 THR A2009 "
     model   vdw
     2.117 3.040
  nonbonded pdb=" NZ  LYS A1765 "
            pdb=" O   ASN A1982 "
     model   vdw
     2.129 3.120
  nonbonded pdb=" OE2 GLU A 880 "
            pdb=" OG  SER A1307 "
     model   vdw
     2.140 3.040
  ... (remaining 137415 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and (resid 199 through 210 or resid 212 through 216 or resid 218 thro \ 
ugh 219 or resid 221 through 227 or resid 229 through 230 or resid 232 through 2 \ 
34 or resid 236 through 270))
  selection = (chain 'C' and (resid 199 through 210 or resid 212 through 216 or resid 218 thro \ 
ugh 219 or resid 221 through 227 or resid 229 through 230 or resid 232 through 2 \ 
34 or resid 236 through 270))
  selection = (chain 'D' and (resid 199 through 210 or resid 212 through 216 or resid 218 thro \ 
ugh 219 or resid 221 through 227 or resid 229 through 230 or resid 232 through 2 \ 
34 or resid 236 through 270))
  selection = (chain 'E' and (resid 199 through 210 or resid 212 through 216 or resid 218 thro \ 
ugh 219 or resid 221 through 227 or resid 229 through 230 or resid 232 through 2 \ 
34 or resid 236 through 270))
}

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=0.26 max=1.00 mean=0.99
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:             2.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     17.040
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.020
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7185
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.479  18210  Z= 0.331
  Angle     :  0.886  10.919  24691  Z= 0.522
  Chirality :  0.052   0.381   2910
  Planarity :  0.005   0.070   3105
  Dihedral  : 14.459  89.986   6769
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 22.21
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  : 13.54 %
    Favored  : 86.05 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  8.67 %
    Favored  : 90.89 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.59 (0.15), residues: 2204
  helix: -1.09 (0.12), residues: 1293
  sheet: -3.04 (0.48), residues: 88
  loop : -4.50 (0.17), residues: 823

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1974 
 TYR   0.021   0.002   TYR A1793 
 PHE   0.024   0.002   PHE A1311 
 TRP   0.047   0.002   TRP A1950 
 HIS   0.010   0.002   HIS A1368 

Details of bonding type rmsd
  covalent geometry    : bond        0.00576 (18207)
  covalent geometry    : angle       0.88567 (24691)
  hydrogen bonds       : bond        0.14294 ( 1028)
  hydrogen bonds       : angle       6.20233 ( 2986)
  metal coordination   : bond        0.30129 (    3)

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

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

  4408 Ramachandran restraints generated.
    2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4408 Ramachandran restraints generated.
    2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  311 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 302
  time to evaluate  : 0.720 
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   44 LEU cc_start: 0.8200 (pt) cc_final: 0.7786 (pp)
REVERT: A   55 GLU cc_start: 0.8996 (tp30) cc_final: 0.8370 (tp30)
REVERT: A  209 ARG cc_start: 0.8277 (tpt170) cc_final: 0.8004 (ttp80)
REVERT: A  236 GLU cc_start: 0.8648 (mp0) cc_final: 0.8201 (mp0)
REVERT: A  363 MET cc_start: 0.7372 (ttp) cc_final: 0.6939 (ttm)
REVERT: A  399 LEU cc_start: 0.9181 (tp) cc_final: 0.8979 (tp)
REVERT: A  421 LEU cc_start: 0.0360 (OUTLIER) cc_final: 0.0059 (tp)
REVERT: A  612 ILE cc_start: 0.7462 (tp) cc_final: 0.7214 (tp)
REVERT: A  689 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.7281 (p90)
REVERT: A  767 MET cc_start: 0.8127 (tpp) cc_final: 0.7860 (mmm)
REVERT: A  775 GLN cc_start: 0.7477 (pt0) cc_final: 0.7212 (pt0)
REVERT: A  830 PHE cc_start: 0.7962 (t80) cc_final: 0.7589 (t80)
REVERT: A  891 LEU cc_start: 0.9266 (tp) cc_final: 0.8919 (tt)
REVERT: A  947 ARG cc_start: 0.8047 (mtt180) cc_final: 0.7827 (mtt180)
REVERT: A 1111 LEU cc_start: 0.9259 (mt) cc_final: 0.8871 (mt)
REVERT: A 1828 TYR cc_start: 0.7735 (m-10) cc_final: 0.7257 (m-80)
REVERT: A 1920 GLN cc_start: 0.6449 (tt0) cc_final: 0.6074 (tt0)
REVERT: F  362 LYS cc_start: 0.8764 (mttt) cc_final: 0.8482 (ttmm)
REVERT: F  387 ILE cc_start: 0.8868 (mm) cc_final: 0.8646 (mm)
REVERT: C  218 ASN cc_start: 0.0665 (m-40) cc_final: 0.0099 (m110)
REVERT: C  233 MET cc_start: 0.6365 (mtp) cc_final: 0.5841 (mtm)
REVERT: C  247 GLN cc_start: 0.7851 (mm110) cc_final: 0.6966 (pp30)
REVERT: C  252 THR cc_start: 0.6561 (p) cc_final: 0.6001 (m)
REVERT: C  264 MET cc_start: 0.7478 (ttm) cc_final: 0.7066 (ttm)
REVERT: D  249 LEU cc_start: 0.7954 (mt) cc_final: 0.7669 (pp)
REVERT: D  270 MET cc_start: 0.5900 (mtt) cc_final: 0.5189 (tpt)
  outliers start: 9
  outliers final: 4
  residues processed: 309
  average time/residue: 0.1355
  time to fit residues: 63.5334
Evaluate side-chains
  211 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 205
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 216 optimal weight:    8.9990
   chunk 98 optimal weight:    4.9990
   chunk 194 optimal weight:   10.0000
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    3.9990
   chunk 200 optimal weight:    2.9990
   chunk 212 optimal weight:    4.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A  61 GLN
A 104 ASN
** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 315 HIS
A 368 HIS
A 403 HIS
A 436 ASN
A 531 GLN
A 583 HIS
A 591 ASN
A 774 ASN
A 849 ASN
A 870 ASN
A 925 HIS
A1107 ASN
A1272 ASN
A1289 ASN
A1339 GLN
** A1368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1688 ASN
A1850 GLN
A1898 ASN
A1920 GLN
A2025 GLN
** A2057 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2144 ASN
A2212 GLN
F 372 ASN
F 379 GLN
B 234 ASN
B 235 GLN
D 201 GLN

Total number of N/Q/H flips: 29

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.090658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.072997 restraints weight = 326358.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.076341 restraints weight = 162124.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.077479 restraints weight = 82368.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.078115 restraints weight = 57132.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.079087 restraints weight = 45959.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3420
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3420 r_free = 0.3420    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3421 r_free = 0.3421    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3421
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  18210  Z= 0.262
  Angle     :  0.828  10.838  24691  Z= 0.430
  Chirality :  0.047   0.340   2910
  Planarity :  0.006   0.082   3105
  Dihedral  :  6.440  85.206   2425
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 16.79
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  : 12.29 %
    Favored  : 87.66 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  7.13 %
    Favored  : 92.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -2.13 (0.17), residues: 2204
  helix:  0.24 (0.14), residues: 1308
  sheet: -2.65 (0.52), residues: 88
  loop : -4.21 (0.18), residues: 808

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E 232 
 TYR   0.020   0.002   TYR A1793 
 PHE   0.025   0.002   PHE A  69 
 TRP   0.067   0.002   TRP A1950 
 HIS   0.009   0.002   HIS A1539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00570 (18207)
  covalent geometry    : angle       0.82813 (24691)
  hydrogen bonds       : bond        0.06291 ( 1028)
  hydrogen bonds       : angle       5.09996 ( 2986)
  metal coordination   : bond        0.01258 (    3)

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

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

  4408 Ramachandran restraints generated.
    2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4408 Ramachandran restraints generated.
    2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 271
  time to evaluate  : 0.683 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 LEU cc_start: 0.8178 (pt) cc_final: 0.7827 (pp)
REVERT: A  209 ARG cc_start: 0.8479 (tpt170) cc_final: 0.8157 (ttp80)
REVERT: A  245 TYR cc_start: 0.8638 (m-10) cc_final: 0.8184 (m-80)
REVERT: A  777 ILE cc_start: 0.9170 (mp) cc_final: 0.8546 (mp)
REVERT: A  830 PHE cc_start: 0.7928 (t80) cc_final: 0.7593 (t80)
REVERT: A 1111 LEU cc_start: 0.9227 (mt) cc_final: 0.8872 (mt)
REVERT: A 1131 MET cc_start: 0.7298 (mmt) cc_final: 0.7050 (mmp)
REVERT: A 1249 TYR cc_start: 0.8167 (t80) cc_final: 0.7943 (t80)
REVERT: A 1520 MET cc_start: 0.8241 (mmm) cc_final: 0.7807 (tmm)
REVERT: A 1958 THR cc_start: 0.8744 (p) cc_final: 0.8543 (t)
REVERT: F  362 LYS cc_start: 0.8918 (mttt) cc_final: 0.8704 (ttmm)
REVERT: F  382 ASP cc_start: 0.8766 (m-30) cc_final: 0.8538 (m-30)
REVERT: F  387 ILE cc_start: 0.8967 (mm) cc_final: 0.8744 (mm)
REVERT: B  254 LYS cc_start: 0.8578 (tptt) cc_final: 0.7922 (tppp)
REVERT: C  233 MET cc_start: 0.6922 (mtp) cc_final: 0.6376 (mtt)
REVERT: C  247 GLN cc_start: 0.9055 (mm110) cc_final: 0.7727 (pp30)
REVERT: D  242 ARG cc_start: 0.7416 (ttt-90) cc_final: 0.7032 (ttt-90)
REVERT: D  246 SER cc_start: 0.8294 (t) cc_final: 0.7987 (p)
REVERT: D  249 LEU cc_start: 0.8000 (mt) cc_final: 0.7645 (pp)
REVERT: D  270 MET cc_start: 0.6669 (mtt) cc_final: 0.5863 (tpt)
  outliers start: 3
  outliers final: 1
  residues processed: 274
  average time/residue: 0.1380
  time to fit residues: 57.3439
Evaluate side-chains
  208 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 207
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 124 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 161 optimal weight:    4.9990
   chunk 129 optimal weight:    6.9990
   chunk 180 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 209 optimal weight:    1.9990
   chunk 160 optimal weight:    0.6980
   chunk 107 optimal weight:    2.9990
   chunk 200 optimal weight:    0.8980
   chunk 187 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  65 ASN
A 208 ASN
A 531 GLN
A 681 GLN
A 870 ASN
** A1209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1272 ASN
A1338 GLN
** A1621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1919 ASN
A1920 GLN
A2033 GLN
A2053 ASN
A2057 ASN
B 235 GLN
C 228 ASN
D 234 ASN
E 235 GLN    B

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.094510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.076227 restraints weight = 393649.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.079832 restraints weight = 194701.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.081059 restraints weight = 99970.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.081830 restraints weight = 66713.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.083245 restraints weight = 51142.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3501
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3501 r_free = 0.3501    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3501 r_free = 0.3501    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3501
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.2672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  18210  Z= 0.155
  Angle     :  0.724  12.082  24691  Z= 0.368
  Chirality :  0.044   0.295   2910
  Planarity :  0.006   0.084   3105
  Dihedral  :  6.009  88.934   2425
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 13.32
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  9.44 %
    Favored  : 90.52 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  5.20 %
    Favored  : 94.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.26 (0.18), residues: 2204
  helix:  0.97 (0.14), residues: 1309
  sheet: -2.48 (0.51), residues: 91
  loop : -3.89 (0.19), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1544 
 TYR   0.020   0.001   TYR A1793 
 PHE   0.019   0.001   PHE A 401 
 TRP   0.047   0.002   TRP A1950 
 HIS   0.007   0.001   HIS A1539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (18207)
  covalent geometry    : angle       0.72388 (24691)
  hydrogen bonds       : bond        0.05367 ( 1028)
  hydrogen bonds       : angle       4.55680 ( 2986)
  metal coordination   : bond        0.00321 (    3)

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

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

  4408 Ramachandran restraints generated.
    2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4408 Ramachandran restraints generated.
    2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 304
  time to evaluate  : 0.484 
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: A   44 LEU cc_start: 0.8126 (pt) cc_final: 0.7799 (pp)
REVERT: A   98 ILE cc_start: 0.8520 (tp) cc_final: 0.8194 (mm)
REVERT: A  209 ARG cc_start: 0.8548 (tpt170) cc_final: 0.8214 (ttp80)
REVERT: A  453 VAL cc_start: 0.7497 (p) cc_final: 0.7268 (t)
REVERT: A  575 ILE cc_start: 0.9618 (mt) cc_final: 0.9353 (tt)
REVERT: A  686 MET cc_start: 0.8082 (tpp) cc_final: 0.7735 (tpp)
REVERT: A  891 LEU cc_start: 0.9129 (tp) cc_final: 0.8551 (tt)
REVERT: A  950 ASN cc_start: 0.8914 (t0) cc_final: 0.8708 (t0)
REVERT: A 1106 TYR cc_start: 0.7725 (t80) cc_final: 0.7388 (t80)
REVERT: A 1111 LEU cc_start: 0.9064 (mt) cc_final: 0.8745 (mt)
REVERT: A 1272 ASN cc_start: 0.7369 (t160) cc_final: 0.6901 (t0)
REVERT: A 1958 THR cc_start: 0.8592 (p) cc_final: 0.8374 (t)
REVERT: A 2006 MET cc_start: 0.7951 (tpt) cc_final: 0.7299 (tpt)
REVERT: A 2009 THR cc_start: 0.8558 (p) cc_final: 0.8245 (p)
REVERT: A 2159 ASP cc_start: 0.7829 (m-30) cc_final: 0.7565 (m-30)
REVERT: F  362 LYS cc_start: 0.8928 (mttt) cc_final: 0.8509 (ttmm)
REVERT: F  363 MET cc_start: 0.8696 (mmm) cc_final: 0.8286 (mmm)
REVERT: F  382 ASP cc_start: 0.8713 (m-30) cc_final: 0.8470 (m-30)
REVERT: B  254 LYS cc_start: 0.8629 (tptt) cc_final: 0.7996 (tppp)
REVERT: C  233 MET cc_start: 0.6658 (mtp) cc_final: 0.6341 (mtp)
REVERT: C  247 GLN cc_start: 0.8640 (mm110) cc_final: 0.7423 (pp30)
REVERT: C  261 LYS cc_start: 0.8124 (pttt) cc_final: 0.7713 (pttt)
REVERT: D  230 ASP cc_start: 0.7868 (t0) cc_final: 0.7457 (m-30)
REVERT: D  242 ARG cc_start: 0.7231 (ttt-90) cc_final: 0.6872 (tpp80)
REVERT: D  249 LEU cc_start: 0.7965 (mt) cc_final: 0.7688 (pp)
REVERT: D  270 MET cc_start: 0.6626 (mtt) cc_final: 0.5921 (tpt)
  outliers start: 2
  outliers final: 0
  residues processed: 305
  average time/residue: 0.1322
  time to fit residues: 61.3072
Evaluate side-chains
  214 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 199 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 217 optimal weight:    4.9990
   chunk 127 optimal weight:    0.0170
   chunk 177 optimal weight:    0.5980
   chunk 57 optimal weight:    0.7980
   chunk 89 optimal weight:    6.9990
   chunk 113 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9990
   overall best weight:    0.6822

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

Flipped N/Q/H residues before XYZ refinement:
A  73 HIS
A 300 GLN
A 436 ASN
A 531 GLN
A 870 ASN
A1209 ASN
A1272 ASN
** A1621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1622 HIS
** A1771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1920 GLN
A2057 ASN
B 235 GLN
D 228 ASN    A
** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.095302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.077181 restraints weight = 288125.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.081124 restraints weight = 137581.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.082526 restraints weight = 69011.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.082827 restraints weight = 49151.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.083098 restraints weight = 44752.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3513
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3513 r_free = 0.3513    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3513 r_free = 0.3513    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3513
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.3112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  18210  Z= 0.146
  Angle     :  0.688  10.314  24691  Z= 0.351
  Chirality :  0.043   0.253   2910
  Planarity :  0.005   0.081   3105
  Dihedral  :  5.825  88.563   2425
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  9.71 %
    Favored  : 90.24 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  3.22 %
    Favored  : 96.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.84 (0.19), residues: 2204
  helix:  1.33 (0.15), residues: 1299
  sheet: -2.19 (0.51), residues: 91
  loop : -3.71 (0.20), residues: 814

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1376 
 TYR   0.018   0.001   TYR A 894 
 PHE   0.016   0.001   PHE A2052 
 TRP   0.047   0.002   TRP A1950 
 HIS   0.005   0.001   HIS A 415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (18207)
  covalent geometry    : angle       0.68820 (24691)
  hydrogen bonds       : bond        0.05082 ( 1028)
  hydrogen bonds       : angle       4.37531 ( 2986)
  metal coordination   : bond        0.00247 (    3)

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

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

  4408 Ramachandran restraints generated.
    2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4408 Ramachandran restraints generated.
    2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 284
  time to evaluate  : 0.655 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 LEU cc_start: 0.7951 (pt) cc_final: 0.7633 (pp)
REVERT: A  209 ARG cc_start: 0.8498 (tpt170) cc_final: 0.8131 (ttp80)
REVERT: A  363 MET cc_start: 0.8057 (ttp) cc_final: 0.7599 (ttm)
REVERT: A  575 ILE cc_start: 0.9562 (mt) cc_final: 0.9314 (tt)
REVERT: A  891 LEU cc_start: 0.9124 (tp) cc_final: 0.8396 (tt)
REVERT: A 1111 LEU cc_start: 0.9018 (mt) cc_final: 0.8693 (mt)
REVERT: A 1646 LEU cc_start: 0.8102 (tt) cc_final: 0.7710 (mt)
REVERT: A 1958 THR cc_start: 0.8657 (p) cc_final: 0.8435 (t)
REVERT: A 2006 MET cc_start: 0.7957 (tpt) cc_final: 0.7329 (tpt)
REVERT: A 2009 THR cc_start: 0.8564 (p) cc_final: 0.8245 (p)
REVERT: A 2034 GLU cc_start: 0.8417 (pt0) cc_final: 0.7804 (pt0)
REVERT: A 2159 ASP cc_start: 0.7913 (m-30) cc_final: 0.7706 (m-30)
REVERT: A 2197 LYS cc_start: 0.8623 (mttt) cc_final: 0.8318 (tptt)
REVERT: F  362 LYS cc_start: 0.8917 (mttt) cc_final: 0.8575 (ttmm)
REVERT: F  363 MET cc_start: 0.8679 (mmm) cc_final: 0.8408 (mmm)
REVERT: F  382 ASP cc_start: 0.8712 (m-30) cc_final: 0.8458 (m-30)
REVERT: B  254 LYS cc_start: 0.8628 (tptt) cc_final: 0.8045 (tppp)
REVERT: B  264 MET cc_start: 0.8711 (ppp) cc_final: 0.8502 (ppp)
REVERT: C  233 MET cc_start: 0.6780 (mtp) cc_final: 0.6378 (mtm)
REVERT: C  234 ASN cc_start: 0.8437 (t0) cc_final: 0.7928 (m-40)
REVERT: C  247 GLN cc_start: 0.8686 (mm110) cc_final: 0.7507 (pp30)
REVERT: C  261 LYS cc_start: 0.7939 (pttt) cc_final: 0.7597 (pmtt)
REVERT: D  230 ASP cc_start: 0.7948 (t0) cc_final: 0.7634 (m-30)
REVERT: D  237 GLU cc_start: 0.7960 (pt0) cc_final: 0.7610 (tm-30)
REVERT: D  242 ARG cc_start: 0.7462 (ttt-90) cc_final: 0.7101 (tpp80)
REVERT: D  243 ILE cc_start: 0.8335 (mt) cc_final: 0.8098 (mt)
REVERT: D  249 LEU cc_start: 0.8089 (mt) cc_final: 0.7713 (pp)
REVERT: D  266 THR cc_start: 0.8644 (m) cc_final: 0.8406 (p)
REVERT: D  270 MET cc_start: 0.6654 (mtt) cc_final: 0.5979 (tpt)
REVERT: E  232 ARG cc_start: 0.8253 (ptt180) cc_final: 0.7667 (ptt180)
REVERT: E  242 ARG cc_start: 0.7403 (mtt180) cc_final: 0.6527 (tpt170)
REVERT: E  243 ILE cc_start: 0.7709 (mm) cc_final: 0.7340 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 284
  average time/residue: 0.1332
  time to fit residues: 58.0217
Evaluate side-chains
  213 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 165 optimal weight:    0.9990
   chunk 175 optimal weight:    0.8980
   chunk 208 optimal weight:    5.9990
   chunk 193 optimal weight:    4.9990
   chunk 162 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 115 optimal weight:    0.8980
   chunk 49 optimal weight:    0.0020
   chunk 103 optimal weight:    1.9990
   overall best weight:    0.7592

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

Flipped N/Q/H residues before XYZ refinement:
A  73 HIS
A 531 GLN
A 681 GLN
A 870 ASN
A1272 ASN
A1353 ASN
** A1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1762 HIS
** A1771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1920 GLN
** A2033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2057 ASN
B 235 GLN
D 234 ASN
** E 213 GLN ** 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 = 0.3780 r_free = 0.3780 target = 0.095315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.077216 restraints weight = 339556.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.080762 restraints weight = 179248.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.082200 restraints weight = 86132.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.082914 restraints weight = 57194.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.083234 restraints weight = 53316.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3525
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3525 r_free = 0.3525    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3525 r_free = 0.3525    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3525
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.3371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  18210  Z= 0.147
  Angle     :  0.686  10.302  24691  Z= 0.351
  Chirality :  0.042   0.198   2910
  Planarity :  0.005   0.084   3105
  Dihedral  :  5.750  87.188   2425
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  : 10.08 %
    Favored  : 89.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.65 (0.19), residues: 2204
  helix:  1.47 (0.15), residues: 1299
  sheet: -2.02 (0.50), residues: 100
  loop : -3.63 (0.20), residues: 805

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG C 232 
 TYR   0.018   0.001   TYR A1565 
 PHE   0.033   0.001   PHE A  69 
 TRP   0.045   0.002   TRP A1950 
 HIS   0.005   0.001   HIS A1539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (18207)
  covalent geometry    : angle       0.68584 (24691)
  hydrogen bonds       : bond        0.04949 ( 1028)
  hydrogen bonds       : angle       4.32963 ( 2986)
  metal coordination   : bond        0.00317 (    3)

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

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

  4408 Ramachandran restraints generated.
    2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4408 Ramachandran restraints generated.
    2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 291
  time to evaluate  : 0.758 
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: A   44 LEU cc_start: 0.7915 (pt) cc_final: 0.7605 (pp)
REVERT: A   98 ILE cc_start: 0.8276 (tp) cc_final: 0.7996 (mm)
REVERT: A  209 ARG cc_start: 0.8504 (tpt170) cc_final: 0.8129 (ttp80)
REVERT: A  244 MET cc_start: 0.8077 (ttp) cc_final: 0.7553 (ttt)
REVERT: A  384 MET cc_start: 0.8189 (tmm) cc_final: 0.7823 (tmm)
REVERT: A  575 ILE cc_start: 0.9609 (mt) cc_final: 0.9357 (tt)
REVERT: A  891 LEU cc_start: 0.9184 (tp) cc_final: 0.8472 (tt)
REVERT: A  950 ASN cc_start: 0.8791 (t0) cc_final: 0.8522 (t0)
REVERT: A 1111 LEU cc_start: 0.9014 (mt) cc_final: 0.8720 (mt)
REVERT: A 1120 ASN cc_start: 0.9021 (t0) cc_final: 0.8809 (t0)
REVERT: A 1501 TYR cc_start: 0.6028 (t80) cc_final: 0.5785 (t80)
REVERT: A 1633 PHE cc_start: 0.7605 (m-10) cc_final: 0.7387 (m-80)
REVERT: A 1646 LEU cc_start: 0.7983 (tt) cc_final: 0.7594 (mt)
REVERT: A 1815 MET cc_start: 0.8814 (ptm) cc_final: 0.8531 (ptp)
REVERT: A 1818 ILE cc_start: 0.9124 (mp) cc_final: 0.8626 (tp)
REVERT: A 1962 PHE cc_start: 0.8660 (t80) cc_final: 0.8307 (t80)
REVERT: A 2165 PHE cc_start: 0.7099 (t80) cc_final: 0.6634 (t80)
REVERT: A 2197 LYS cc_start: 0.8596 (mttt) cc_final: 0.8352 (tptp)
REVERT: F  362 LYS cc_start: 0.8900 (mttt) cc_final: 0.8543 (ttmm)
REVERT: F  363 MET cc_start: 0.8664 (mmm) cc_final: 0.8407 (mmm)
REVERT: F  382 ASP cc_start: 0.8662 (m-30) cc_final: 0.8417 (m-30)
REVERT: B  254 LYS cc_start: 0.8651 (tptt) cc_final: 0.8063 (tppp)
REVERT: C  233 MET cc_start: 0.6633 (mtp) cc_final: 0.5874 (mtp)
REVERT: C  234 ASN cc_start: 0.8411 (t0) cc_final: 0.7933 (m-40)
REVERT: C  247 GLN cc_start: 0.8658 (mm110) cc_final: 0.7549 (pp30)
REVERT: C  261 LYS cc_start: 0.7802 (pttt) cc_final: 0.7543 (pmtt)
REVERT: D  233 MET cc_start: 0.7769 (tmm) cc_final: 0.7371 (tmm)
REVERT: D  242 ARG cc_start: 0.7436 (ttt-90) cc_final: 0.7023 (tpp80)
REVERT: D  243 ILE cc_start: 0.8340 (mt) cc_final: 0.8096 (mt)
REVERT: D  266 THR cc_start: 0.8680 (m) cc_final: 0.8438 (p)
REVERT: D  270 MET cc_start: 0.6396 (mtt) cc_final: 0.5908 (tpt)
REVERT: E  232 ARG cc_start: 0.7863 (ptt180) cc_final: 0.7633 (ptt180)
REVERT: E  242 ARG cc_start: 0.7547 (mtt180) cc_final: 0.6613 (tpt170)
REVERT: E  243 ILE cc_start: 0.7607 (mm) cc_final: 0.7250 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 291
  average time/residue: 0.1293
  time to fit residues: 58.4766
Evaluate side-chains
  215 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 199 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9980
   chunk 101 optimal weight:    5.9990
   chunk 138 optimal weight:    2.9990
   chunk 179 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 114 optimal weight:    0.8980
   chunk 125 optimal weight:    0.8980
   chunk 162 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A  21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  73 HIS
A 436 ASN
A 531 GLN
A 870 ASN
A1209 ASN
A1272 ASN
** A1338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1920 GLN
A2057 ASN
B 235 GLN
** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.094967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.076885 restraints weight = 281160.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.080426 restraints weight = 141225.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.081976 restraints weight = 73073.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.082160 restraints weight = 51159.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.082485 restraints weight = 44364.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3513
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3513 r_free = 0.3513    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3513 r_free = 0.3513    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3513
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.3537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  18210  Z= 0.155
  Angle     :  0.703  12.134  24691  Z= 0.355
  Chirality :  0.043   0.197   2910
  Planarity :  0.005   0.087   3105
  Dihedral  :  5.710  87.384   2425
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  9.94 %
    Favored  : 90.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.61 (0.19), residues: 2204
  helix:  1.47 (0.15), residues: 1303
  sheet: -1.86 (0.51), residues: 100
  loop : -3.60 (0.20), residues: 801

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A2153 
 TYR   0.014   0.001   TYR A  85 
 PHE   0.016   0.002   PHE A2052 
 TRP   0.048   0.002   TRP A1950 
 HIS   0.006   0.001   HIS A1539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (18207)
  covalent geometry    : angle       0.70283 (24691)
  hydrogen bonds       : bond        0.04919 ( 1028)
  hydrogen bonds       : angle       4.32715 ( 2986)
  metal coordination   : bond        0.00233 (    3)

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

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

  4408 Ramachandran restraints generated.
    2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4408 Ramachandran restraints generated.
    2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 284
  time to evaluate  : 0.700 
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   44 LEU cc_start: 0.7992 (pt) cc_final: 0.7753 (pp)
REVERT: A   98 ILE cc_start: 0.8353 (tp) cc_final: 0.8027 (mm)
REVERT: A  209 ARG cc_start: 0.8443 (tpt170) cc_final: 0.8081 (ttp80)
REVERT: A  244 MET cc_start: 0.8117 (ttp) cc_final: 0.7574 (ttt)
REVERT: A  453 VAL cc_start: 0.7835 (p) cc_final: 0.7608 (t)
REVERT: A  575 ILE cc_start: 0.9557 (mt) cc_final: 0.9325 (tt)
REVERT: A  830 PHE cc_start: 0.8022 (t80) cc_final: 0.7799 (t80)
REVERT: A  891 LEU cc_start: 0.9199 (tp) cc_final: 0.8622 (tt)
REVERT: A 1111 LEU cc_start: 0.9036 (mt) cc_final: 0.8730 (mt)
REVERT: A 1501 TYR cc_start: 0.5832 (t80) cc_final: 0.5558 (t80)
REVERT: A 1646 LEU cc_start: 0.7913 (tt) cc_final: 0.7707 (mt)
REVERT: A 1920 GLN cc_start: 0.6132 (tt0) cc_final: 0.5566 (tt0)
REVERT: A 1962 PHE cc_start: 0.8743 (t80) cc_final: 0.8265 (t80)
REVERT: F  362 LYS cc_start: 0.8868 (mttt) cc_final: 0.8533 (ttmm)
REVERT: F  363 MET cc_start: 0.8652 (mmm) cc_final: 0.8374 (mmm)
REVERT: F  382 ASP cc_start: 0.8673 (m-30) cc_final: 0.8437 (m-30)
REVERT: B  254 LYS cc_start: 0.8645 (tptt) cc_final: 0.8073 (tppp)
REVERT: C  233 MET cc_start: 0.6538 (mtp) cc_final: 0.5822 (mtp)
REVERT: C  234 ASN cc_start: 0.8482 (t0) cc_final: 0.8004 (m-40)
REVERT: C  247 GLN cc_start: 0.8701 (mm110) cc_final: 0.7706 (pp30)
REVERT: C  261 LYS cc_start: 0.7661 (pttt) cc_final: 0.7391 (pttt)
REVERT: D  208 LEU cc_start: 0.6355 (tp) cc_final: 0.6097 (mp)
REVERT: D  242 ARG cc_start: 0.7421 (ttt-90) cc_final: 0.6942 (tpp80)
REVERT: D  243 ILE cc_start: 0.8252 (mt) cc_final: 0.8007 (mt)
REVERT: D  249 LEU cc_start: 0.8532 (pp) cc_final: 0.7814 (mm)
REVERT: D  266 THR cc_start: 0.8734 (m) cc_final: 0.8452 (p)
REVERT: D  270 MET cc_start: 0.6310 (mtt) cc_final: 0.5729 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 284
  average time/residue: 0.1250
  time to fit residues: 54.9924
Evaluate side-chains
  210 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 140 optimal weight:    0.0000
   chunk 171 optimal weight:    4.9990
   chunk 182 optimal weight:    2.9990
   chunk 217 optimal weight:    1.9990
   chunk 173 optimal weight:    2.9990
   chunk 108 optimal weight:    1.9990
   chunk 210 optimal weight:    2.9990
   chunk 181 optimal weight:    1.9990
   chunk 126 optimal weight:    6.9990
   chunk 123 optimal weight:    0.0370
   chunk 98 optimal weight:    7.9990
   overall best weight:    1.2068

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

Flipped N/Q/H residues before XYZ refinement:
** A  21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  73 HIS
A 531 GLN
A 870 ASN
** A1272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2033 GLN
** A2057 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 235 GLN
** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.094356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.076473 restraints weight = 334834.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.079866 restraints weight = 177912.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.081069 restraints weight = 96272.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.081846 restraints weight = 66168.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.081989 restraints weight = 62617.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3485
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3485 r_free = 0.3485    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3485 r_free = 0.3485    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3485
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.3620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  18210  Z= 0.166
  Angle     :  0.716  10.570  24691  Z= 0.363
  Chirality :  0.043   0.215   2910
  Planarity :  0.006   0.092   3105
  Dihedral  :  5.783  88.761   2425
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 13.13
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  : 10.36 %
    Favored  : 89.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.71 (0.19), residues: 2204
  helix:  1.40 (0.15), residues: 1300
  sheet: -1.87 (0.51), residues: 100
  loop : -3.66 (0.20), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG C 232 
 TYR   0.015   0.001   TYR A1397 
 PHE   0.029   0.002   PHE A  69 
 TRP   0.067   0.002   TRP A1950 
 HIS   0.007   0.001   HIS A1539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (18207)
  covalent geometry    : angle       0.71600 (24691)
  hydrogen bonds       : bond        0.04918 ( 1028)
  hydrogen bonds       : angle       4.39149 ( 2986)
  metal coordination   : bond        0.00283 (    3)

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

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

  4408 Ramachandran restraints generated.
    2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4408 Ramachandran restraints generated.
    2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 283
  time to evaluate  : 0.667 
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: A   44 LEU cc_start: 0.8018 (pt) cc_final: 0.7733 (pp)
REVERT: A  209 ARG cc_start: 0.8558 (tpt170) cc_final: 0.8125 (ttp80)
REVERT: A  244 MET cc_start: 0.8540 (ttp) cc_final: 0.7523 (ttt)
REVERT: A  245 TYR cc_start: 0.8232 (m-80) cc_final: 0.7922 (m-80)
REVERT: A  575 ILE cc_start: 0.9599 (mt) cc_final: 0.9339 (tt)
REVERT: A  891 LEU cc_start: 0.9094 (tp) cc_final: 0.8349 (tt)
REVERT: A  895 MET cc_start: 0.8600 (mmm) cc_final: 0.8298 (mmm)
REVERT: A 1111 LEU cc_start: 0.9029 (mt) cc_final: 0.8741 (mt)
REVERT: A 1920 GLN cc_start: 0.6159 (tt0) cc_final: 0.5788 (tt0)
REVERT: A 1962 PHE cc_start: 0.8677 (t80) cc_final: 0.8233 (t80)
REVERT: F  362 LYS cc_start: 0.8895 (mttt) cc_final: 0.8561 (ttmm)
REVERT: F  363 MET cc_start: 0.8700 (mmm) cc_final: 0.8384 (mmm)
REVERT: F  382 ASP cc_start: 0.8693 (m-30) cc_final: 0.8468 (m-30)
REVERT: B  227 ARG cc_start: 0.8322 (tpm170) cc_final: 0.7922 (mmm160)
REVERT: B  235 GLN cc_start: 0.6595 (mp10) cc_final: 0.6377 (mm-40)
REVERT: B  254 LYS cc_start: 0.8641 (tptt) cc_final: 0.8075 (tppp)
REVERT: C  233 MET cc_start: 0.6731 (mtp) cc_final: 0.6258 (mtm)
REVERT: C  234 ASN cc_start: 0.8503 (t0) cc_final: 0.8052 (m-40)
REVERT: C  247 GLN cc_start: 0.8754 (mm110) cc_final: 0.7742 (pp30)
REVERT: C  261 LYS cc_start: 0.7742 (pttt) cc_final: 0.7404 (pttt)
REVERT: D  208 LEU cc_start: 0.6015 (tp) cc_final: 0.5810 (mp)
REVERT: D  242 ARG cc_start: 0.7327 (ttt-90) cc_final: 0.6988 (tpp80)
REVERT: D  249 LEU cc_start: 0.8577 (pp) cc_final: 0.7755 (mm)
REVERT: D  266 THR cc_start: 0.8844 (m) cc_final: 0.8529 (p)
REVERT: D  270 MET cc_start: 0.6411 (mtt) cc_final: 0.5873 (tpt)
REVERT: E  233 MET cc_start: 0.9187 (mpp) cc_final: 0.8618 (mpp)
REVERT: E  242 ARG cc_start: 0.7698 (ptp90) cc_final: 0.7155 (tpt170)
  outliers start: 0
  outliers final: 0
  residues processed: 283
  average time/residue: 0.1276
  time to fit residues: 55.5085
Evaluate side-chains
  210 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 198 optimal weight:    0.8980
   chunk 91 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 141 optimal weight:   10.0000
   chunk 83 optimal weight:    0.9990
   chunk 214 optimal weight:    0.7980
   chunk 52 optimal weight:    5.9990
   chunk 146 optimal weight:    8.9990
   chunk 1 optimal weight:    0.7980
   chunk 10 optimal weight:    4.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A  21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  73 HIS
A  81 HIS
A 436 ASN
A 531 GLN
A 870 ASN
A1272 ASN
** A1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2057 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 234 ASN
** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.094056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.075881 restraints weight = 385983.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.079145 restraints weight = 194466.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.080989 restraints weight = 96782.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.081393 restraints weight = 64180.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.081881 restraints weight = 58492.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3497
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3497 r_free = 0.3497    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3497 r_free = 0.3497    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3497
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
moved from start:          0.3775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  18210  Z= 0.162
  Angle     :  0.723  10.759  24691  Z= 0.368
  Chirality :  0.044   0.268   2910
  Planarity :  0.005   0.091   3105
  Dihedral  :  5.801  88.763   2425
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 13.13
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  : 10.45 %
    Favored  : 89.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.68 (0.19), residues: 2204
  helix:  1.40 (0.15), residues: 1295
  sheet: -1.65 (0.53), residues: 95
  loop : -3.59 (0.20), residues: 814

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 232 
 TYR   0.014   0.001   TYR A1231 
 PHE   0.030   0.002   PHE A  69 
 TRP   0.058   0.002   TRP A1950 
 HIS   0.006   0.001   HIS A1539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (18207)
  covalent geometry    : angle       0.72265 (24691)
  hydrogen bonds       : bond        0.04855 ( 1028)
  hydrogen bonds       : angle       4.41902 ( 2986)
  metal coordination   : bond        0.00297 (    3)

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

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

  4408 Ramachandran restraints generated.
    2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4408 Ramachandran restraints generated.
    2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 277
  time to evaluate  : 0.534 
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: A   44 LEU cc_start: 0.7991 (pt) cc_final: 0.7718 (pp)
REVERT: A   98 ILE cc_start: 0.8189 (tp) cc_final: 0.7880 (mm)
REVERT: A  209 ARG cc_start: 0.8519 (tpt170) cc_final: 0.8098 (ttp80)
REVERT: A  244 MET cc_start: 0.8491 (ttp) cc_final: 0.7695 (ttt)
REVERT: A  363 MET cc_start: 0.7872 (ttp) cc_final: 0.7355 (ttm)
REVERT: A  384 MET cc_start: 0.8317 (tmm) cc_final: 0.7581 (tmm)
REVERT: A  575 ILE cc_start: 0.9514 (mt) cc_final: 0.9259 (tt)
REVERT: A  891 LEU cc_start: 0.9110 (tp) cc_final: 0.8393 (tt)
REVERT: A  895 MET cc_start: 0.8659 (mmm) cc_final: 0.8420 (mmm)
REVERT: A 1111 LEU cc_start: 0.9040 (mt) cc_final: 0.8749 (mt)
REVERT: A 1646 LEU cc_start: 0.7860 (tt) cc_final: 0.7487 (mt)
REVERT: A 1920 GLN cc_start: 0.6123 (tt0) cc_final: 0.5614 (tt0)
REVERT: A 1962 PHE cc_start: 0.8682 (t80) cc_final: 0.8257 (t80)
REVERT: F  362 LYS cc_start: 0.8893 (mttt) cc_final: 0.8560 (ttmm)
REVERT: F  363 MET cc_start: 0.8686 (mmm) cc_final: 0.8393 (mmm)
REVERT: F  382 ASP cc_start: 0.8693 (m-30) cc_final: 0.8462 (m-30)
REVERT: B  227 ARG cc_start: 0.8288 (tpm170) cc_final: 0.7808 (mmm160)
REVERT: B  235 GLN cc_start: 0.6614 (mp10) cc_final: 0.6316 (mm-40)
REVERT: B  254 LYS cc_start: 0.8656 (tptt) cc_final: 0.8063 (tppp)
REVERT: C  233 MET cc_start: 0.6990 (mtp) cc_final: 0.6269 (mtp)
REVERT: C  234 ASN cc_start: 0.8563 (t0) cc_final: 0.8216 (m-40)
REVERT: C  247 GLN cc_start: 0.8808 (mm110) cc_final: 0.7765 (pp30)
REVERT: D  208 LEU cc_start: 0.6062 (tp) cc_final: 0.5841 (mp)
REVERT: D  242 ARG cc_start: 0.7371 (ttt-90) cc_final: 0.7060 (tpp80)
REVERT: D  249 LEU cc_start: 0.8592 (pp) cc_final: 0.7783 (mm)
REVERT: D  266 THR cc_start: 0.8817 (m) cc_final: 0.8497 (p)
REVERT: D  270 MET cc_start: 0.6281 (mtt) cc_final: 0.5833 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 277
  average time/residue: 0.1314
  time to fit residues: 55.9530
Evaluate side-chains
  201 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.610 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 211 optimal weight:    6.9990
   chunk 59 optimal weight:    0.6980
   chunk 168 optimal weight:    1.9990
   chunk 200 optimal weight:    2.9990
   chunk 105 optimal weight:    0.1980
   chunk 65 optimal weight:    0.7980
   chunk 188 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A  21 HIS
A  73 HIS
A 531 GLN
A 870 ASN
** A1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1621 HIS
** A1771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1929 ASN
** A2057 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.095437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.077015 restraints weight = 347987.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.080776 restraints weight = 156511.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.082307 restraints weight = 78465.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.083093 restraints weight = 53147.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.084129 restraints weight = 41870.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3546
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3546 r_free = 0.3546    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3546 r_free = 0.3546    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3546
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
moved from start:          0.4019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  18210  Z= 0.145
  Angle     :  0.712  10.483  24691  Z= 0.362
  Chirality :  0.043   0.209   2910
  Planarity :  0.006   0.106   3105
  Dihedral  :  5.673  86.936   2425
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.58 %
    Favored  : 90.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.67 (0.19), residues: 2204
  helix:  1.40 (0.15), residues: 1298
  sheet: -1.59 (0.52), residues: 95
  loop : -3.59 (0.20), residues: 811

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 232 
 TYR   0.023   0.001   TYR A1565 
 PHE   0.028   0.002   PHE A  69 
 TRP   0.060   0.002   TRP A1950 
 HIS   0.005   0.001   HIS A1539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (18207)
  covalent geometry    : angle       0.71182 (24691)
  hydrogen bonds       : bond        0.04694 ( 1028)
  hydrogen bonds       : angle       4.36949 ( 2986)
  metal coordination   : bond        0.00199 (    3)

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

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

  4408 Ramachandran restraints generated.
    2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4408 Ramachandran restraints generated.
    2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 293
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 LEU cc_start: 0.8337 (pt) cc_final: 0.8075 (pp)
REVERT: A   98 ILE cc_start: 0.8103 (tp) cc_final: 0.7781 (mm)
REVERT: A  209 ARG cc_start: 0.8494 (tpt170) cc_final: 0.8112 (ttp80)
REVERT: A  244 MET cc_start: 0.8232 (ttp) cc_final: 0.7528 (ttt)
REVERT: A  363 MET cc_start: 0.8025 (ttp) cc_final: 0.7483 (ttm)
REVERT: A  384 MET cc_start: 0.8340 (tmm) cc_final: 0.7669 (tmm)
REVERT: A  453 VAL cc_start: 0.7974 (p) cc_final: 0.7721 (t)
REVERT: A  575 ILE cc_start: 0.9486 (mt) cc_final: 0.9253 (tt)
REVERT: A  891 LEU cc_start: 0.9070 (tp) cc_final: 0.8297 (tt)
REVERT: A  895 MET cc_start: 0.8659 (mmm) cc_final: 0.8377 (mmm)
REVERT: A 1111 LEU cc_start: 0.9016 (mt) cc_final: 0.8725 (mt)
REVERT: A 1213 ARG cc_start: 0.7174 (mmp-170) cc_final: 0.6780 (mmp-170)
REVERT: A 1568 MET cc_start: 0.7662 (mmt) cc_final: 0.7303 (mmm)
REVERT: A 1915 SER cc_start: 0.6443 (t) cc_final: 0.6040 (p)
REVERT: A 1962 PHE cc_start: 0.8853 (t80) cc_final: 0.8409 (t80)
REVERT: F  362 LYS cc_start: 0.8854 (mttt) cc_final: 0.8517 (ttmm)
REVERT: F  363 MET cc_start: 0.8688 (mmm) cc_final: 0.8384 (mmm)
REVERT: F  382 ASP cc_start: 0.8683 (m-30) cc_final: 0.8449 (m-30)
REVERT: F  383 LEU cc_start: 0.8860 (mt) cc_final: 0.8639 (mt)
REVERT: B  227 ARG cc_start: 0.8244 (tpm170) cc_final: 0.7767 (mmm160)
REVERT: B  249 LEU cc_start: 0.8433 (pp) cc_final: 0.8174 (tp)
REVERT: B  253 ILE cc_start: 0.8792 (mt) cc_final: 0.8566 (mm)
REVERT: B  254 LYS cc_start: 0.8650 (tptt) cc_final: 0.8024 (tppp)
REVERT: C  233 MET cc_start: 0.6864 (mtp) cc_final: 0.6328 (mtp)
REVERT: C  234 ASN cc_start: 0.8751 (t0) cc_final: 0.8315 (m-40)
REVERT: C  247 GLN cc_start: 0.8724 (mm110) cc_final: 0.7710 (pp30)
REVERT: C  252 THR cc_start: 0.7886 (p) cc_final: 0.7650 (p)
REVERT: C  253 ILE cc_start: 0.6601 (mt) cc_final: 0.6333 (mm)
REVERT: D  208 LEU cc_start: 0.6207 (tp) cc_final: 0.5963 (mp)
REVERT: D  242 ARG cc_start: 0.7320 (ttt-90) cc_final: 0.6968 (tpp80)
REVERT: D  249 LEU cc_start: 0.8620 (pp) cc_final: 0.7853 (mm)
REVERT: D  266 THR cc_start: 0.8732 (m) cc_final: 0.8399 (p)
REVERT: D  270 MET cc_start: 0.6062 (mtt) cc_final: 0.5653 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 293
  average time/residue: 0.1340
  time to fit residues: 60.4545
Evaluate side-chains
  216 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 125 optimal weight:    8.9990
   chunk 42 optimal weight:    2.9990
   chunk 136 optimal weight:    0.7980
   chunk 128 optimal weight:    0.2980
   chunk 4 optimal weight:    5.9990
   chunk 206 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 110 optimal weight:    0.9980
   chunk 82 optimal weight:    0.5980
   chunk 197 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  73 HIS
A 436 ASN
A 531 GLN
A 870 ASN
A1272 ASN
** A1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2057 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 235 GLN    B

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.095263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.077040 restraints weight = 301509.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.081318 restraints weight = 142620.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.082176 restraints weight = 67507.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.082927 restraints weight = 47561.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.083748 restraints weight = 39447.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3542
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3542 r_free = 0.3542    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3542 r_free = 0.3542    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3542
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.4154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  18210  Z= 0.146
  Angle     :  0.717  12.106  24691  Z= 0.364
  Chirality :  0.043   0.208   2910
  Planarity :  0.007   0.232   3105
  Dihedral  :  5.655  86.594   2425
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.67 %
    Favored  : 90.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.66 (0.18), residues: 2204
  helix:  1.38 (0.14), residues: 1303
  sheet: -1.39 (0.53), residues: 95
  loop : -3.61 (0.20), residues: 806

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.027   0.001   ARG E 232 
 TYR   0.017   0.001   TYR A1501 
 PHE   0.029   0.002   PHE A  69 
 TRP   0.059   0.002   TRP A1950 
 HIS   0.006   0.001   HIS A1539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (18207)
  covalent geometry    : angle       0.71746 (24691)
  hydrogen bonds       : bond        0.04716 ( 1028)
  hydrogen bonds       : angle       4.36455 ( 2986)
  metal coordination   : bond        0.00217 (    3)

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

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

  4408 Ramachandran restraints generated.
    2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4408 Ramachandran restraints generated.
    2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 273
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 LEU cc_start: 0.8024 (pt) cc_final: 0.7637 (pp)
REVERT: A   98 ILE cc_start: 0.7989 (tp) cc_final: 0.7679 (mm)
REVERT: A  209 ARG cc_start: 0.8396 (tpt170) cc_final: 0.8062 (ttp80)
REVERT: A  244 MET cc_start: 0.7937 (ttp) cc_final: 0.7242 (ttt)
REVERT: A  363 MET cc_start: 0.7793 (ttp) cc_final: 0.7361 (ttm)
REVERT: A  384 MET cc_start: 0.8257 (tmm) cc_final: 0.7568 (tmm)
REVERT: A  575 ILE cc_start: 0.9482 (mt) cc_final: 0.9240 (tt)
REVERT: A  891 LEU cc_start: 0.9171 (tp) cc_final: 0.8323 (tt)
REVERT: A  895 MET cc_start: 0.8444 (mmm) cc_final: 0.8232 (mmm)
REVERT: A 1111 LEU cc_start: 0.8992 (mt) cc_final: 0.8705 (mt)
REVERT: A 1213 ARG cc_start: 0.6799 (mmp-170) cc_final: 0.6537 (mmp-170)
REVERT: A 1568 MET cc_start: 0.7755 (mmt) cc_final: 0.7411 (mmm)
REVERT: A 1646 LEU cc_start: 0.7808 (tt) cc_final: 0.7369 (mt)
REVERT: A 1915 SER cc_start: 0.6745 (t) cc_final: 0.6471 (p)
REVERT: F  362 LYS cc_start: 0.8811 (mttt) cc_final: 0.8474 (ttmm)
REVERT: F  363 MET cc_start: 0.8582 (mmm) cc_final: 0.8316 (mmm)
REVERT: F  382 ASP cc_start: 0.8572 (m-30) cc_final: 0.8344 (m-30)
REVERT: B  227 ARG cc_start: 0.8236 (tpm170) cc_final: 0.7742 (mmm160)
REVERT: B  249 LEU cc_start: 0.8491 (pp) cc_final: 0.8104 (mp)
REVERT: B  254 LYS cc_start: 0.8645 (tptt) cc_final: 0.8047 (tppp)
REVERT: C  233 MET cc_start: 0.7254 (mtp) cc_final: 0.6522 (mtp)
REVERT: C  234 ASN cc_start: 0.9075 (t0) cc_final: 0.8700 (m110)
REVERT: C  247 GLN cc_start: 0.8707 (mm110) cc_final: 0.7703 (pp30)
REVERT: D  208 LEU cc_start: 0.6406 (tp) cc_final: 0.6150 (mp)
REVERT: D  242 ARG cc_start: 0.7273 (ttt-90) cc_final: 0.6927 (tpp80)
REVERT: D  249 LEU cc_start: 0.8557 (pp) cc_final: 0.7685 (mm)
REVERT: D  266 THR cc_start: 0.8678 (m) cc_final: 0.8303 (p)
REVERT: D  270 MET cc_start: 0.6040 (mtt) cc_final: 0.5514 (tpt)
REVERT: E  242 ARG cc_start: 0.7265 (ptt180) cc_final: 0.6162 (tpt170)
  outliers start: 0
  outliers final: 0
  residues processed: 273
  average time/residue: 0.1319
  time to fit residues: 55.7191
Evaluate side-chains
  208 residues out of total 1987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 222
   random chunks:
   chunk 161 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 139 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0470
   chunk 47 optimal weight:    0.8980
   chunk 1 optimal weight:    0.3980
   chunk 216 optimal weight:    4.9990
   chunk 151 optimal weight:    0.0670
   chunk 174 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   overall best weight:    0.4616

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

Flipped N/Q/H residues before XYZ refinement:
A  73 HIS
A 531 GLN
A 870 ASN
** A1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2057 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 235 GLN    B

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.096438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.078091 restraints weight = 331938.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.082331 restraints weight = 152184.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.083549 restraints weight = 71615.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.084298 restraints weight = 49741.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.085286 restraints weight = 39743.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3571
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3571 r_free = 0.3571    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3571 r_free = 0.3571    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3571
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7344
moved from start:          0.4366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  18210  Z= 0.139
  Angle     :  0.706  11.587  24691  Z= 0.357
  Chirality :  0.043   0.203   2910
  Planarity :  0.005   0.095   3105
  Dihedral  :  5.496  85.087   2425
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 12.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.02 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.58 (0.19), residues: 2204
  helix:  1.44 (0.14), residues: 1311
  sheet: -1.54 (0.52), residues: 100
  loop : -3.59 (0.20), residues: 793

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 232 
 TYR   0.014   0.001   TYR A1231 
 PHE   0.028   0.002   PHE A  69 
 TRP   0.051   0.002   TRP A1950 
 HIS   0.006   0.001   HIS A1539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (18207)
  covalent geometry    : angle       0.70565 (24691)
  hydrogen bonds       : bond        0.04599 ( 1028)
  hydrogen bonds       : angle       4.31660 ( 2986)
  metal coordination   : bond        0.00152 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2764.08 seconds
wall clock time: 48 minutes 49.56 seconds (2929.56 seconds total)