Starting phenix.real_space_refine
on Sun Aug 24 19:35:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8glk_40196/08_2025/8glk_40196.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8glk_40196/08_2025/8glk_40196.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8glk_40196/08_2025/8glk_40196.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8glk_40196/08_2025/8glk_40196.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8glk_40196/08_2025/8glk_40196.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8glk_40196/08_2025/8glk_40196.map"
  }
  resolution = 2.8
  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: 4
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     C   13852      2.51       5
     N    3661      2.21       5
     O    4340      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 21899
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "D"
      Number of atoms: 599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 599
          Classifications: {'peptide': 75}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 70}
    Chain: "A"
      Number of atoms: 17380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2191, 17380
          Classifications: {'peptide': 2191}
          Link IDs: {'PCIS': 3, 'PTRANS': 99, 'TRANS': 2088}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 990
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 990
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 2861
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 367, 2861
          Classifications: {'peptide': 367}
          Link IDs: {'PTRANS': 17, 'TRANS': 349}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 69
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 69
          Unusual residues: {'LMN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.01, per 1000 atoms: 0.18
  Number of scatterers: 21899
  At special positions: 0
  Unit cell: (122.304, 128.96, 143.104, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      46     16.00
     O    4340      8.00
     N    3661      7.00
     C   13852      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: 1.77
  Conformation dependent library (CDL) restraints added in 880.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  5486 Ramachandran restraints generated.
    2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5118

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 21 sheets defined
      14.6% alpha, 31.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'A' and resid 160 through 164
    Processing helix  chain 'A' and resid 284 through 286
      No H-bonds generated for 'chain 'A' and resid 284 through 286'
    Processing helix  chain 'A' and resid 295 through 306
      removed outlier: 4.602A  pdb=" N   ASP A 303 " --> pdb=" O   ARG A 299 " (cutoff:3.500A)
      removed outlier: 4.896A  pdb=" N   VAL A 304 " --> pdb=" O   ASN A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 363
    Processing helix  chain 'A' and resid 382 through 386
      removed outlier: 4.199A  pdb=" N   ASN A 386 " --> pdb=" O   ASN A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
      removed outlier: 3.633A  pdb=" N   ILE A 393 " --> pdb=" O   PRO A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 406
    Processing helix  chain 'A' and resid 410 through 414
      removed outlier: 3.678A  pdb=" N   PHE A 414 " --> pdb=" O   LYS A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 437
      No H-bonds generated for 'chain 'A' and resid 435 through 437'
    Processing helix  chain 'A' and resid 517 through 522
      removed outlier: 3.902A  pdb=" N   ASN A 521 " --> pdb=" O   ASN A 517 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 569 through 573
      removed outlier: 3.969A  pdb=" N   LYS A 573 " --> pdb=" O   PRO A 570 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 583
    Processing helix  chain 'A' and resid 626 through 633
    Processing helix  chain 'A' and resid 643 through 647
    Processing helix  chain 'A' and resid 650 through 655
    Processing helix  chain 'A' and resid 657 through 662
    Processing helix  chain 'A' and resid 663 through 668
    Processing helix  chain 'A' and resid 669 through 674
      removed outlier: 6.089A  pdb=" N   ASP A 672 " --> pdb=" O   GLN A 669 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   LYS A 673 " --> pdb=" O   ASP A 670 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ASN A 674 " --> pdb=" O   SER A 671 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 669 through 674'
    Processing helix  chain 'A' and resid 730 through 735
      removed outlier: 3.599A  pdb=" N   ALA A 735 " --> pdb=" O   PRO A 731 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 810 through 819
      removed outlier: 3.811A  pdb=" N   THR A 814 " --> pdb=" O   VAL A 810 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 845 through 847
      No H-bonds generated for 'chain 'A' and resid 845 through 847'
    Processing helix  chain 'A' and resid 872 through 876
    Processing helix  chain 'A' and resid 898 through 903
    Processing helix  chain 'A' and resid 926 through 931
      removed outlier: 3.586A  pdb=" N   SER A 931 " --> pdb=" O   ASP A 928 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 940 through 944
    Processing helix  chain 'A' and resid 982 through 985
    Processing helix  chain 'A' and resid 998 through 1003
    Processing helix  chain 'A' and resid 1048 through 1052
      removed outlier: 3.663A  pdb=" N   LEU A1052 " --> pdb=" O   GLU A1049 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1081 through 1089
    Processing helix  chain 'A' and resid 1099 through 1103
      removed outlier: 3.511A  pdb=" N   SER A1102 " --> pdb=" O   ARG A1099 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1104 through 1108
      removed outlier: 3.690A  pdb=" N   ALA A1108 " --> pdb=" O   THR A1105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1127 through 1132
    Processing helix  chain 'A' and resid 1412 through 1417
    Processing helix  chain 'A' and resid 1418 through 1422
    Processing helix  chain 'A' and resid 1427 through 1438
    Processing helix  chain 'A' and resid 1454 through 1458
    Processing helix  chain 'A' and resid 1573 through 1576
    Processing helix  chain 'A' and resid 1577 through 1580
      removed outlier: 3.628A  pdb=" N   TRP A1580 " --> pdb=" O   PRO A1577 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1577 through 1580'
    Processing helix  chain 'A' and resid 1607 through 1614
    Processing helix  chain 'A' and resid 1617 through 1629
      removed outlier: 3.542A  pdb=" N   ILE A1629 " --> pdb=" O   ARG A1625 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1656 through 1658
      No H-bonds generated for 'chain 'A' and resid 1656 through 1658'
    Processing helix  chain 'A' and resid 1830 through 1834
      removed outlier: 3.603A  pdb=" N   LYS A1833 " --> pdb=" O   PRO A1830 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1856 through 1861
    Processing helix  chain 'A' and resid 1976 through 1981
    Processing helix  chain 'A' and resid 1987 through 1995
    Processing helix  chain 'A' and resid 2071 through 2075
      removed outlier: 3.512A  pdb=" N   THR A2074 " --> pdb=" O   MET A2071 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2084 through 2106
      removed outlier: 3.788A  pdb=" N   ARG A2094 " --> pdb=" O   PHE A2090 " (cutoff:3.500A)
      removed outlier: 4.858A  pdb=" N   LEU A2095 " --> pdb=" O   ARG A2091 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   ILE A2096 " --> pdb=" O   SER A2092 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2129 through 2136
      removed outlier: 3.804A  pdb=" N   ASN A2136 " --> pdb=" O   VAL A2132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2147 through 2161
      Proline residue:  A2153  - end of helix
    Processing helix  chain 'A' and resid 2186 through 2190
    Processing helix  chain 'B' and resid 27 through 42
    Processing helix  chain 'B' and resid 126 through 133
    Processing helix  chain 'B' and resid 134 through 136
      No H-bonds generated for 'chain 'B' and resid 134 through 136'
    Processing helix  chain 'F' and resid 30 through 35
    Processing helix  chain 'F' and resid 38 through 44
    Processing helix  chain 'F' and resid 61 through 68
      removed outlier: 3.551A  pdb=" N   LYS F  64 " --> pdb=" O   ASN F  61 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   ALA F  66 " --> pdb=" O   ALA F  63 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 284 through 297
      removed outlier: 4.129A  pdb=" N   ASP F 288 " --> pdb=" O   GLN F 284 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 299 through 307
      removed outlier: 3.811A  pdb=" N   PHE F 305 " --> pdb=" O   VAL F 301 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 314 through 319
    Processing sheet with id=AA1, first strand: chain 'D' and resid 547 through 548
      removed outlier: 8.941A  pdb=" N   SER D 548 " --> pdb=" O   LYS D 610 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   ILE D 612 " --> pdb=" O   SER D 548 " (cutoff:3.500A)
      removed outlier: 5.789A  pdb=" N   TYR D 563 " --> pdb=" O   ASN D 580 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   ASN D 580 " --> pdb=" O   TYR D 563 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 551 through 553
    Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 154
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 166 through 173
    current: chain 'A' and resid 187 through 194
      removed outlier: 6.555A  pdb=" N   PHE A 205 " --> pdb=" O   ASN A 224 " (cutoff:3.500A)
      removed outlier: 5.750A  pdb=" N   ILE A 217 " --> pdb=" O   GLN A 248 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   GLN A 248 " --> pdb=" O   ILE A 217 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LYS A 219 " --> pdb=" O   GLN A 246 " (cutoff:3.500A)
      removed outlier: 4.872A  pdb=" N   MET A 227 " --> pdb=" O   GLN A 238 " (cutoff:3.500A)
      removed outlier: 5.238A  pdb=" N   GLN A 238 " --> pdb=" O   MET A 227 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   THR A 253 " --> pdb=" O   GLU A 763 " (cutoff:3.500A)
      removed outlier: 4.725A  pdb=" N   ARG A 755 " --> pdb=" O   GLN A 261 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   PHE A 770 " --> pdb=" O   ILE A 766 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 770 through 773
    current: chain 'A' and resid 796 through 809
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 1559 through 1571
    current: chain 'A' and resid 1630 through 1644
      removed outlier: 5.433A  pdb=" N   THR A1632 " --> pdb=" O   HIS A1672 " (cutoff:3.500A)
      removed outlier: 7.421A  pdb=" N   HIS A1672 " --> pdb=" O   THR A1632 " (cutoff:3.500A)
      removed outlier: 5.392A  pdb=" N   ARG A1634 " --> pdb=" O   GLU A1670 " (cutoff:3.500A)
      removed outlier: 7.183A  pdb=" N   GLU A1670 " --> pdb=" O   ARG A1634 " (cutoff:3.500A)
      removed outlier: 5.452A  pdb=" N   SER A1636 " --> pdb=" O   GLN A1668 " (cutoff:3.500A)
      removed outlier: 7.462A  pdb=" N   GLN A1668 " --> pdb=" O   SER A1636 " (cutoff:3.500A)
      removed outlier: 5.358A  pdb=" N   ASN A1638 " --> pdb=" O   TYR A1666 " (cutoff:3.500A)
      removed outlier: 7.423A  pdb=" N   TYR A1666 " --> pdb=" O   ASN A1638 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   ILE A1640 " --> pdb=" O   GLN A1664 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   GLN A1664 " --> pdb=" O   ILE A1640 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   LYS A1644 " --> pdb=" O   PHE A1660 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   PHE A1660 " --> pdb=" O   LYS A1644 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 1757 through 1760
    current: chain 'A' and resid 1779 through 1789
      removed outlier: 5.588A  pdb=" N   ILE A1789 " --> pdb=" O   PRO A1816 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   THR A1847 " --> pdb=" O   SER A1881 " (cutoff:3.500A)
      removed outlier: 5.141A  pdb=" N   ASN A1874 " --> pdb=" O   GLY A1962 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   ILE A1945 " --> pdb=" O   ASP A2022 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   ASP A2022 " --> pdb=" O   ILE A1945 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   ASN A1947 " --> pdb=" O   ASN A2020 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ASN A1951 " --> pdb=" O   LYS A2016 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   LEU A2023 " --> pdb=" O   LEU A2027 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   LEU A2027 " --> pdb=" O   LEU A2023 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   ASP A2034 " --> pdb=" O   SER A2068 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   GLN A2044 " --> pdb=" O   SER A2058 " (cutoff:3.500A)
      removed outlier: 5.162A  pdb=" N   SER A2058 " --> pdb=" O   GLN A2044 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   SER A2046 " --> pdb=" O   PRO A2056 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 2054 through 2069
    current: chain 'A' and resid 2197 through 2217
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 2238 through 2240
    current: chain 'A' and resid 2264 through 2278
      removed outlier: 4.018A  pdb=" N   VAL A2287 " --> pdb=" O   ALA A2274 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   ASP A2302 " --> pdb=" O   SER A2319 " (cutoff:3.500A)
      removed outlier: 5.670A  pdb=" N   SER A2319 " --> pdb=" O   ASP A2302 " (cutoff:3.500A)
      removed outlier: 7.842A  pdb=" N   ASP A2320 " --> pdb=" O   TYR A2361 " (cutoff:3.500A)
      removed outlier: 4.767A  pdb=" N   TYR A2361 " --> pdb=" O   ASP A2320 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   ASN A2322 " --> pdb=" O   ALA A2359 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   ALA A2359 " --> pdb=" O   ASN A2322 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   LYS A2324 " --> pdb=" O   LEU A2357 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   LEU A2357 " --> pdb=" O   LYS A2324 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   ASP A2326 " --> pdb=" O   LEU A2355 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   LEU A2355 " --> pdb=" O   ASP A2326 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   SER A2328 " --> pdb=" O   TRP A2353 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   TRP A2353 " --> pdb=" O   SER A2328 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   ARG A2330 " --> pdb=" O   ASN A2351 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ASN A2351 " --> pdb=" O   ARG A2330 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   ASN A2332 " --> pdb=" O   GLY A2349 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   GLY A2349 " --> pdb=" O   ASN A2332 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   THR A2334 " --> pdb=" O   ALA A2347 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ASN A2351 " --> pdb=" O   LYS A2379 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 264 through 270
    Processing sheet with id=AA5, first strand: chain 'A' and resid 275 through 282
    Processing sheet with id=AA6, first strand: chain 'A' and resid 291 through 293
      removed outlier: 3.909A  pdb=" N   TYR A 447 " --> pdb=" O   ASN A 442 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 471 through 474
      removed outlier: 6.387A  pdb=" N   LEU A 460 " --> pdb=" O   LEU A 508 " (cutoff:3.500A)
      removed outlier: 7.984A  pdb=" N   PHE A 464 " --> pdb=" O   VAL A 504 " (cutoff:3.500A)
      removed outlier: 11.849A  pdb=" N   VAL A 504 " --> pdb=" O   PHE A 464 " (cutoff:3.500A)
      removed outlier: 19.571A  pdb=" N   TYR A 466 " --> pdb=" O   SER A 502 " (cutoff:3.500A)
      removed outlier: 23.900A  pdb=" N   SER A 502 " --> pdb=" O   TYR A 466 " (cutoff:3.500A)
      removed outlier: 5.196A  pdb=" N   ARG A 342 " --> pdb=" O   ASN A 430 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   ASN A 430 " --> pdb=" O   ARG A 342 " (cutoff:3.500A)
      removed outlier: 5.492A  pdb=" N   ILE A 318 " --> pdb=" O   THR A 467 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   THR A 467 " --> pdb=" O   ILE A 318 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 486 through 489
    Processing sheet with id=AA9, first strand: chain 'A' and resid 527 through 529
    Processing sheet with id=AB1, first strand: chain 'A' and resid 690 through 691
    Processing sheet with id=AB2, first strand: chain 'A' and resid 849 through 850
    Processing sheet with id=AB3, first strand: chain 'A' and resid 856 through 859
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 856 through 859
    current: chain 'A' and resid 1326 through 1337
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 1326 through 1337
    current: chain 'A' and resid 1423 through 1426
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'A' and resid 866 through 869
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 866 through 869
    current: chain 'A' and resid 960 through 969
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 960 through 969
    current: chain 'A' and resid 1208 through 1219
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'A' and resid 877 through 878
    Processing sheet with id=AB6, first strand: chain 'A' and resid 938 through 939
      removed outlier: 4.536A  pdb=" N   ILE A 938 " --> pdb=" O   VAL A 957 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1265 through 1266
      removed outlier: 7.069A  pdb=" N   ARG A1343 " --> pdb=" O   LYS A1491 " (cutoff:3.500A)
      removed outlier: 5.304A  pdb=" N   LYS A1491 " --> pdb=" O   ARG A1343 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   VAL A1345 " --> pdb=" O   GLY A1489 " (cutoff:3.500A)
      removed outlier: 5.125A  pdb=" N   GLY A1489 " --> pdb=" O   VAL A1345 " (cutoff:3.500A)
      removed outlier: 7.292A  pdb=" N   LYS A1347 " --> pdb=" O   MET A1487 " (cutoff:3.500A)
      removed outlier: 5.323A  pdb=" N   MET A1487 " --> pdb=" O   LYS A1347 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   VAL A1349 " --> pdb=" O   ASN A1485 " (cutoff:3.500A)
      removed outlier: 4.670A  pdb=" N   ASN A1485 " --> pdb=" O   VAL A1349 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 1313 through 1315
    Processing sheet with id=AB9, first strand: chain 'A' and resid 1862 through 1863
    Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 48
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 54 through 59
    current: chain 'B' and resid 110 through 113
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 110 through 113
    current: chain 'B' and resid 166 through 174
    Processing sheet with id=AC2, first strand: chain 'F' and resid 193 through 194
      removed outlier: 3.590A  pdb=" N   ASN F 199 " --> pdb=" O   ILE F 240 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ILE F 240 " --> pdb=" O   ASN F 199 " (cutoff:3.500A)
      removed outlier: 7.186A  pdb=" N   ASP F 397 " --> pdb=" O   ASP F  70 " (cutoff:3.500A)
      removed outlier: 5.245A  pdb=" N   ASP F  70 " --> pdb=" O   ASP F 397 " (cutoff:3.500A)
      removed outlier: 5.860A  pdb=" N   VAL F 182 " --> pdb=" O   ASN F 210 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ASN F 210 " --> pdb=" O   VAL F 182 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'F' and resid 118 through 120
      removed outlier: 3.582A  pdb=" N   ARG F 131 " --> pdb=" O   LEU F 120 " (cutoff:3.500A)

    722 hydrogen bonds defined for protein.
    1911 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: 4.93

  Time building geometry restraints manager: 2.31 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 7244
        1.34 -     1.46: 4722
        1.46 -     1.57: 10320
        1.57 -     1.69: 8
        1.69 -     1.81: 90
  Bond restraints: 22384
  Sorted by residual:
  bond pdb=" C1  LMN A2501 "
       pdb=" O5  LMN A2501 "
    ideal  model  delta    sigma   weight residual
    1.403  1.564 -0.161 2.00e-02 2.50e+03 6.48e+01
  bond pdb=" C4  LMN A2501 "
       pdb=" O4  LMN A2501 "
    ideal  model  delta    sigma   weight residual
    1.409  1.507 -0.098 2.00e-02 2.50e+03 2.39e+01
  bond pdb=" CCF LMN A2501 "
       pdb=" OBX LMN A2501 "
    ideal  model  delta    sigma   weight residual
    1.410  1.500 -0.090 2.00e-02 2.50e+03 2.02e+01
  bond pdb=" CCS LMN A2501 "
       pdb=" OBZ LMN A2501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.482 -0.088 2.00e-02 2.50e+03 1.92e+01
  bond pdb=" CCR LMN A2501 "
       pdb=" OBY LMN A2501 "
    ideal  model  delta    sigma   weight residual
    1.393  1.474 -0.081 2.00e-02 2.50e+03 1.63e+01
  ... (remaining 22379 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 29957
        1.99 -     3.99: 389
        3.99 -     5.98: 36
        5.98 -     7.98: 6
        7.98 -     9.97: 2
  Bond angle restraints: 30390
  Sorted by residual:
  angle pdb=" C4  LMN A2501 "
        pdb=" O4  LMN A2501 "
        pdb=" CCR LMN A2501 "
      ideal   model   delta    sigma   weight residual
     120.22  110.25    9.97 3.00e+00 1.11e-01 1.11e+01
  angle pdb=" CCQ LMN A2501 "
        pdb=" OCB LMN A2501 "
        pdb=" CCS LMN A2501 "
      ideal   model   delta    sigma   weight residual
     119.65  110.02    9.63 3.00e+00 1.11e-01 1.03e+01
  angle pdb=" C   SER A2050 "
        pdb=" N   THR A2051 "
        pdb=" CA  THR A2051 "
      ideal   model   delta    sigma   weight residual
     121.54  127.28   -5.74 1.91e+00 2.74e-01 9.03e+00
  angle pdb=" N   GLY D 550 "
        pdb=" CA  GLY D 550 "
        pdb=" C   GLY D 550 "
      ideal   model   delta    sigma   weight residual
     114.48  111.01    3.47 1.19e+00 7.06e-01 8.52e+00
  angle pdb=" N   VAL D 575 "
        pdb=" CA  VAL D 575 "
        pdb=" C   VAL D 575 "
      ideal   model   delta    sigma   weight residual
     113.53  110.74    2.79 9.80e-01 1.04e+00 8.08e+00
  ... (remaining 30385 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.51: 12865
       24.51 -    49.01: 436
       49.01 -    73.52: 55
       73.52 -    98.03: 38
       98.03 -   122.53: 15
  Dihedral angle restraints: 13409
    sinusoidal: 5388
      harmonic: 8021
  Sorted by residual:
  dihedral pdb=" CA  PHE D 544 "
           pdb=" C   PHE D 544 "
           pdb=" N   PRO D 545 "
           pdb=" CA  PRO D 545 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -141.33  -38.67     0      5.00e+00 4.00e-02 5.98e+01
  dihedral pdb=" CA  PRO A1063 "
           pdb=" C   PRO A1063 "
           pdb=" N   LEU A1064 "
           pdb=" CA  LEU A1064 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.60   21.40     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CCC LMN A2501 "
           pdb=" CCR LMN A2501 "
           pdb=" OBY LMN A2501 "
           pdb=" O4  LMN A2501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.74 -176.73 -122.53     1      3.00e+01 1.11e-03 1.64e+01
  ... (remaining 13406 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 2000
       0.033 -    0.066: 863
       0.066 -    0.099: 239
       0.099 -    0.132: 189
       0.132 -    0.165: 11
  Chirality restraints: 3302
  Sorted by residual:
  chirality pdb=" CCV LMN A2501 "
            pdb=" CCR LMN A2501 "
            pdb=" CCT LMN A2501 "
            pdb=" OAU LMN A2501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.28    2.45   -0.16 2.00e-01 2.50e+01 6.78e-01
  chirality pdb=" CB  ILE B 100 "
            pdb=" CA  ILE B 100 "
            pdb=" CG1 ILE B 100 "
            pdb=" CG2 ILE B 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.80   -0.15 2.00e-01 2.50e+01 5.74e-01
  chirality pdb=" CCW LMN A2501 "
            pdb=" CCS LMN A2501 "
            pdb=" CCU LMN A2501 "
            pdb=" OAV LMN A2501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.30    2.45   -0.15 2.00e-01 2.50e+01 5.36e-01
  ... (remaining 3299 not shown)

  Planarity restraints: 4025
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE D 544 "    0.061 5.00e-02 4.00e+02   9.36e-02 1.40e+01
        pdb=" N   PRO D 545 "   -0.162 5.00e-02 4.00e+02
        pdb=" CA  PRO D 545 "    0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO D 545 "    0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A1639 "   -0.012 2.00e-02 2.50e+03   2.49e-02 6.21e+00
        pdb=" C   PHE A1639 "    0.043 2.00e-02 2.50e+03
        pdb=" O   PHE A1639 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ILE A1640 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 176 "    0.011 2.00e-02 2.50e+03   2.20e-02 4.83e+00
        pdb=" C   SER A 176 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   SER A 176 "    0.014 2.00e-02 2.50e+03
        pdb=" N   MET A 177 "    0.013 2.00e-02 2.50e+03
  ... (remaining 4022 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 560
        2.70 -     3.25: 20837
        3.25 -     3.80: 35517
        3.80 -     4.35: 49146
        4.35 -     4.90: 80838
  Nonbonded interactions: 186898
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A 865 "
            pdb=" OH  TYR A1006 "
     model   vdw
     2.154 3.040
  nonbonded pdb=" OG  SER A 231 "
            pdb=" OE2 GLU A 836 "
     model   vdw
     2.161 3.040
  nonbonded pdb=" OD2 ASP A 539 "
            pdb=" OH  TYR A 590 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" O   VAL A 810 "
            pdb=" OG  SER A 829 "
     model   vdw
     2.184 3.040
  nonbonded pdb=" O   LEU A2156 "
            pdb=" OG1 THR A2160 "
     model   vdw
     2.184 3.040
  ... (remaining 186893 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             3.850
  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:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.060
  Process input model:                     18.270
  Find NCS groups from input model:        0.080
  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:             0.010
  Load rotamer database and sin/cos tables:7.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.161  22384  Z= 0.173
  Angle     :  0.557   9.973  30390  Z= 0.293
  Chirality :  0.045   0.165   3302
  Planarity :  0.004   0.094   4025
  Dihedral  : 14.056 122.534   8291
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.25 %
    Favored  : 99.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.78 %
    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 aren not related in a simple way.
  whole: -0.46 (0.16), residues: 2743
  helix: -0.92 (0.30), residues: 297
  sheet:  0.34 (0.16), residues: 1057
  loop : -0.61 (0.16), residues: 1389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F 232 
 TYR   0.019   0.001   TYR A1679 
 PHE   0.031   0.001   PHE A 656 
 TRP   0.030   0.002   TRP A1996 
 HIS   0.007   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (22384)
  covalent geometry    : angle       0.55720 (30390)
  hydrogen bonds       : bond        0.11736 (  722)
  hydrogen bonds       : angle       5.96528 ( 1911)

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

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

  5486 Ramachandran restraints generated.
    2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5486 Ramachandran restraints generated.
    2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  375 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 373
  time to evaluate  : 0.955 
Fit side-chains
REVERT: A 1724 TYR cc_start: 0.7491 (m-80) cc_final: 0.7210 (m-80)
REVERT: B   47 GLN cc_start: 0.7953 (mt0) cc_final: 0.7745 (mt0)
REVERT: B  104 TYR cc_start: 0.8576 (p90) cc_final: 0.8337 (p90)
REVERT: F  304 ILE cc_start: 0.8723 (mt) cc_final: 0.8517 (mp)
  outliers start: 2
  outliers final: 1
  residues processed: 374
  average time/residue: 0.6642
  time to fit residues: 280.7212
Evaluate side-chains
  236 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 235
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   39 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 274
   random chunks:
   chunk 197 optimal weight:    8.9990
   chunk 215 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 132 optimal weight:    5.9990
   chunk 261 optimal weight:    3.9990
   chunk 248 optimal weight:    8.9990
   chunk 207 optimal weight:    4.9990
   chunk 155 optimal weight:    5.9990
   chunk 244 optimal weight:    3.9990
   chunk 183 optimal weight:    0.0010
   chunk 111 optimal weight:    2.9990
   overall best weight:    2.1994

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

Flipped N/Q/H residues before XYZ refinement:
D 553 ASN
D 579 GLN
A 133 ASN
A 196 GLN
A 272 ASN
A 613 GLN
A 752 GLN
A 792 GLN
A1653 HIS
A1781 ASN
A1955 ASN
** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2366 ASN
** F  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 291 ASN
F 385 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.098069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.072614 restraints weight = 35720.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.2835 rms_B_bonded: 2.38
r_work: 0.2707 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2571 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8902
moved from start:          0.1264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  22384  Z= 0.213
  Angle     :  0.593   8.905  30390  Z= 0.307
  Chirality :  0.047   0.222   3302
  Planarity :  0.004   0.085   4025
  Dihedral  :  9.358 106.322   3146
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  :  8.33 %
    Favored  : 90.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.78 %
    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 aren not related in a simple way.
  whole: -0.49 (0.16), residues: 2743
  helix: -0.88 (0.30), residues: 290
  sheet:  0.25 (0.16), residues: 1060
  loop : -0.57 (0.17), residues: 1393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F 232 
 TYR   0.018   0.001   TYR D 563 
 PHE   0.025   0.002   PHE A 656 
 TRP   0.029   0.002   TRP A1996 
 HIS   0.006   0.002   HIS A2375 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 (22384)
  covalent geometry    : angle       0.59324 (30390)
  hydrogen bonds       : bond        0.03377 (  722)
  hydrogen bonds       : angle       5.34439 ( 1911)

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

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

  5486 Ramachandran restraints generated.
    2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5486 Ramachandran restraints generated.
    2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 256
  time to evaluate  : 0.955 
Fit side-chains
REVERT: D  560 ASN cc_start: 0.7542 (m-40) cc_final: 0.6903 (p0)
REVERT: A  170 ASP cc_start: 0.8596 (m-30) cc_final: 0.8386 (m-30)
REVERT: A  713 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8271 (tm-30)
REVERT: A  750 PHE cc_start: 0.7829 (m-10) cc_final: 0.7368 (m-10)
REVERT: A 1197 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8573 (mt-10)
REVERT: A 1263 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8745 (mt-10)
REVERT: A 1724 TYR cc_start: 0.8189 (m-80) cc_final: 0.7622 (m-80)
REVERT: A 1970 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8886 (mm)
REVERT: A 2199 ARG cc_start: 0.7385 (ttp-110) cc_final: 0.7125 (ttm110)
REVERT: B   47 GLN cc_start: 0.8196 (mt0) cc_final: 0.7774 (mt0)
REVERT: B   55 TYR cc_start: 0.9063 (p90) cc_final: 0.8852 (p90)
REVERT: B  104 TYR cc_start: 0.9197 (p90) cc_final: 0.8827 (p90)
REVERT: B  116 GLU cc_start: 0.8849 (pm20) cc_final: 0.8616 (mp0)
REVERT: B  169 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8013 (mt-10)
REVERT: F  304 ILE cc_start: 0.8314 (mt) cc_final: 0.8004 (mp)
REVERT: F  353 GLN cc_start: 0.8811 (pt0) cc_final: 0.8559 (pt0)
REVERT: F  365 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.7764 (ppp)
  outliers start: 38
  outliers final: 13
  residues processed: 274
  average time/residue: 0.6815
  time to fit residues: 212.4014
Evaluate side-chains
  255 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 239
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  556 LEU
Chi-restraints excluded: chain D residue  607 THR
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  235 ARG
Chi-restraints excluded: chain A residue  266 LYS
Chi-restraints excluded: chain A residue 1197 GLU
Chi-restraints excluded: chain A residue 1428 ASP
Chi-restraints excluded: chain A residue 1555 GLU
Chi-restraints excluded: chain A residue 1970 LEU
Chi-restraints excluded: chain A residue 2267 SER
Chi-restraints excluded: chain A residue 2357 LEU
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain F residue   85 LEU
Chi-restraints excluded: chain F residue  250 SER
Chi-restraints excluded: chain F residue  323 THR
Chi-restraints excluded: chain F residue  365 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 274
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 131 optimal weight:    0.0980
   chunk 56 optimal weight:    0.8980
   chunk 197 optimal weight:    7.9990
   chunk 221 optimal weight:    8.9990
   chunk 201 optimal weight:    0.9990
   chunk 215 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 85 optimal weight:    4.9990
   chunk 223 optimal weight:    2.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
D 553 ASN
A 511 ASN
A 532 GLN
A 613 GLN
A 752 GLN
A1200 ASN
A1302 ASN
A1653 HIS
A1734 ASN
** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2331 ASN
B  94 ASN
** F  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 209 GLN
** F 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 385 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.099830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.074645 restraints weight = 35661.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.2875 rms_B_bonded: 2.38
r_work: 0.2748 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2612 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8872
moved from start:          0.1394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  22384  Z= 0.112
  Angle     :  0.536   8.021  30390  Z= 0.275
  Chirality :  0.045   0.317   3302
  Planarity :  0.004   0.069   4025
  Dihedral  :  7.516  88.816   3144
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  :  8.91 %
    Favored  : 89.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.78 %
    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 aren not related in a simple way.
  whole: -0.44 (0.16), residues: 2743
  helix: -0.79 (0.30), residues: 291
  sheet:  0.28 (0.16), residues: 1064
  loop : -0.56 (0.17), residues: 1388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  48 
 TYR   0.013   0.001   TYR B  54 
 PHE   0.016   0.001   PHE A1242 
 TRP   0.018   0.001   TRP A1996 
 HIS   0.003   0.001   HIS A1653 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (22384)
  covalent geometry    : angle       0.53621 (30390)
  hydrogen bonds       : bond        0.02757 (  722)
  hydrogen bonds       : angle       5.13032 ( 1911)

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

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

  5486 Ramachandran restraints generated.
    2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5486 Ramachandran restraints generated.
    2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 250
  time to evaluate  : 0.843 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  599 LYS cc_start: 0.9064 (ttpt) cc_final: 0.8486 (ttmt)
REVERT: A  260 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8868 (mm-30)
REVERT: A  560 GLN cc_start: 0.8752 (tt0) cc_final: 0.8462 (tm-30)
REVERT: A  713 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8293 (tm-30)
REVERT: A  737 ASN cc_start: 0.8307 (t0) cc_final: 0.8085 (t0)
REVERT: A  750 PHE cc_start: 0.7564 (m-10) cc_final: 0.7300 (m-10)
REVERT: A 1263 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8705 (mt-10)
REVERT: A 1970 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8880 (mm)
REVERT: A 2016 LYS cc_start: 0.8691 (tppp) cc_final: 0.8417 (tppp)
REVERT: A 2198 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7519 (mttm)
REVERT: A 2199 ARG cc_start: 0.7377 (ttp-110) cc_final: 0.6965 (ttm110)
REVERT: B   30 GLU cc_start: 0.7691 (mp0) cc_final: 0.7428 (mp0)
REVERT: B   47 GLN cc_start: 0.8173 (mt0) cc_final: 0.7859 (mt0)
REVERT: B   59 LYS cc_start: 0.8626 (pttm) cc_final: 0.8107 (pptt)
REVERT: B  104 TYR cc_start: 0.9241 (p90) cc_final: 0.9011 (p90)
REVERT: B  116 GLU cc_start: 0.8805 (pm20) cc_final: 0.8533 (mp0)
REVERT: B  169 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8179 (mt-10)
REVERT: F   84 ASP cc_start: 0.7229 (p0) cc_final: 0.6962 (p0)
REVERT: F  304 ILE cc_start: 0.8275 (mt) cc_final: 0.7985 (mp)
REVERT: F  353 GLN cc_start: 0.8840 (pt0) cc_final: 0.8589 (pt0)
  outliers start: 40
  outliers final: 12
  residues processed: 271
  average time/residue: 0.6518
  time to fit residues: 201.2499
Evaluate side-chains
  249 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 235
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  593 SER
Chi-restraints excluded: chain D residue  607 THR
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  235 ARG
Chi-restraints excluded: chain A residue 1243 MET
Chi-restraints excluded: chain A residue 1428 ASP
Chi-restraints excluded: chain A residue 1970 LEU
Chi-restraints excluded: chain A residue 2198 LYS
Chi-restraints excluded: chain A residue 2267 SER
Chi-restraints excluded: chain A residue 2357 LEU
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain F residue   85 LEU
Chi-restraints excluded: chain F residue  250 SER
Chi-restraints excluded: chain F residue  323 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 274
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 75 optimal weight:    4.9990
   chunk 209 optimal weight:    6.9990
   chunk 181 optimal weight:   10.0000
   chunk 27 optimal weight:    0.1980
   chunk 238 optimal weight:   20.0000
   chunk 129 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9990
   chunk 47 optimal weight:    6.9990
   chunk 105 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    2.8388

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

Flipped N/Q/H residues before XYZ refinement:
D 553 ASN
** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 511 ASN
A 613 GLN
A 752 GLN
A1018 ASN
A1062 GLN
** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2331 ASN
** F  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 291 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.096344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.070946 restraints weight = 36032.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.2813 rms_B_bonded: 2.37
r_work: 0.2684 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2548 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8953
moved from start:          0.1659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  22384  Z= 0.254
  Angle     :  0.596   8.139  30390  Z= 0.309
  Chirality :  0.048   0.362   3302
  Planarity :  0.004   0.075   4025
  Dihedral  :  6.939  75.158   3144
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 10.45 %
    Favored  : 87.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.78 %
    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 aren not related in a simple way.
  whole: -0.54 (0.16), residues: 2743
  helix: -0.85 (0.30), residues: 296
  sheet:  0.16 (0.16), residues: 1064
  loop : -0.57 (0.17), residues: 1383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A2189 
 TYR   0.016   0.002   TYR A1104 
 PHE   0.023   0.002   PHE A1480 
 TRP   0.025   0.002   TRP A1996 
 HIS   0.006   0.002   HIS A2375 

Details of bonding type rmsd
  covalent geometry    : bond        0.00583 (22384)
  covalent geometry    : angle       0.59616 (30390)
  hydrogen bonds       : bond        0.03270 (  722)
  hydrogen bonds       : angle       5.27617 ( 1911)

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

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

  5486 Ramachandran restraints generated.
    2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5486 Ramachandran restraints generated.
    2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 243
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
REVERT: D  578 LYS cc_start: 0.8863 (tptp) cc_final: 0.8627 (tppp)
REVERT: D  599 LYS cc_start: 0.9060 (ttpt) cc_final: 0.8776 (ttmt)
REVERT: A  560 GLN cc_start: 0.8758 (tt0) cc_final: 0.8504 (tm-30)
REVERT: A  713 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8328 (tm-30)
REVERT: A  737 ASN cc_start: 0.8543 (t0) cc_final: 0.8236 (t0)
REVERT: A  786 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8378 (pp30)
REVERT: A 1263 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8720 (mt-10)
REVERT: A 1949 GLN cc_start: 0.7535 (tt0) cc_final: 0.7277 (tp40)
REVERT: A 2016 LYS cc_start: 0.8721 (tppp) cc_final: 0.8440 (tppp)
REVERT: B   30 GLU cc_start: 0.7779 (mp0) cc_final: 0.7477 (mp0)
REVERT: B   47 GLN cc_start: 0.8115 (mt0) cc_final: 0.7806 (mt0)
REVERT: B   59 LYS cc_start: 0.8667 (pttm) cc_final: 0.8227 (pptt)
REVERT: B  116 GLU cc_start: 0.8871 (pm20) cc_final: 0.8568 (mp0)
REVERT: B  169 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8192 (mt-10)
REVERT: F   84 ASP cc_start: 0.7425 (p0) cc_final: 0.7221 (p0)
REVERT: F  304 ILE cc_start: 0.8294 (mt) cc_final: 0.7976 (mp)
REVERT: F  353 GLN cc_start: 0.8922 (pt0) cc_final: 0.8641 (pt0)
REVERT: F  365 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.7586 (ppp)
  outliers start: 42
  outliers final: 14
  residues processed: 265
  average time/residue: 0.6380
  time to fit residues: 192.8924
Evaluate side-chains
  244 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 228
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  542 VAL
Chi-restraints excluded: chain D residue  556 LEU
Chi-restraints excluded: chain D residue  593 SER
Chi-restraints excluded: chain D residue  607 THR
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  786 GLN
Chi-restraints excluded: chain A residue 1286 ASP
Chi-restraints excluded: chain A residue 1428 ASP
Chi-restraints excluded: chain A residue 2267 SER
Chi-restraints excluded: chain A residue 2357 LEU
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain F residue   85 LEU
Chi-restraints excluded: chain F residue  250 SER
Chi-restraints excluded: chain F residue  323 THR
Chi-restraints excluded: chain F residue  365 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 274
   random chunks:
   chunk 214 optimal weight:    4.9990
   chunk 211 optimal weight:    2.9990
   chunk 244 optimal weight:    5.9990
   chunk 190 optimal weight:    6.9990
   chunk 66 optimal weight:    8.9990
   chunk 228 optimal weight:    9.9990
   chunk 260 optimal weight:    7.9990
   chunk 121 optimal weight:    0.6980
   chunk 81 optimal weight:    6.9990
   chunk 54 optimal weight:    3.9990
   chunk 70 optimal weight:    0.6980
   overall best weight:    2.6786

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

Flipped N/Q/H residues before XYZ refinement:
D 553 ASN
A 264 GLN
A 511 ASN
A 532 GLN
A 613 GLN
A 752 GLN
A1348 ASN
A1485 ASN
A1740 ASN
A1767 GLN
** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2331 ASN
B  94 ASN
F  47 GLN
F 209 GLN
** F 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 385 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.096120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.070733 restraints weight = 35923.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.2803 rms_B_bonded: 2.38
r_work: 0.2673 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2536 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8939
moved from start:          0.1796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  22384  Z= 0.241
  Angle     :  0.588   8.204  30390  Z= 0.306
  Chirality :  0.048   0.374   3302
  Planarity :  0.004   0.074   4025
  Dihedral  :  6.557  74.383   3144
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 10.91 %
    Favored  : 87.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.78 %
    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 aren not related in a simple way.
  whole: -0.60 (0.16), residues: 2743
  helix: -0.95 (0.30), residues: 302
  sheet:  0.11 (0.16), residues: 1059
  loop : -0.58 (0.17), residues: 1382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 164 
 TYR   0.016   0.001   TYR A1104 
 PHE   0.020   0.002   PHE A1480 
 TRP   0.021   0.002   TRP A1996 
 HIS   0.005   0.001   HIS A2375 

Details of bonding type rmsd
  covalent geometry    : bond        0.00549 (22384)
  covalent geometry    : angle       0.58785 (30390)
  hydrogen bonds       : bond        0.03201 (  722)
  hydrogen bonds       : angle       5.30771 ( 1911)

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

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

  5486 Ramachandran restraints generated.
    2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5486 Ramachandran restraints generated.
    2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 234
  time to evaluate  : 0.950 
Fit side-chains
   revert: symmetry clash
REVERT: D  578 LYS cc_start: 0.8866 (tptp) cc_final: 0.8613 (tppp)
REVERT: D  599 LYS cc_start: 0.9051 (ttpt) cc_final: 0.8800 (ttmt)
REVERT: A  260 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8854 (mm-30)
REVERT: A  560 GLN cc_start: 0.8776 (tt0) cc_final: 0.8514 (tm-30)
REVERT: A  713 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8336 (tm-30)
REVERT: A  786 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8361 (pp30)
REVERT: A  809 GLU cc_start: 0.8579 (tt0) cc_final: 0.7949 (tm-30)
REVERT: A 1197 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8698 (mt-10)
REVERT: A 1263 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8709 (mt-10)
REVERT: A 1580 TRP cc_start: 0.8254 (OUTLIER) cc_final: 0.6968 (p-90)
REVERT: A 1949 GLN cc_start: 0.7536 (tt0) cc_final: 0.7259 (tp40)
REVERT: A 2016 LYS cc_start: 0.8747 (tppp) cc_final: 0.8470 (tppp)
REVERT: B   30 GLU cc_start: 0.7834 (mp0) cc_final: 0.7545 (mp0)
REVERT: B   47 GLN cc_start: 0.8108 (mt0) cc_final: 0.7780 (mt0)
REVERT: B   59 LYS cc_start: 0.8689 (pttm) cc_final: 0.8229 (pptt)
REVERT: B  104 TYR cc_start: 0.9251 (p90) cc_final: 0.9017 (p90)
REVERT: B  116 GLU cc_start: 0.8869 (pm20) cc_final: 0.8548 (mp0)
REVERT: B  169 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8218 (mt-10)
REVERT: F  304 ILE cc_start: 0.8268 (mt) cc_final: 0.7969 (mp)
REVERT: F  365 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.7531 (ppp)
  outliers start: 49
  outliers final: 17
  residues processed: 261
  average time/residue: 0.7173
  time to fit residues: 213.2718
Evaluate side-chains
  244 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 223
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  542 VAL
Chi-restraints excluded: chain D residue  593 SER
Chi-restraints excluded: chain D residue  607 THR
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  554 ASN
Chi-restraints excluded: chain A residue  697 VAL
Chi-restraints excluded: chain A residue  786 GLN
Chi-restraints excluded: chain A residue  954 ILE
Chi-restraints excluded: chain A residue 1197 GLU
Chi-restraints excluded: chain A residue 1286 ASP
Chi-restraints excluded: chain A residue 1428 ASP
Chi-restraints excluded: chain A residue 1580 TRP
Chi-restraints excluded: chain A residue 2267 SER
Chi-restraints excluded: chain A residue 2357 LEU
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain F residue   85 LEU
Chi-restraints excluded: chain F residue  250 SER
Chi-restraints excluded: chain F residue  323 THR
Chi-restraints excluded: chain F residue  365 MET
Chi-restraints excluded: chain F residue  392 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 274
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 98 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 145 optimal weight:    8.9990
   chunk 215 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 118 optimal weight:    0.5980
   chunk 243 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   chunk 6 optimal weight:    0.6980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
D 553 ASN
A 511 ASN
A 532 GLN
A 613 GLN
A 752 GLN
A 818 ASN
A1740 ASN
** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2331 ASN
F  47 GLN
F  72 GLN
F 209 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.097925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.072718 restraints weight = 35726.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.2843 rms_B_bonded: 2.38
r_work: 0.2714 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2577 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8908
moved from start:          0.1785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  22384  Z= 0.131
  Angle     :  0.541   8.572  30390  Z= 0.280
  Chirality :  0.046   0.350   3302
  Planarity :  0.004   0.069   4025
  Dihedral  :  6.175  75.199   3144
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 11.75 %
    Favored  : 86.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.78 %
    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 aren not related in a simple way.
  whole: -0.52 (0.16), residues: 2743
  helix: -0.77 (0.30), residues: 294
  sheet:  0.14 (0.16), residues: 1064
  loop : -0.55 (0.17), residues: 1385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 164 
 TYR   0.011   0.001   TYR A1394 
 PHE   0.016   0.001   PHE A1480 
 TRP   0.015   0.001   TRP A2353 
 HIS   0.003   0.001   HIS A1672 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (22384)
  covalent geometry    : angle       0.54078 (30390)
  hydrogen bonds       : bond        0.02734 (  722)
  hydrogen bonds       : angle       5.13371 ( 1911)

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

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

  5486 Ramachandran restraints generated.
    2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5486 Ramachandran restraints generated.
    2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 247
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
REVERT: D  599 LYS cc_start: 0.8981 (ttpt) cc_final: 0.8756 (ttmt)
REVERT: A  260 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8868 (mm-30)
REVERT: A  277 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8700 (mm-40)
REVERT: A  560 GLN cc_start: 0.8760 (tt0) cc_final: 0.8501 (tm-30)
REVERT: A  573 LYS cc_start: 0.8942 (mttm) cc_final: 0.8625 (mtpp)
REVERT: A  713 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8296 (tm-30)
REVERT: A  723 LEU cc_start: 0.8509 (tp) cc_final: 0.8302 (mt)
REVERT: A  809 GLU cc_start: 0.8578 (tt0) cc_final: 0.7929 (tm-30)
REVERT: A  870 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8770 (mmp)
REVERT: A 1263 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8702 (mt-10)
REVERT: A 1526 ASP cc_start: 0.8353 (m-30) cc_final: 0.8151 (m-30)
REVERT: A 1580 TRP cc_start: 0.8206 (OUTLIER) cc_final: 0.6986 (p-90)
REVERT: A 1949 GLN cc_start: 0.7521 (tt0) cc_final: 0.7245 (tp40)
REVERT: A 1970 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8887 (mm)
REVERT: A 2016 LYS cc_start: 0.8733 (tppp) cc_final: 0.8463 (tppp)
REVERT: A 2248 GLN cc_start: 0.8853 (tt0) cc_final: 0.8455 (tt0)
REVERT: A 2333 GLU cc_start: 0.8762 (tt0) cc_final: 0.8474 (mp0)
REVERT: B   30 GLU cc_start: 0.7862 (mp0) cc_final: 0.7581 (mp0)
REVERT: B   47 GLN cc_start: 0.8057 (mt0) cc_final: 0.7720 (mt0)
REVERT: B   59 LYS cc_start: 0.8691 (pttm) cc_final: 0.8251 (pptt)
REVERT: B  104 TYR cc_start: 0.9217 (p90) cc_final: 0.8852 (p90)
REVERT: B  116 GLU cc_start: 0.8854 (pm20) cc_final: 0.8582 (mp0)
REVERT: B  169 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8139 (mt-10)
REVERT: F   84 ASP cc_start: 0.7209 (p0) cc_final: 0.6956 (p0)
REVERT: F  141 ASP cc_start: 0.8760 (p0) cc_final: 0.8555 (p0)
REVERT: F  304 ILE cc_start: 0.8231 (mt) cc_final: 0.7924 (mp)
REVERT: F  365 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.7470 (ppp)
  outliers start: 44
  outliers final: 19
  residues processed: 268
  average time/residue: 0.6989
  time to fit residues: 213.4563
Evaluate side-chains
  263 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 239
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  542 VAL
Chi-restraints excluded: chain D residue  591 LEU
Chi-restraints excluded: chain D residue  607 THR
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  235 ARG
Chi-restraints excluded: chain A residue  277 GLN
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  697 VAL
Chi-restraints excluded: chain A residue  870 MET
Chi-restraints excluded: chain A residue 1286 ASP
Chi-restraints excluded: chain A residue 1428 ASP
Chi-restraints excluded: chain A residue 1580 TRP
Chi-restraints excluded: chain A residue 1609 ASP
Chi-restraints excluded: chain A residue 1970 LEU
Chi-restraints excluded: chain A residue 2126 THR
Chi-restraints excluded: chain A residue 2357 LEU
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain F residue   85 LEU
Chi-restraints excluded: chain F residue  250 SER
Chi-restraints excluded: chain F residue  323 THR
Chi-restraints excluded: chain F residue  365 MET
Chi-restraints excluded: chain F residue  392 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 274
   random chunks:
   chunk 168 optimal weight:    3.9990
   chunk 270 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0470
   chunk 6 optimal weight:    0.9990
   chunk 120 optimal weight:    0.8980
   chunk 259 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 248 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.7884

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

Flipped N/Q/H residues before XYZ refinement:
D 553 ASN
A 511 ASN
A 532 GLN
A 613 GLN
A 752 GLN
A1740 ASN
** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2136 ASN
A2331 ASN
F  47 GLN
F 209 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.099002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.073839 restraints weight = 35721.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.2865 rms_B_bonded: 2.39
r_work: 0.2736 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2602 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8890
moved from start:          0.1855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  22384  Z= 0.112
  Angle     :  0.525   8.831  30390  Z= 0.271
  Chirality :  0.045   0.322   3302
  Planarity :  0.004   0.066   4025
  Dihedral  :  5.886  74.776   3144
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 12.54 %
    Favored  : 85.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.78 %
    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 aren not related in a simple way.
  whole: -0.44 (0.16), residues: 2743
  helix: -0.65 (0.30), residues: 298
  sheet:  0.20 (0.16), residues: 1062
  loop : -0.51 (0.17), residues: 1383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A2189 
 TYR   0.012   0.001   TYR A1394 
 PHE   0.015   0.001   PHE A1242 
 TRP   0.014   0.001   TRP A2353 
 HIS   0.003   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (22384)
  covalent geometry    : angle       0.52484 (30390)
  hydrogen bonds       : bond        0.02562 (  722)
  hydrogen bonds       : angle       4.97300 ( 1911)

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

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

  5486 Ramachandran restraints generated.
    2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5486 Ramachandran restraints generated.
    2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 252
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  260 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8866 (mm-30)
REVERT: A  264 GLN cc_start: 0.8578 (pt0) cc_final: 0.8294 (pt0)
REVERT: A  560 GLN cc_start: 0.8749 (tt0) cc_final: 0.8466 (tm-30)
REVERT: A  573 LYS cc_start: 0.8888 (mttm) cc_final: 0.8543 (mtpp)
REVERT: A  713 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8262 (tm-30)
REVERT: A  723 LEU cc_start: 0.8553 (tp) cc_final: 0.8322 (mt)
REVERT: A  809 GLU cc_start: 0.8556 (tt0) cc_final: 0.7923 (tm-30)
REVERT: A  870 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8724 (mmp)
REVERT: A 1263 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8682 (mt-10)
REVERT: A 1580 TRP cc_start: 0.8189 (OUTLIER) cc_final: 0.6812 (p-90)
REVERT: A 1949 GLN cc_start: 0.7563 (tt0) cc_final: 0.7284 (tp40)
REVERT: A 1970 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8884 (mm)
REVERT: A 2016 LYS cc_start: 0.8707 (tppp) cc_final: 0.8466 (tppp)
REVERT: A 2190 TYR cc_start: 0.6887 (m-80) cc_final: 0.6473 (m-80)
REVERT: A 2199 ARG cc_start: 0.7565 (ttp-110) cc_final: 0.6931 (ttp80)
REVERT: A 2333 GLU cc_start: 0.8745 (tt0) cc_final: 0.8473 (mp0)
REVERT: B   30 GLU cc_start: 0.7873 (mp0) cc_final: 0.7592 (mp0)
REVERT: B   47 GLN cc_start: 0.8065 (mt0) cc_final: 0.7700 (mt0)
REVERT: B   59 LYS cc_start: 0.8665 (pttm) cc_final: 0.8206 (pptt)
REVERT: B  116 GLU cc_start: 0.8867 (pm20) cc_final: 0.8568 (mp0)
REVERT: B  169 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8356 (mt-10)
REVERT: F   84 ASP cc_start: 0.7115 (p0) cc_final: 0.6907 (p0)
REVERT: F  141 ASP cc_start: 0.8687 (p0) cc_final: 0.8474 (p0)
REVERT: F  293 LYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6845 (ttmm)
REVERT: F  304 ILE cc_start: 0.8224 (mt) cc_final: 0.7914 (mp)
REVERT: F  365 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.7480 (ppp)
  outliers start: 39
  outliers final: 17
  residues processed: 273
  average time/residue: 0.6408
  time to fit residues: 199.2012
Evaluate side-chains
  266 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 244
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  542 VAL
Chi-restraints excluded: chain D residue  607 THR
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  235 ARG
Chi-restraints excluded: chain A residue  277 GLN
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  697 VAL
Chi-restraints excluded: chain A residue  870 MET
Chi-restraints excluded: chain A residue 1243 MET
Chi-restraints excluded: chain A residue 1286 ASP
Chi-restraints excluded: chain A residue 1428 ASP
Chi-restraints excluded: chain A residue 1580 TRP
Chi-restraints excluded: chain A residue 1970 LEU
Chi-restraints excluded: chain A residue 2267 SER
Chi-restraints excluded: chain A residue 2357 LEU
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain F residue   85 LEU
Chi-restraints excluded: chain F residue  250 SER
Chi-restraints excluded: chain F residue  293 LYS
Chi-restraints excluded: chain F residue  323 THR
Chi-restraints excluded: chain F residue  365 MET
Chi-restraints excluded: chain F residue  392 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 274
   random chunks:
   chunk 205 optimal weight:    0.0570
   chunk 166 optimal weight:    6.9990
   chunk 94 optimal weight:    0.4980
   chunk 87 optimal weight:    0.6980
   chunk 206 optimal weight:    3.9990
   chunk 254 optimal weight:    8.9990
   chunk 217 optimal weight:    0.7980
   chunk 158 optimal weight:    3.9990
   chunk 194 optimal weight:    7.9990
   chunk 238 optimal weight:    6.9990
   chunk 115 optimal weight:    0.9980
   overall best weight:    0.6098

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

Flipped N/Q/H residues before XYZ refinement:
D 553 ASN
A 511 ASN
A 613 GLN
A 752 GLN
A1667 ASN
A1732 ASN
A1740 ASN
** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2331 ASN
F  47 GLN
F 209 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.099704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.074661 restraints weight = 35561.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.2881 rms_B_bonded: 2.38
r_work: 0.2754 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2620 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8877
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  22384  Z= 0.102
  Angle     :  0.522   8.932  30390  Z= 0.269
  Chirality :  0.045   0.295   3302
  Planarity :  0.003   0.062   4025
  Dihedral  :  5.685  74.132   3144
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 12.70 %
    Favored  : 85.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.78 %
    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 aren not related in a simple way.
  whole: -0.38 (0.16), residues: 2743
  helix: -0.61 (0.30), residues: 298
  sheet:  0.26 (0.16), residues: 1059
  loop : -0.48 (0.17), residues: 1386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A2398 
 TYR   0.011   0.001   TYR A2159 
 PHE   0.019   0.001   PHE A 750 
 TRP   0.013   0.001   TRP A2353 
 HIS   0.003   0.001   HIS A1672 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (22384)
  covalent geometry    : angle       0.52234 (30390)
  hydrogen bonds       : bond        0.02462 (  722)
  hydrogen bonds       : angle       4.86733 ( 1911)

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

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

  5486 Ramachandran restraints generated.
    2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5486 Ramachandran restraints generated.
    2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 251
  time to evaluate  : 0.978 
Fit side-chains
   revert: symmetry clash
REVERT: D  578 LYS cc_start: 0.8919 (tptp) cc_final: 0.8478 (mmmt)
REVERT: A  170 ASP cc_start: 0.8507 (m-30) cc_final: 0.8259 (m-30)
REVERT: A  260 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8910 (mm-30)
REVERT: A  264 GLN cc_start: 0.8586 (pt0) cc_final: 0.8290 (pt0)
REVERT: A  560 GLN cc_start: 0.8728 (tt0) cc_final: 0.8446 (tm-30)
REVERT: A  573 LYS cc_start: 0.8843 (mttm) cc_final: 0.8517 (mtpp)
REVERT: A  713 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8253 (tm-30)
REVERT: A  723 LEU cc_start: 0.8541 (tp) cc_final: 0.8312 (mt)
REVERT: A  809 GLU cc_start: 0.8544 (tt0) cc_final: 0.7913 (tm-30)
REVERT: A 1197 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8614 (mt-10)
REVERT: A 1263 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8665 (mt-10)
REVERT: A 1580 TRP cc_start: 0.8160 (OUTLIER) cc_final: 0.6772 (p-90)
REVERT: A 1949 GLN cc_start: 0.7587 (tt0) cc_final: 0.7308 (tp40)
REVERT: A 1970 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8884 (mm)
REVERT: A 2190 TYR cc_start: 0.6881 (m-80) cc_final: 0.6473 (m-80)
REVERT: A 2248 GLN cc_start: 0.8885 (tt0) cc_final: 0.8423 (tt0)
REVERT: A 2333 GLU cc_start: 0.8702 (tt0) cc_final: 0.8464 (mp0)
REVERT: B   30 GLU cc_start: 0.7883 (mp0) cc_final: 0.7592 (mp0)
REVERT: B   47 GLN cc_start: 0.7999 (mt0) cc_final: 0.7618 (mt0)
REVERT: B   59 LYS cc_start: 0.8675 (pttm) cc_final: 0.8223 (pptt)
REVERT: B  116 GLU cc_start: 0.8864 (pm20) cc_final: 0.8548 (mp0)
REVERT: B  169 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8359 (mt-10)
REVERT: F  304 ILE cc_start: 0.8262 (mt) cc_final: 0.7990 (mp)
REVERT: F  365 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.7473 (ppp)
  outliers start: 34
  outliers final: 17
  residues processed: 270
  average time/residue: 0.7258
  time to fit residues: 223.1552
Evaluate side-chains
  265 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 244
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  542 VAL
Chi-restraints excluded: chain D residue  607 THR
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  235 ARG
Chi-restraints excluded: chain A residue  554 ASN
Chi-restraints excluded: chain A residue  697 VAL
Chi-restraints excluded: chain A residue 1197 GLU
Chi-restraints excluded: chain A residue 1243 MET
Chi-restraints excluded: chain A residue 1286 ASP
Chi-restraints excluded: chain A residue 1428 ASP
Chi-restraints excluded: chain A residue 1580 TRP
Chi-restraints excluded: chain A residue 1609 ASP
Chi-restraints excluded: chain A residue 1970 LEU
Chi-restraints excluded: chain A residue 2290 MET
Chi-restraints excluded: chain A residue 2357 LEU
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain F residue   85 LEU
Chi-restraints excluded: chain F residue  250 SER
Chi-restraints excluded: chain F residue  323 THR
Chi-restraints excluded: chain F residue  365 MET
Chi-restraints excluded: chain F residue  392 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 274
   random chunks:
   chunk 248 optimal weight:    7.9990
   chunk 88 optimal weight:    1.9990
   chunk 103 optimal weight:    0.0670
   chunk 45 optimal weight:    4.9990
   chunk 100 optimal weight:    4.9990
   chunk 202 optimal weight:    0.6980
   chunk 199 optimal weight:    0.3980
   chunk 67 optimal weight:    4.9990
   chunk 138 optimal weight:    0.0270
   chunk 144 optimal weight:    2.9990
   chunk 161 optimal weight:    7.9990
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
D 551 ASN
D 553 ASN
A 511 ASN
A 532 GLN
A 613 GLN
A 752 GLN
A1740 ASN
** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2331 ASN
F  47 GLN
F 209 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.099928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.074960 restraints weight = 35515.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.2888 rms_B_bonded: 2.37
r_work: 0.2760 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2624 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8875
moved from start:          0.1984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  22384  Z= 0.103
  Angle     :  0.527   9.210  30390  Z= 0.272
  Chirality :  0.045   0.293   3302
  Planarity :  0.004   0.080   4025
  Dihedral  :  5.589  73.614   3144
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 13.66 %
    Favored  : 85.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.78 %
    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 aren not related in a simple way.
  whole: -0.34 (0.16), residues: 2743
  helix: -0.59 (0.30), residues: 298
  sheet:  0.27 (0.16), residues: 1064
  loop : -0.45 (0.17), residues: 1381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A2189 
 TYR   0.013   0.001   TYR D 563 
 PHE   0.024   0.001   PHE A 750 
 TRP   0.013   0.001   TRP A1996 
 HIS   0.003   0.001   HIS A1672 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 (22384)
  covalent geometry    : angle       0.52749 (30390)
  hydrogen bonds       : bond        0.02476 (  722)
  hydrogen bonds       : angle       4.83055 ( 1911)

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

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

  5486 Ramachandran restraints generated.
    2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5486 Ramachandran restraints generated.
    2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 251
  time to evaluate  : 0.872 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  578 LYS cc_start: 0.8913 (tptp) cc_final: 0.8684 (tppp)
REVERT: A  260 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8909 (mm-30)
REVERT: A  264 GLN cc_start: 0.8552 (pt0) cc_final: 0.8296 (pt0)
REVERT: A  560 GLN cc_start: 0.8738 (tt0) cc_final: 0.8448 (tm-30)
REVERT: A  573 LYS cc_start: 0.8835 (mttm) cc_final: 0.8521 (mtpp)
REVERT: A  713 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8275 (tm-30)
REVERT: A  723 LEU cc_start: 0.8559 (tp) cc_final: 0.8320 (mt)
REVERT: A  749 ILE cc_start: 0.8262 (pt) cc_final: 0.8015 (pp)
REVERT: A  809 GLU cc_start: 0.8533 (tt0) cc_final: 0.7898 (tm-30)
REVERT: A 1197 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8633 (mt-10)
REVERT: A 1263 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8671 (mt-10)
REVERT: A 1580 TRP cc_start: 0.8151 (OUTLIER) cc_final: 0.6767 (p-90)
REVERT: A 1949 GLN cc_start: 0.7574 (tt0) cc_final: 0.7295 (tp40)
REVERT: A 1970 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8876 (mm)
REVERT: A 2189 ARG cc_start: 0.8326 (ttm-80) cc_final: 0.7648 (mtt90)
REVERT: A 2190 TYR cc_start: 0.6900 (m-80) cc_final: 0.6466 (m-80)
REVERT: A 2199 ARG cc_start: 0.7510 (ttp-110) cc_final: 0.7246 (ttp-110)
REVERT: A 2333 GLU cc_start: 0.8678 (tt0) cc_final: 0.8450 (mp0)
REVERT: B   30 GLU cc_start: 0.7887 (mp0) cc_final: 0.7599 (mp0)
REVERT: B   47 GLN cc_start: 0.7958 (mt0) cc_final: 0.7600 (mt0)
REVERT: B   59 LYS cc_start: 0.8690 (pttm) cc_final: 0.8267 (pptt)
REVERT: B  102 LYS cc_start: 0.9084 (tttt) cc_final: 0.8750 (tmmm)
REVERT: B  104 TYR cc_start: 0.9183 (p90) cc_final: 0.8811 (p90)
REVERT: B  116 GLU cc_start: 0.8869 (pm20) cc_final: 0.8545 (mp0)
REVERT: B  169 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8185 (mt-10)
REVERT: F  304 ILE cc_start: 0.8241 (mt) cc_final: 0.7964 (mp)
  outliers start: 28
  outliers final: 17
  residues processed: 268
  average time/residue: 0.6509
  time to fit residues: 199.3652
Evaluate side-chains
  263 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 243
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  542 VAL
Chi-restraints excluded: chain D residue  565 LEU
Chi-restraints excluded: chain D residue  607 THR
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  235 ARG
Chi-restraints excluded: chain A residue  554 ASN
Chi-restraints excluded: chain A residue  697 VAL
Chi-restraints excluded: chain A residue 1197 GLU
Chi-restraints excluded: chain A residue 1243 MET
Chi-restraints excluded: chain A residue 1428 ASP
Chi-restraints excluded: chain A residue 1580 TRP
Chi-restraints excluded: chain A residue 1970 LEU
Chi-restraints excluded: chain A residue 2024 LEU
Chi-restraints excluded: chain A residue 2290 MET
Chi-restraints excluded: chain A residue 2357 LEU
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain F residue   85 LEU
Chi-restraints excluded: chain F residue  250 SER
Chi-restraints excluded: chain F residue  323 THR
Chi-restraints excluded: chain F residue  392 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 274
   random chunks:
   chunk 97 optimal weight:    0.9980
   chunk 138 optimal weight:    0.0670
   chunk 59 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0670
   chunk 129 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 219 optimal weight:    6.9990
   chunk 144 optimal weight:    2.9990
   chunk 206 optimal weight:    9.9990
   chunk 29 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.7858

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

Flipped N/Q/H residues before XYZ refinement:
D 553 ASN
D 579 GLN
A 511 ASN
A 532 GLN
A 613 GLN
A 851 GLN
A1740 ASN
** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 209 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.099820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.074675 restraints weight = 35674.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.2881 rms_B_bonded: 2.39
r_work: 0.2755 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2621 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8878
moved from start:          0.2008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  22384  Z= 0.110
  Angle     :  0.527   9.364  30390  Z= 0.272
  Chirality :  0.045   0.293   3302
  Planarity :  0.004   0.079   4025
  Dihedral  :  5.522  72.968   3144
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 13.87 %
    Favored  : 85.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.78 %
    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 aren not related in a simple way.
  whole: -0.33 (0.16), residues: 2743
  helix: -0.57 (0.30), residues: 298
  sheet:  0.26 (0.16), residues: 1066
  loop : -0.42 (0.17), residues: 1379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A2189 
 TYR   0.012   0.001   TYR A 806 
 PHE   0.016   0.001   PHE A1242 
 TRP   0.013   0.001   TRP A1996 
 HIS   0.003   0.001   HIS A1672 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (22384)
  covalent geometry    : angle       0.52700 (30390)
  hydrogen bonds       : bond        0.02507 (  722)
  hydrogen bonds       : angle       4.82287 ( 1911)

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

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

  5486 Ramachandran restraints generated.
    2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5486 Ramachandran restraints generated.
    2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 247
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  578 LYS cc_start: 0.8907 (tptp) cc_final: 0.8674 (tppp)
REVERT: A  260 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8913 (mm-30)
REVERT: A  264 GLN cc_start: 0.8580 (pt0) cc_final: 0.8373 (pt0)
REVERT: A  560 GLN cc_start: 0.8735 (tt0) cc_final: 0.8441 (tm-30)
REVERT: A  573 LYS cc_start: 0.8848 (mttm) cc_final: 0.8549 (mtpp)
REVERT: A  713 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8269 (tm-30)
REVERT: A  723 LEU cc_start: 0.8567 (tp) cc_final: 0.8318 (mt)
REVERT: A  749 ILE cc_start: 0.8310 (pt) cc_final: 0.8025 (pp)
REVERT: A  809 GLU cc_start: 0.8538 (tt0) cc_final: 0.7887 (tm-30)
REVERT: A 1197 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8615 (mt-10)
REVERT: A 1263 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8674 (mt-10)
REVERT: A 1580 TRP cc_start: 0.8154 (OUTLIER) cc_final: 0.6794 (p-90)
REVERT: A 1949 GLN cc_start: 0.7603 (tt0) cc_final: 0.7326 (tp40)
REVERT: A 1970 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8896 (mm)
REVERT: A 2016 LYS cc_start: 0.8710 (tptm) cc_final: 0.8429 (tppp)
REVERT: A 2190 TYR cc_start: 0.6917 (m-80) cc_final: 0.6471 (m-80)
REVERT: A 2199 ARG cc_start: 0.7544 (ttp-110) cc_final: 0.6911 (ttp80)
REVERT: A 2333 GLU cc_start: 0.8706 (tt0) cc_final: 0.8468 (mp0)
REVERT: B   30 GLU cc_start: 0.7908 (mp0) cc_final: 0.7635 (mp0)
REVERT: B   47 GLN cc_start: 0.7895 (mt0) cc_final: 0.7549 (mt0)
REVERT: B   59 LYS cc_start: 0.8676 (pttm) cc_final: 0.8174 (pptt)
REVERT: B  102 LYS cc_start: 0.9072 (tttt) cc_final: 0.8746 (tmmm)
REVERT: B  116 GLU cc_start: 0.8858 (pm20) cc_final: 0.8530 (mp0)
REVERT: B  169 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8239 (mt-10)
REVERT: F  293 LYS cc_start: 0.7189 (OUTLIER) cc_final: 0.6920 (ttmm)
REVERT: F  304 ILE cc_start: 0.8262 (mt) cc_final: 0.7985 (mp)
  outliers start: 26
  outliers final: 19
  residues processed: 264
  average time/residue: 0.6257
  time to fit residues: 188.6448
Evaluate side-chains
  267 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 244
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  542 VAL
Chi-restraints excluded: chain D residue  565 LEU
Chi-restraints excluded: chain D residue  607 THR
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  235 ARG
Chi-restraints excluded: chain A residue  554 ASN
Chi-restraints excluded: chain A residue  697 VAL
Chi-restraints excluded: chain A residue 1197 GLU
Chi-restraints excluded: chain A residue 1243 MET
Chi-restraints excluded: chain A residue 1428 ASP
Chi-restraints excluded: chain A residue 1580 TRP
Chi-restraints excluded: chain A residue 1609 ASP
Chi-restraints excluded: chain A residue 1970 LEU
Chi-restraints excluded: chain A residue 2024 LEU
Chi-restraints excluded: chain A residue 2267 SER
Chi-restraints excluded: chain A residue 2290 MET
Chi-restraints excluded: chain A residue 2357 LEU
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain F residue   85 LEU
Chi-restraints excluded: chain F residue  250 SER
Chi-restraints excluded: chain F residue  293 LYS
Chi-restraints excluded: chain F residue  323 THR
Chi-restraints excluded: chain F residue  392 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 274
   random chunks:
   chunk 129 optimal weight:    3.9990
   chunk 225 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9990
   chunk 113 optimal weight:    5.9990
   chunk 157 optimal weight:    2.9990
   chunk 178 optimal weight:    3.9990
   chunk 4 optimal weight:   10.0000
   chunk 60 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   chunk 15 optimal weight:    9.9990
   chunk 256 optimal weight:    0.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
D 553 ASN
A 511 ASN
A 532 GLN
A 613 GLN
A1740 ASN
** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 209 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.097730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.072426 restraints weight = 35700.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.2837 rms_B_bonded: 2.37
r_work: 0.2706 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2571 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8916
moved from start:          0.2021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  22384  Z= 0.174
  Angle     :  0.562   9.535  30390  Z= 0.291
  Chirality :  0.046   0.299   3302
  Planarity :  0.004   0.077   4025
  Dihedral  :  5.728  71.633   3144
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 13.95 %
    Favored  : 84.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.78 %
    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 aren not related in a simple way.
  whole: -0.40 (0.16), residues: 2743
  helix: -0.58 (0.31), residues: 299
  sheet:  0.18 (0.16), residues: 1065
  loop : -0.46 (0.17), residues: 1379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A2398 
 TYR   0.014   0.001   TYR A1104 
 PHE   0.019   0.001   PHE A1480 
 TRP   0.019   0.001   TRP A1996 
 HIS   0.003   0.001   HIS A 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 (22384)
  covalent geometry    : angle       0.56177 (30390)
  hydrogen bonds       : bond        0.02884 (  722)
  hydrogen bonds       : angle       5.00974 ( 1911)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7290.77 seconds
wall clock time: 125 minutes 5.09 seconds (7505.09 seconds total)