Starting phenix.real_space_refine
on Thu Jun 12 14:49:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g5i_29745/06_2025/8g5i_29745.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g5i_29745/06_2025/8g5i_29745.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g5i_29745/06_2025/8g5i_29745.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g5i_29745/06_2025/8g5i_29745.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g5i_29745/06_2025/8g5i_29745.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g5i_29745/06_2025/8g5i_29745.cif"
  }
  resolution = 2.75
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      38      5.49       5
     S      80      5.16       5
     C    8859      2.51       5
     N    2480      2.21       5
     O    2627      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 14084
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 7430
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 941, 7430
          Classifications: {'peptide': 941}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 63, 'TRANS': 877}
          Chain breaks: 6
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 62
          Unresolved non-hydrogen angles: 80
          Unresolved non-hydrogen dihedrals: 56
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 37
    Chain: "B"
      Number of atoms: 2986
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 372, 2986
          Classifications: {'peptide': 372}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 16, 'TRANS': 355}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 20
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "C"
      Number of atoms: 2890
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 358, 2890
          Classifications: {'peptide': 358}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 340}
          Chain breaks: 3
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 2
    Chain: "P"
      Number of atoms: 392
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 18, 372
          Classifications: {'DNA': 18}
          Link IDs: {'rna3p': 17}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
      Conformer: "B"
        Number of residues, atoms: 18, 372
          Classifications: {'DNA': 18}
          Link IDs: {'rna3p': 17}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
          bond proxies already assigned to first conformer: 395
    Chain: "T"
      Number of atoms: 386
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 386
          Classifications: {'DNA': 19}
          Link IDs: {'rna3p': 18}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" P  A DA P  27 " occ=0.50
      ... (38 atoms not shown)
      pdb=" C4 B DA P  27 " occ=0.50
  Time building chain proxies: 7.66, per 1000 atoms: 0.54
  Number of scatterers: 14084
  At special positions: 0
  Unit cell: (94.164, 106.554, 141.246, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      80     16.00
     P      38     15.00
     O    2627      8.00
     N    2480      7.00
     C    8859      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: 3.05
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3104

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 9 sheets defined
      41.6% alpha, 11.3% beta
      17 base pairs and 30 stacking pairs defined.
    Time for finding SS restraints: 5.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 99 through 109
      removed outlier: 4.277A  pdb=" N   SER A 103 " --> pdb=" O   ALA A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 159
      Proline residue:  A 149  - end of helix
      removed outlier: 3.503A  pdb=" N   GLN A 159 " --> pdb=" O   ASN A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 182
      No H-bonds generated for 'chain 'A' and resid 180 through 182'
    Processing helix  chain 'A' and resid 271 through 276
    Processing helix  chain 'A' and resid 277 through 283
      removed outlier: 6.875A  pdb=" N   GLU A 280 " --> pdb=" O   HIS A 277 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   TYR A 282 " --> pdb=" O   ARG A 279 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LEU A 283 " --> pdb=" O   GLU A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 302
    Processing helix  chain 'A' and resid 306 through 315
    Processing helix  chain 'A' and resid 345 through 350
    Processing helix  chain 'A' and resid 355 through 364
    Processing helix  chain 'A' and resid 375 through 380
    Processing helix  chain 'A' and resid 381 through 388
      removed outlier: 3.501A  pdb=" N   ILE A 385 " --> pdb=" O   THR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 418
      Proline residue:  A 412  - end of helix
    Processing helix  chain 'A' and resid 420 through 431
      removed outlier: 4.000A  pdb=" N   LEU A 424 " --> pdb=" O   HIS A 420 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   GLY A 431 " --> pdb=" O   MET A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 471
      removed outlier: 3.599A  pdb=" N   ARG A 443 " --> pdb=" O   GLN A 439 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LEU A 466 " --> pdb=" O   SER A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 488
      removed outlier: 4.414A  pdb=" N   ASP A 487 " --> pdb=" O   TRP A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 538
      removed outlier: 3.767A  pdb=" N   GLU A 538 " --> pdb=" O   GLU A 535 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 535 through 538'
    Processing helix  chain 'A' and resid 539 through 556
      removed outlier: 3.676A  pdb=" N   LEU A 549 " --> pdb=" O   ALA A 545 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LYS A 553 " --> pdb=" O   LEU A 549 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   GLY A 554 " --> pdb=" O   GLN A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 577
      removed outlier: 3.623A  pdb=" N   LEU A 576 " --> pdb=" O   TRP A 572 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   CYS A 577 " --> pdb=" O   TYR A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 603
      removed outlier: 3.656A  pdb=" N   MET A 603 " --> pdb=" O   THR A 599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 655
    Processing helix  chain 'A' and resid 754 through 758
      removed outlier: 3.875A  pdb=" N   ASN A 758 " --> pdb=" O   LYS A 755 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 786 through 810
      removed outlier: 4.715A  pdb=" N   PHE A 800 " --> pdb=" O   LYS A 796 " (cutoff:3.500A)
      removed outlier: 5.089A  pdb=" N   TRP A 801 " --> pdb=" O   MET A 797 " (cutoff:3.500A)
      removed outlier: 5.569A  pdb=" N   LYS A 806 " --> pdb=" O   ARG A 802 " (cutoff:3.500A)
      removed outlier: 5.584A  pdb=" N   ARG A 807 " --> pdb=" O   ASN A 803 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 828
      removed outlier: 3.548A  pdb=" N   ILE A 826 " --> pdb=" O   PRO A 822 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 871 through 878
      removed outlier: 3.527A  pdb=" N   LEU A 874 " --> pdb=" O   GLY A 871 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   LYS A 875 " --> pdb=" O   SER A 872 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 893 through 908
    Processing helix  chain 'A' and resid 914 through 921
    Processing helix  chain 'A' and resid 944 through 954
    Processing helix  chain 'A' and resid 958 through 969
      removed outlier: 3.896A  pdb=" N   LEU A 965 " --> pdb=" O   PHE A 961 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   LEU A 966 " --> pdb=" O   ALA A 962 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 973 through 984
    Processing helix  chain 'A' and resid 1057 through 1066
      removed outlier: 4.133A  pdb=" N   LEU A1061 " --> pdb=" O   MET A1057 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1092 through 1123
      removed outlier: 3.667A  pdb=" N   VAL A1100 " --> pdb=" O   ARG A1096 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   VAL A1101 " --> pdb=" O   VAL A1097 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1145 through 1167
      removed outlier: 3.729A  pdb=" N   ARG A1161 " --> pdb=" O   ASN A1157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1217 through 1221
      removed outlier: 4.113A  pdb=" N   ILE A1220 " --> pdb=" O   ALA A1217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 77
    Processing helix  chain 'B' and resid 87 through 94
    Processing helix  chain 'B' and resid 100 through 119
    Processing helix  chain 'B' and resid 185 through 200
      removed outlier: 3.552A  pdb=" N   ALA B 189 " --> pdb=" O   LEU B 185 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   VAL B 194 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 4.793A  pdb=" N   ASN B 195 " --> pdb=" O   GLU B 191 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ASP B 198 " --> pdb=" O   VAL B 194 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   LEU B 199 " --> pdb=" O   ASN B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 265
    Processing helix  chain 'B' and resid 269 through 271
      No H-bonds generated for 'chain 'B' and resid 269 through 271'
    Processing helix  chain 'B' and resid 308 through 315
      removed outlier: 3.547A  pdb=" N   LEU B 312 " --> pdb=" O   ASP B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 323
      removed outlier: 3.637A  pdb=" N   HIS B 323 " --> pdb=" O   SER B 320 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 354
    Processing helix  chain 'B' and resid 395 through 410
    Processing helix  chain 'B' and resid 421 through 425
      removed outlier: 4.570A  pdb=" N   SER B 424 " --> pdb=" O   MET B 421 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 426 through 435
    Processing helix  chain 'B' and resid 445 through 450
      removed outlier: 4.147A  pdb=" N   GLU B 449 " --> pdb=" O   GLU B 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 470 through 484
      removed outlier: 4.184A  pdb=" N   LYS B 483 " --> pdb=" O   ILE B 479 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   ASN B 484 " --> pdb=" O   SER B 480 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 68 through 76
    Processing helix  chain 'C' and resid 82 through 87
      removed outlier: 4.364A  pdb=" N   SER C  87 " --> pdb=" O   LYS C  83 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 88 through 93
    Processing helix  chain 'C' and resid 100 through 119
    Processing helix  chain 'C' and resid 184 through 191
      removed outlier: 4.213A  pdb=" N   GLY C 188 " --> pdb=" O   ASN C 184 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLU C 191 " --> pdb=" O   HIS C 187 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 192 through 200
      removed outlier: 3.717A  pdb=" N   ASP C 198 " --> pdb=" O   VAL C 194 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LEU C 199 " --> pdb=" O   ASN C 195 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 247 through 266
      removed outlier: 4.233A  pdb=" N   PHE C 266 " --> pdb=" O   TRP C 262 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 269 through 271
      No H-bonds generated for 'chain 'C' and resid 269 through 271'
    Processing helix  chain 'C' and resid 342 through 354
    Processing helix  chain 'C' and resid 393 through 409
      removed outlier: 3.643A  pdb=" N   ASN C 409 " --> pdb=" O   GLU C 405 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 425 through 435
    Processing helix  chain 'C' and resid 444 through 449
    Processing helix  chain 'C' and resid 470 through 485
    Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187
      removed outlier: 3.868A  pdb=" N   TRP A 175 " --> pdb=" O   VAL A 187 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   LEU A 195 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   GLN A 264 " --> pdb=" O   ARG A 290 " (cutoff:3.500A)
      removed outlier: 7.963A  pdb=" N   LEU A 292 " --> pdb=" O   GLN A 264 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   VAL A 266 " --> pdb=" O   LEU A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 438
      removed outlier: 4.785A  pdb=" N   TYR A 837 " --> pdb=" O   LEU A 816 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   VAL A 814 " --> pdb=" O   ALA A 839 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 605 through 606
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1130 through 1133
      removed outlier: 3.641A  pdb=" N   ARG A1138 " --> pdb=" O   ILE A1131 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ILE A1133 " --> pdb=" O   GLU A1136 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   GLU A1136 " --> pdb=" O   ILE A1133 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL A1137 " --> pdb=" O   ALA A 889 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 127
      removed outlier: 6.127A  pdb=" N   PHE B 126 " --> pdb=" O   ALA B 209 " (cutoff:3.500A)
      removed outlier: 8.422A  pdb=" N   ILE B 211 " --> pdb=" O   PHE B 126 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   ILE B 300 " --> pdb=" O   ASP B 341 " (cutoff:3.500A)
      removed outlier: 5.555A  pdb=" N   LEU B 299 " --> pdb=" O   TYR B 291 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   TYR B 291 " --> pdb=" O   LEU B 299 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   LYS B 285 " --> pdb=" O   ASN B 305 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 325
    Processing sheet with id=AA7, first strand: chain 'B' and resid 413 through 414
      removed outlier: 7.068A  pdb=" N   TRP B 414 " --> pdb=" O   ILE B 381 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   VAL B 383 " --> pdb=" O   TRP B 414 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   LYS B 382 " --> pdb=" O   ILE B 437 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 126 through 127
      removed outlier: 6.269A  pdb=" N   PHE C 126 " --> pdb=" O   ALA C 209 " (cutoff:3.500A)
      removed outlier: 8.696A  pdb=" N   ILE C 211 " --> pdb=" O   PHE C 126 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   ILE C 300 " --> pdb=" O   ASP C 341 " (cutoff:3.500A)
      removed outlier: 5.565A  pdb=" N   LEU C 299 " --> pdb=" O   TYR C 291 " (cutoff:3.500A)
      removed outlier: 6.160A  pdb=" N   TYR C 291 " --> pdb=" O   LEU C 299 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 413 through 415
      removed outlier: 7.111A  pdb=" N   VAL C 383 " --> pdb=" O   TRP C 414 " (cutoff:3.500A)
      removed outlier: 6.030A  pdb=" N   ALA C 384 " --> pdb=" O   VAL C 441 " (cutoff:3.500A)
      removed outlier: 7.387A  pdb=" N   VAL C 443 " --> pdb=" O   ALA C 384 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   ASP C 386 " --> pdb=" O   VAL C 443 " (cutoff:3.500A)

    536 hydrogen bonds defined for protein.
    1524 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      46 hydrogen bonds
      92 hydrogen bond angles
      0 basepair planarities
      17 basepair parallelities
      31 stacking parallelities
  Total time for adding SS restraints: 5.42

  Time building geometry restraints manager: 3.60 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4439
        1.34 -     1.46: 2856
        1.46 -     1.58: 7023
        1.58 -     1.70: 73
        1.70 -     1.82: 125
  Bond restraints: 14516
  Sorted by residual:
  bond pdb=" O3'  DG P  26 "
       pdb=" P  A DA P  27 "
    ideal  model  delta    sigma   weight residual
    1.607  1.524  0.083 1.50e-02 4.44e+03 3.07e+01
  bond pdb=" N   ARG A 852 "
       pdb=" CA  ARG A 852 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.15e-02 7.56e+03 7.68e+00
  bond pdb=" N   LEU A 605 "
       pdb=" CA  LEU A 605 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.032 1.21e-02 6.83e+03 7.20e+00
  bond pdb=" N   ARG A 853 "
       pdb=" CA  ARG A 853 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.033 1.22e-02 6.72e+03 7.14e+00
  bond pdb=" N   VAL A1101 "
       pdb=" CA  VAL A1101 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.034 1.30e-02 5.92e+03 6.94e+00
  ... (remaining 14511 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.79: 19454
        2.79 -     5.57: 353
        5.57 -     8.36: 22
        8.36 -    11.14: 2
       11.14 -    13.93: 1
  Bond angle restraints: 19832
  Sorted by residual:
  angle pdb=" N   PRO A 560 "
        pdb=" CA  PRO A 560 "
        pdb=" CB  PRO A 560 "
      ideal   model   delta    sigma   weight residual
     103.25  111.48   -8.23 1.05e+00 9.07e-01 6.15e+01
  angle pdb=" N   PRO A 625 "
        pdb=" CA  PRO A 625 "
        pdb=" CB  PRO A 625 "
      ideal   model   delta    sigma   weight residual
     103.33  110.42   -7.09 9.30e-01 1.16e+00 5.81e+01
  angle pdb=" N   PRO A 250 "
        pdb=" CA  PRO A 250 "
        pdb=" CB  PRO A 250 "
      ideal   model   delta    sigma   weight residual
     103.25  111.10   -7.85 1.05e+00 9.07e-01 5.59e+01
  angle pdb=" C3'  DG P  26 "
        pdb=" O3'  DG P  26 "
        pdb=" P  B DA P  27 "
      ideal   model   delta    sigma   weight residual
     120.20  111.04    9.16 1.50e+00 4.44e-01 3.73e+01
  angle pdb=" N   ILE A 954 "
        pdb=" CA  ILE A 954 "
        pdb=" C   ILE A 954 "
      ideal   model   delta    sigma   weight residual
     110.21  104.84    5.37 1.13e+00 7.83e-01 2.26e+01
  ... (remaining 19827 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.68: 8015
       30.68 -    61.36: 487
       61.36 -    92.04: 27
       92.04 -   122.72: 0
      122.72 -   153.41: 2
  Dihedral angle restraints: 8531
    sinusoidal: 3718
      harmonic: 4813
  Sorted by residual:
  dihedral pdb=" CA  PRO A1070 "
           pdb=" C   PRO A1070 "
           pdb=" N   ARG A1071 "
           pdb=" CA  ARG A1071 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.51  -25.49     0      5.00e+00 4.00e-02 2.60e+01
  dihedral pdb=" CD  ARG B  75 "
           pdb=" NE  ARG B  75 "
           pdb=" CZ  ARG B  75 "
           pdb=" NH1 ARG B  75 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -37.38   37.38     1      1.00e+01 1.00e-02 1.97e+01
  dihedral pdb=" CA  LEU B 393 "
           pdb=" C   LEU B 393 "
           pdb=" N   GLU B 394 "
           pdb=" CA  GLU B 394 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.68  -19.32     0      5.00e+00 4.00e-02 1.49e+01
  ... (remaining 8528 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.111: 2088
       0.111 -    0.222: 49
       0.222 -    0.333: 0
       0.333 -    0.444: 0
       0.444 -    0.555: 1
  Chirality restraints: 2138
  Sorted by residual:
  chirality pdb=" P    DG P  26 "
            pdb=" OP1  DG P  26 "
            pdb=" OP2  DG P  26 "
            pdb=" O5'  DG P  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.90   -0.56 2.00e-01 2.50e+01 7.71e+00
  chirality pdb=" CA  PRO A 625 "
            pdb=" N   PRO A 625 "
            pdb=" C   PRO A 625 "
            pdb=" CB  PRO A 625 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.52    0.20 2.00e-01 2.50e+01 9.75e-01
  chirality pdb=" CA  LEU A 605 "
            pdb=" N   LEU A 605 "
            pdb=" C   LEU A 605 "
            pdb=" CB  LEU A 605 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.13e-01
  ... (remaining 2135 not shown)

  Planarity restraints: 2416
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  75 "    0.665 9.50e-02 1.11e+02   2.98e-01 5.43e+01
        pdb=" NE  ARG B  75 "   -0.038 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  75 "   -0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  75 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  75 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 363 "    0.546 9.50e-02 1.11e+02   2.45e-01 3.66e+01
        pdb=" NE  ARG B 363 "   -0.033 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 363 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 363 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 363 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 852 "   -0.406 9.50e-02 1.11e+02   1.82e-01 2.03e+01
        pdb=" NE  ARG A 852 "    0.025 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 852 "    0.001 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 852 "    0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 852 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 2413 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 261
        2.65 -     3.21: 13315
        3.21 -     3.77: 22571
        3.77 -     4.34: 30448
        4.34 -     4.90: 49068
  Nonbonded interactions: 115663
  Sorted by model distance:
  nonbonded pdb=" OG  SER C  90 "
            pdb=" O   CYS C  95 "
     model   vdw
     2.085 3.040
  nonbonded pdb=" O   PRO A 857 "
            pdb=" OG1 THR A 861 "
     model   vdw
     2.107 3.040
  nonbonded pdb=" OG1 THR A 885 "
            pdb=" O   ASP A1186 "
     model   vdw
     2.121 3.040
  nonbonded pdb=" O   LYS A 553 "
            pdb=" NZ  LYS A 553 "
     model   vdw
     2.122 3.120
  nonbonded pdb=" N   GLU A 280 "
            pdb=" OE1 GLU A 280 "
     model   vdw
     2.153 3.120
  ... (remaining 115658 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and (resid 68 through 104 or (resid 105 and (name N or name CA or nam \ 
e C or name O or name CB or name CG or name CD )) or resid 106 through 136 or re \ 
sid 180 through 219 or resid 227 through 355 or resid 368 through 420 or (resid  \ 
421 and (name N or name CA or name C or name O or name CB )) or resid 422 throug \ 
h 485))
  selection = (chain 'C' and (resid 68 through 136 or resid 180 through 227 or (resid 228 and  \ 
(name N or name CA or name C or name O or name CB )) or resid 229 through 485))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.300
  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:          0.500
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     35.140
  Find NCS groups from input model:        0.380
  Set up NCS constraints:                  0.070
  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:11.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6859
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      :  0.004   0.083  14516  Z= 0.192
  Angle     :  0.800  13.928  19832  Z= 0.433
  Chirality :  0.044   0.555   2138
  Planarity :  0.010   0.298   2416
  Dihedral  : 17.633 153.406   5427
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.76 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 26.97 %
    Favored  : 71.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.21), residues: 1643
  helix:  1.15 (0.22), residues: 595
  sheet:  0.04 (0.37), residues: 194
  loop : -1.18 (0.21), residues: 854

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1118 
 HIS   0.010   0.001   HIS C 313 
 PHE   0.037   0.001   PHE A 539 
 TYR   0.014   0.001   TYR A1108 
 ARG   0.013   0.001   ARG B 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14606 (  582)
  hydrogen bonds       : angle       6.03594 ( 1616)
  covalent geometry    : bond        0.00389 (14516)
  covalent geometry    : angle       0.80024 (19832)

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

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

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 217
  time to evaluate  : 1.519 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  539 PHE cc_start: 0.6585 (p90) cc_final: 0.5406 (p90)
REVERT: A  579 ARG cc_start: 0.8022 (mmm160) cc_final: 0.7730 (mmm160)
REVERT: A 1195 MET cc_start: 0.7873 (ttm) cc_final: 0.7600 (ptp)
REVERT: C  422 GLN cc_start: 0.5878 (tp-100) cc_final: 0.5364 (tp40)
  outliers start: 19
  outliers final: 9
  residues processed: 234
  average time/residue: 1.1731
  time to fit residues: 303.3209
Evaluate side-chains
  201 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 192
  time to evaluate  : 1.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  741 ASP
Chi-restraints excluded: chain A residue 1132 SER
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  306 LEU
Chi-restraints excluded: chain C residue  377 CYS
Chi-restraints excluded: chain C residue  459 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 141 optimal weight:    3.9990
   chunk 127 optimal weight:    4.9990
   chunk 70 optimal weight:   20.0000
   chunk 43 optimal weight:    0.9980
   chunk 85 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 131 optimal weight:    6.9990
   chunk 50 optimal weight:    8.9990
   chunk 80 optimal weight:    0.1980
   chunk 98 optimal weight:    2.9990
   chunk 152 optimal weight:    6.9990
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
A  90 GLN
A 134 ASN
A 138 HIS
A 144 GLN
A 226 GLN
A 394 GLN
A 472 GLN
A 493 GLN
** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 618 HIS
A 843 GLN
** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 959 GLN
** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1102 GLN
** A1110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1134 HIS
** B  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 216 HIS
** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 272 ASN
B 305 ASN
B 355 GLN
** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 313 HIS

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.152407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.118920 restraints weight = 38155.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.3717 rms_B_bonded: 4.13
r_work: 0.3573 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3579
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3579 r_free = 0.3579    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3579 r_free = 0.3579    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       20 |
|-----------------------------------------------------------------------------|
r_final: 0.3579
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.1512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  14516  Z= 0.216
  Angle     :  0.733  12.537  19832  Z= 0.369
  Chirality :  0.046   0.189   2138
  Planarity :  0.005   0.051   2416
  Dihedral  : 15.095 150.917   2221
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.82 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 23.31 %
    Favored  : 71.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.21), residues: 1643
  helix:  1.14 (0.21), residues: 607
  sheet: -0.02 (0.35), residues: 208
  loop : -1.19 (0.22), residues: 828

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 607 
 HIS   0.009   0.001   HIS A1134 
 PHE   0.014   0.002   PHE B 266 
 TYR   0.014   0.002   TYR A1108 
 ARG   0.008   0.001   ARG A 275 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04110 (  582)
  hydrogen bonds       : angle       4.77175 ( 1616)
  covalent geometry    : bond        0.00493 (14516)
  covalent geometry    : angle       0.73317 (19832)

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

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

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 209
  time to evaluate  : 1.687 
Fit side-chains
REVERT: A   78 MET cc_start: 0.5998 (ppp) cc_final: 0.5636 (ppp)
REVERT: A  544 MET cc_start: 0.8725 (ppp) cc_final: 0.8483 (ppp)
REVERT: A  647 CYS cc_start: 0.7009 (t) cc_final: 0.6678 (p)
REVERT: A  762 VAL cc_start: 0.7821 (OUTLIER) cc_final: 0.7607 (t)
REVERT: A  975 GLN cc_start: 0.8615 (pm20) cc_final: 0.8234 (pm20)
REVERT: A 1098 ASN cc_start: 0.9128 (m-40) cc_final: 0.8922 (m-40)
REVERT: A 1144 GLU cc_start: 0.8444 (pt0) cc_final: 0.8077 (pm20)
REVERT: B   74 GLN cc_start: 0.8269 (mm-40) cc_final: 0.8047 (mm-40)
REVERT: B   75 ARG cc_start: 0.7821 (mmm160) cc_final: 0.7614 (tpt90)
REVERT: B  445 GLU cc_start: 0.8693 (pm20) cc_final: 0.7661 (pm20)
REVERT: B  465 MET cc_start: 0.8089 (mmm) cc_final: 0.7840 (mmm)
REVERT: B  472 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8314 (tmmm)
REVERT: C  310 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7686 (pm20)
REVERT: C  396 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7051 (mpp80)
  outliers start: 68
  outliers final: 26
  residues processed: 251
  average time/residue: 1.1749
  time to fit residues: 325.5209
Evaluate side-chains
  214 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 184
  time to evaluate  : 1.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  433 SER
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  774 MET
Chi-restraints excluded: chain A residue  948 ILE
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1141 VAL
Chi-restraints excluded: chain A residue 1206 MET
Chi-restraints excluded: chain A residue 1218 LEU
Chi-restraints excluded: chain B residue   72 ILE
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  352 ASP
Chi-restraints excluded: chain B residue  371 VAL
Chi-restraints excluded: chain B residue  377 CYS
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  459 ASP
Chi-restraints excluded: chain B residue  472 LYS
Chi-restraints excluded: chain B residue  484 ASN
Chi-restraints excluded: chain C residue   89 ASP
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  278 CYS
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  331 VAL
Chi-restraints excluded: chain C residue  338 VAL
Chi-restraints excluded: chain C residue  377 CYS
Chi-restraints excluded: chain C residue  396 ARG
Chi-restraints excluded: chain C residue  413 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 87 optimal weight:    5.9990
   chunk 40 optimal weight:    0.3980
   chunk 114 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   chunk 110 optimal weight:    5.9990
   chunk 95 optimal weight:    4.9990
   chunk 9 optimal weight:    6.9990
   chunk 153 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    1.6186

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

Flipped N/Q/H residues before XYZ refinement:
A 298 HIS
** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1110 HIS
A1134 HIS
** B  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 133 HIS
B 258 HIS
** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 309 HIS
** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.153270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.121857 restraints weight = 28647.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3723 rms_B_bonded: 3.46
r_work: 0.3589 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3604
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3604 r_free = 0.3604    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       20 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3604 r_free = 0.3604    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       20 |
|-----------------------------------------------------------------------------|
r_final: 0.3604
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  14516  Z= 0.177
  Angle     :  0.688  11.622  19832  Z= 0.345
  Chirality :  0.044   0.162   2138
  Planarity :  0.005   0.047   2416
  Dihedral  : 15.113 150.593   2214
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.12 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 24.09 %
    Favored  : 70.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.21), residues: 1643
  helix:  1.09 (0.21), residues: 612
  sheet:  0.07 (0.35), residues: 206
  loop : -1.24 (0.22), residues: 825

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 607 
 HIS   0.009   0.001   HIS A1134 
 PHE   0.016   0.001   PHE A 610 
 TYR   0.011   0.001   TYR B 206 
 ARG   0.005   0.000   ARG B 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03848 (  582)
  hydrogen bonds       : angle       4.65325 ( 1616)
  covalent geometry    : bond        0.00402 (14516)
  covalent geometry    : angle       0.68825 (19832)

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

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

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 198
  time to evaluate  : 1.742 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.6100 (OUTLIER) cc_final: 0.5685 (ppp)
REVERT: A  544 MET cc_start: 0.8530 (ppp) cc_final: 0.8316 (pp-130)
REVERT: A  552 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7597 (mp)
REVERT: A  647 CYS cc_start: 0.6976 (t) cc_final: 0.6670 (p)
REVERT: A  975 GLN cc_start: 0.8659 (pm20) cc_final: 0.8287 (pm20)
REVERT: A 1098 ASN cc_start: 0.9074 (m-40) cc_final: 0.8740 (m110)
REVERT: A 1144 GLU cc_start: 0.8435 (pt0) cc_final: 0.8050 (pm20)
REVERT: B   74 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7885 (mm-40)
REVERT: B  325 ARG cc_start: 0.7797 (ptp-110) cc_final: 0.7484 (mtm180)
REVERT: B  465 MET cc_start: 0.8096 (mmm) cc_final: 0.7689 (mmm)
REVERT: B  472 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8366 (tmmm)
REVERT: C  310 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7657 (pm20)
REVERT: C  396 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7114 (mpp80)
  outliers start: 77
  outliers final: 33
  residues processed: 239
  average time/residue: 1.4248
  time to fit residues: 377.9028
Evaluate side-chains
  219 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 181
  time to evaluate  : 1.731 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 MET
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  433 SER
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  858 THR
Chi-restraints excluded: chain A residue  885 THR
Chi-restraints excluded: chain A residue  910 MET
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  948 ILE
Chi-restraints excluded: chain A residue  973 LEU
Chi-restraints excluded: chain A residue 1057 MET
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1141 VAL
Chi-restraints excluded: chain A residue 1193 VAL
Chi-restraints excluded: chain A residue 1206 MET
Chi-restraints excluded: chain A residue 1218 LEU
Chi-restraints excluded: chain B residue  371 VAL
Chi-restraints excluded: chain B residue  377 CYS
Chi-restraints excluded: chain B residue  386 ASP
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  459 ASP
Chi-restraints excluded: chain B residue  472 LYS
Chi-restraints excluded: chain B residue  484 ASN
Chi-restraints excluded: chain C residue   80 SER
Chi-restraints excluded: chain C residue   89 ASP
Chi-restraints excluded: chain C residue  278 CYS
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  331 VAL
Chi-restraints excluded: chain C residue  338 VAL
Chi-restraints excluded: chain C residue  377 CYS
Chi-restraints excluded: chain C residue  396 ARG
Chi-restraints excluded: chain C residue  413 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 84 optimal weight:    4.9990
   chunk 158 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 160 optimal weight:    0.1980
   chunk 19 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   chunk 94 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0770
   chunk 68 optimal weight:    1.9990
   chunk 53 optimal weight:    7.9990
   overall best weight:    1.0544

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

Flipped N/Q/H residues before XYZ refinement:
** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 740 ASN
** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1134 HIS
A1222 GLN
** B  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 330 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.153471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.121478 restraints weight = 26698.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3745 rms_B_bonded: 3.47
r_work: 0.3611 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3627
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3627 r_free = 0.3627    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       20 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3627 r_free = 0.3627    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       20 |
|-----------------------------------------------------------------------------|
r_final: 0.3627
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.1953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14516  Z= 0.146
  Angle     :  0.679  13.785  19832  Z= 0.336
  Chirality :  0.043   0.170   2138
  Planarity :  0.005   0.048   2416
  Dihedral  : 15.080 150.505   2212
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.12 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 24.51 %
    Favored  : 70.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.21), residues: 1643
  helix:  1.11 (0.21), residues: 617
  sheet:  0.04 (0.35), residues: 194
  loop : -1.23 (0.22), residues: 832

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 607 
 HIS   0.005   0.001   HIS A1134 
 PHE   0.008   0.001   PHE B 266 
 TYR   0.012   0.001   TYR A1108 
 ARG   0.008   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03543 (  582)
  hydrogen bonds       : angle       4.54711 ( 1616)
  covalent geometry    : bond        0.00331 (14516)
  covalent geometry    : angle       0.67937 (19832)

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

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

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 191
  time to evaluate  : 1.714 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.6076 (OUTLIER) cc_final: 0.5646 (ppp)
REVERT: A  544 MET cc_start: 0.8522 (ppp) cc_final: 0.8281 (pp-130)
REVERT: A  550 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7322 (mp10)
REVERT: A 1098 ASN cc_start: 0.9055 (m-40) cc_final: 0.8694 (m110)
REVERT: A 1136 GLU cc_start: 0.7960 (tt0) cc_final: 0.7624 (tm-30)
REVERT: A 1144 GLU cc_start: 0.8421 (pt0) cc_final: 0.8014 (pm20)
REVERT: B   74 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7805 (mm-40)
REVERT: B  325 ARG cc_start: 0.7739 (ptp-110) cc_final: 0.7413 (mtm180)
REVERT: B  445 GLU cc_start: 0.8639 (pm20) cc_final: 0.8432 (pm20)
REVERT: B  465 MET cc_start: 0.8018 (mmm) cc_final: 0.7648 (mmm)
REVERT: B  472 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8369 (tmmm)
REVERT: C  310 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7728 (pm20)
REVERT: C  396 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7111 (mpp80)
  outliers start: 77
  outliers final: 34
  residues processed: 236
  average time/residue: 1.2241
  time to fit residues: 318.8377
Evaluate side-chains
  225 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 186
  time to evaluate  : 1.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 MET
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  433 SER
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain A residue  540 GLN
Chi-restraints excluded: chain A residue  550 GLN
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  858 THR
Chi-restraints excluded: chain A residue  910 MET
Chi-restraints excluded: chain A residue  948 ILE
Chi-restraints excluded: chain A residue 1057 MET
Chi-restraints excluded: chain A residue 1063 SER
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1141 VAL
Chi-restraints excluded: chain A residue 1168 LEU
Chi-restraints excluded: chain A residue 1193 VAL
Chi-restraints excluded: chain A residue 1206 MET
Chi-restraints excluded: chain A residue 1218 LEU
Chi-restraints excluded: chain B residue  268 MET
Chi-restraints excluded: chain B residue  352 ASP
Chi-restraints excluded: chain B residue  371 VAL
Chi-restraints excluded: chain B residue  377 CYS
Chi-restraints excluded: chain B residue  386 ASP
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  459 ASP
Chi-restraints excluded: chain B residue  472 LYS
Chi-restraints excluded: chain B residue  484 ASN
Chi-restraints excluded: chain C residue   80 SER
Chi-restraints excluded: chain C residue  278 CYS
Chi-restraints excluded: chain C residue  306 LEU
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  338 VAL
Chi-restraints excluded: chain C residue  377 CYS
Chi-restraints excluded: chain C residue  396 ARG
Chi-restraints excluded: chain C residue  413 VAL
Chi-restraints excluded: chain C residue  459 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 100 optimal weight:    2.9990
   chunk 87 optimal weight:    6.9990
   chunk 54 optimal weight:    4.9990
   chunk 30 optimal weight:    0.5980
   chunk 50 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 113 optimal weight:    4.9990
   chunk 8 optimal weight:    5.9990
   chunk 159 optimal weight:    0.9980
   chunk 57 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
A  77 GLN
** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1134 HIS
** B  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 261 GLN
** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 192 HIS
** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.150353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.117873 restraints weight = 27947.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 3.52
r_work: 0.3565 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3571
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3571 r_free = 0.3571    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       20 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3571 r_free = 0.3571    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       20 |
|-----------------------------------------------------------------------------|
r_final: 0.3571
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.2226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  14516  Z= 0.208
  Angle     :  0.717  11.511  19832  Z= 0.359
  Chirality :  0.045   0.174   2138
  Planarity :  0.005   0.052   2416
  Dihedral  : 15.148 151.224   2210
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.91 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  6.18 %
    Allowed  : 23.67 %
    Favored  : 70.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.21), residues: 1643
  helix:  0.97 (0.21), residues: 618
  sheet: -0.01 (0.35), residues: 194
  loop : -1.33 (0.22), residues: 831

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 607 
 HIS   0.006   0.001   HIS B  77 
 PHE   0.017   0.002   PHE A 610 
 TYR   0.015   0.002   TYR A 573 
 ARG   0.006   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03847 (  582)
  hydrogen bonds       : angle       4.63554 ( 1616)
  covalent geometry    : bond        0.00478 (14516)
  covalent geometry    : angle       0.71716 (19832)

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

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

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 186
  time to evaluate  : 1.545 
Fit side-chains
   revert: symmetry clash
REVERT: A  544 MET cc_start: 0.8571 (ppp) cc_final: 0.8330 (pp-130)
REVERT: A  552 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7747 (mp)
REVERT: A  594 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7215 (mm)
REVERT: A  774 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7700 (ptm)
REVERT: A 1098 ASN cc_start: 0.9074 (m-40) cc_final: 0.8671 (m110)
REVERT: A 1144 GLU cc_start: 0.8445 (pt0) cc_final: 0.8088 (pm20)
REVERT: A 1208 ARG cc_start: 0.6107 (OUTLIER) cc_final: 0.5870 (ptt180)
REVERT: B   69 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8378 (tm)
REVERT: B   74 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7887 (mm-40)
REVERT: B  325 ARG cc_start: 0.7778 (ptp-110) cc_final: 0.7475 (mtm180)
REVERT: B  386 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8344 (t70)
REVERT: B  465 MET cc_start: 0.8094 (mmm) cc_final: 0.7661 (mmm)
REVERT: B  472 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8472 (ttpp)
REVERT: C  310 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7751 (pm20)
REVERT: C  329 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.6918 (pmtt)
REVERT: C  386 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7507 (t0)
REVERT: C  396 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7120 (mpp80)
  outliers start: 88
  outliers final: 38
  residues processed: 241
  average time/residue: 1.1652
  time to fit residues: 311.1934
Evaluate side-chains
  220 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 171
  time to evaluate  : 1.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  152 GLU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  433 SER
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain A residue  540 GLN
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  605 LEU
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  774 MET
Chi-restraints excluded: chain A residue  858 THR
Chi-restraints excluded: chain A residue  885 THR
Chi-restraints excluded: chain A residue  948 ILE
Chi-restraints excluded: chain A residue 1057 MET
Chi-restraints excluded: chain A residue 1063 SER
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1141 VAL
Chi-restraints excluded: chain A residue 1163 MET
Chi-restraints excluded: chain A residue 1193 VAL
Chi-restraints excluded: chain A residue 1206 MET
Chi-restraints excluded: chain A residue 1208 ARG
Chi-restraints excluded: chain A residue 1218 LEU
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   72 ILE
Chi-restraints excluded: chain B residue  268 MET
Chi-restraints excluded: chain B residue  352 ASP
Chi-restraints excluded: chain B residue  371 VAL
Chi-restraints excluded: chain B residue  377 CYS
Chi-restraints excluded: chain B residue  386 ASP
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  459 ASP
Chi-restraints excluded: chain B residue  472 LYS
Chi-restraints excluded: chain B residue  484 ASN
Chi-restraints excluded: chain C residue   80 SER
Chi-restraints excluded: chain C residue  278 CYS
Chi-restraints excluded: chain C residue  306 LEU
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  329 LYS
Chi-restraints excluded: chain C residue  331 VAL
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain C residue  338 VAL
Chi-restraints excluded: chain C residue  377 CYS
Chi-restraints excluded: chain C residue  386 ASP
Chi-restraints excluded: chain C residue  396 ARG
Chi-restraints excluded: chain C residue  413 VAL
Chi-restraints excluded: chain C residue  459 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 112 optimal weight:    3.9990
   chunk 105 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9980
   chunk 161 optimal weight:    0.8980
   chunk 38 optimal weight:    0.2980
   chunk 136 optimal weight:    4.9990
   chunk 104 optimal weight:    1.9990
   chunk 119 optimal weight:    6.9990
   chunk 45 optimal weight:    0.0040
   overall best weight:    0.6192

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

Flipped N/Q/H residues before XYZ refinement:
A 264 GLN
** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 740 ASN
** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 318 ASN
** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.154462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.122265 restraints weight = 28397.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3751 rms_B_bonded: 3.56
r_work: 0.3617 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3629
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3629 r_free = 0.3629    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       20 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3629 r_free = 0.3629    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       20 |
|-----------------------------------------------------------------------------|
r_final: 0.3629
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14516  Z= 0.132
  Angle     :  0.688  15.011  19832  Z= 0.339
  Chirality :  0.043   0.161   2138
  Planarity :  0.004   0.046   2416
  Dihedral  : 15.076 150.465   2210
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.18 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 24.93 %
    Favored  : 70.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.21), residues: 1643
  helix:  1.10 (0.21), residues: 616
  sheet:  0.02 (0.36), residues: 197
  loop : -1.26 (0.22), residues: 830

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A 748 
 HIS   0.004   0.001   HIS B  77 
 PHE   0.009   0.001   PHE B 254 
 TYR   0.018   0.001   TYR B 193 
 ARG   0.006   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03385 (  582)
  hydrogen bonds       : angle       4.50742 ( 1616)
  covalent geometry    : bond        0.00295 (14516)
  covalent geometry    : angle       0.68754 (19832)

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

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

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 194
  time to evaluate  : 1.789 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 LEU cc_start: 0.5992 (OUTLIER) cc_final: 0.5301 (tp)
REVERT: A  544 MET cc_start: 0.8486 (ppp) cc_final: 0.8263 (pp-130)
REVERT: A  552 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7699 (mp)
REVERT: A 1078 CYS cc_start: 0.7962 (m) cc_final: 0.7744 (m)
REVERT: A 1098 ASN cc_start: 0.9035 (m-40) cc_final: 0.8609 (m110)
REVERT: A 1136 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7646 (tm-30)
REVERT: A 1144 GLU cc_start: 0.8442 (pt0) cc_final: 0.8066 (pm20)
REVERT: B   69 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8300 (tm)
REVERT: B   74 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7811 (mm-40)
REVERT: B  191 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8140 (mt-10)
REVERT: B  325 ARG cc_start: 0.7772 (ptp-110) cc_final: 0.7490 (mtm180)
REVERT: B  465 MET cc_start: 0.7965 (mmm) cc_final: 0.7537 (mmm)
REVERT: B  472 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8447 (tmmm)
REVERT: C  310 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7751 (pm20)
REVERT: C  329 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.6906 (pmtt)
REVERT: C  386 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.6825 (t0)
REVERT: C  396 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7102 (mpp80)
  outliers start: 72
  outliers final: 36
  residues processed: 239
  average time/residue: 1.5317
  time to fit residues: 402.6873
Evaluate side-chains
  220 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 176
  time to evaluate  : 1.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  152 GLU
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  433 SER
Chi-restraints excluded: chain A residue  540 GLN
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  605 LEU
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  831 TYR
Chi-restraints excluded: chain A residue  858 THR
Chi-restraints excluded: chain A residue  885 THR
Chi-restraints excluded: chain A residue  948 ILE
Chi-restraints excluded: chain A residue 1057 MET
Chi-restraints excluded: chain A residue 1063 SER
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1141 VAL
Chi-restraints excluded: chain A residue 1163 MET
Chi-restraints excluded: chain A residue 1168 LEU
Chi-restraints excluded: chain A residue 1193 VAL
Chi-restraints excluded: chain A residue 1206 MET
Chi-restraints excluded: chain A residue 1218 LEU
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   72 ILE
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue  371 VAL
Chi-restraints excluded: chain B residue  386 ASP
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  472 LYS
Chi-restraints excluded: chain C residue   80 SER
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  278 CYS
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  329 LYS
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain C residue  335 VAL
Chi-restraints excluded: chain C residue  338 VAL
Chi-restraints excluded: chain C residue  386 ASP
Chi-restraints excluded: chain C residue  396 ARG
Chi-restraints excluded: chain C residue  413 VAL
Chi-restraints excluded: chain C residue  459 ASP
Chi-restraints excluded: chain C residue  468 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 157 optimal weight:    5.9990
   chunk 60 optimal weight:    8.9990
   chunk 71 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   chunk 56 optimal weight:    4.9990
   chunk 107 optimal weight:    6.9990
   chunk 147 optimal weight:    6.9990
   chunk 100 optimal weight:    3.9990
   chunk 1 optimal weight:    0.2980
   chunk 99 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 740 ASN
** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.153211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.121871 restraints weight = 27599.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3731 rms_B_bonded: 3.40
r_work: 0.3601 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3612
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3612 r_free = 0.3612    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       20 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3612 r_free = 0.3612    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       20 |
|-----------------------------------------------------------------------------|
r_final: 0.3612
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.2334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  14516  Z= 0.162
  Angle     :  0.705  14.305  19832  Z= 0.348
  Chirality :  0.043   0.167   2138
  Planarity :  0.005   0.051   2416
  Dihedral  : 15.090 150.808   2209
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.61 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 25.56 %
    Favored  : 69.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.21), residues: 1643
  helix:  1.05 (0.21), residues: 624
  sheet:  0.04 (0.36), residues: 197
  loop : -1.27 (0.22), residues: 822

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 607 
 HIS   0.004   0.001   HIS B  77 
 PHE   0.010   0.001   PHE A 389 
 TYR   0.017   0.001   TYR B 193 
 ARG   0.008   0.000   ARG A1148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03523 (  582)
  hydrogen bonds       : angle       4.50389 ( 1616)
  covalent geometry    : bond        0.00372 (14516)
  covalent geometry    : angle       0.70499 (19832)

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

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

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 177
  time to evaluate  : 1.592 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 LEU cc_start: 0.6047 (OUTLIER) cc_final: 0.5301 (tp)
REVERT: A  536 GLU cc_start: 0.8107 (tp30) cc_final: 0.7306 (pt0)
REVERT: A  544 MET cc_start: 0.8460 (ppp) cc_final: 0.8251 (pp-130)
REVERT: A  550 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7420 (mp10)
REVERT: A  552 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7741 (mp)
REVERT: A 1098 ASN cc_start: 0.9019 (m-40) cc_final: 0.8549 (m-40)
REVERT: A 1136 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7626 (tm-30)
REVERT: A 1144 GLU cc_start: 0.8471 (pt0) cc_final: 0.8136 (pm20)
REVERT: B   69 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8302 (tm)
REVERT: B   74 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7838 (mm-40)
REVERT: B  191 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8117 (mt-10)
REVERT: B  325 ARG cc_start: 0.7744 (ptp-110) cc_final: 0.7466 (mtm180)
REVERT: B  386 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8294 (t70)
REVERT: B  465 MET cc_start: 0.7994 (mmm) cc_final: 0.7726 (mmt)
REVERT: B  472 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8470 (tmmm)
REVERT: C  310 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7770 (pm20)
REVERT: C  329 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.6878 (pmtt)
REVERT: C  386 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.6834 (t0)
REVERT: C  396 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7080 (mpp80)
  outliers start: 72
  outliers final: 42
  residues processed: 227
  average time/residue: 1.1630
  time to fit residues: 292.3482
Evaluate side-chains
  220 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 168
  time to evaluate  : 1.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  152 GLU
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  433 SER
Chi-restraints excluded: chain A residue  550 GLN
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  605 LEU
Chi-restraints excluded: chain A residue  615 SER
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  831 TYR
Chi-restraints excluded: chain A residue  858 THR
Chi-restraints excluded: chain A residue  885 THR
Chi-restraints excluded: chain A residue  948 ILE
Chi-restraints excluded: chain A residue  992 LEU
Chi-restraints excluded: chain A residue 1057 MET
Chi-restraints excluded: chain A residue 1063 SER
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1079 ILE
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1141 VAL
Chi-restraints excluded: chain A residue 1163 MET
Chi-restraints excluded: chain A residue 1168 LEU
Chi-restraints excluded: chain A residue 1193 VAL
Chi-restraints excluded: chain A residue 1206 MET
Chi-restraints excluded: chain A residue 1218 LEU
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   72 ILE
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue  268 MET
Chi-restraints excluded: chain B residue  371 VAL
Chi-restraints excluded: chain B residue  386 ASP
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  472 LYS
Chi-restraints excluded: chain B residue  484 ASN
Chi-restraints excluded: chain C residue   80 SER
Chi-restraints excluded: chain C residue  113 GLU
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  278 CYS
Chi-restraints excluded: chain C residue  306 LEU
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  329 LYS
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain C residue  335 VAL
Chi-restraints excluded: chain C residue  338 VAL
Chi-restraints excluded: chain C residue  377 CYS
Chi-restraints excluded: chain C residue  386 ASP
Chi-restraints excluded: chain C residue  396 ARG
Chi-restraints excluded: chain C residue  413 VAL
Chi-restraints excluded: chain C residue  459 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9980
   chunk 112 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   chunk 75 optimal weight:    0.4980
   chunk 33 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 118 optimal weight:    0.9980
   chunk 58 optimal weight:    0.2980
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 740 ASN
** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.154855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.123023 restraints weight = 27601.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 3.49
r_work: 0.3634 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3641
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3641 r_free = 0.3641    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       20 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3641 r_free = 0.3641    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       20 |
|-----------------------------------------------------------------------------|
r_final: 0.3641
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.2374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14516  Z= 0.133
  Angle     :  0.682  13.028  19832  Z= 0.338
  Chirality :  0.042   0.168   2138
  Planarity :  0.004   0.047   2416
  Dihedral  : 15.057 150.420   2209
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.94 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 26.76 %
    Favored  : 68.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.21), residues: 1643
  helix:  1.17 (0.22), residues: 616
  sheet:  0.09 (0.36), residues: 198
  loop : -1.23 (0.22), residues: 829

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 607 
 HIS   0.004   0.001   HIS A  84 
 PHE   0.009   0.001   PHE C 403 
 TYR   0.020   0.001   TYR B 193 
 ARG   0.005   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03330 (  582)
  hydrogen bonds       : angle       4.44876 ( 1616)
  covalent geometry    : bond        0.00301 (14516)
  covalent geometry    : angle       0.68213 (19832)

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

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

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 179
  time to evaluate  : 1.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 LEU cc_start: 0.5998 (OUTLIER) cc_final: 0.5286 (tp)
REVERT: A  536 GLU cc_start: 0.8141 (tp30) cc_final: 0.7292 (pt0)
REVERT: A  544 MET cc_start: 0.8451 (ppp) cc_final: 0.8241 (pp-130)
REVERT: A  546 ARG cc_start: 0.8280 (ttp80) cc_final: 0.7959 (ttp80)
REVERT: A  550 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.6872 (mp10)
REVERT: A  552 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7746 (mp)
REVERT: A  934 LYS cc_start: 0.8874 (ttmm) cc_final: 0.8591 (ttmm)
REVERT: A 1136 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7534 (tm-30)
REVERT: A 1144 GLU cc_start: 0.8474 (pt0) cc_final: 0.8112 (pm20)
REVERT: B   69 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8298 (tm)
REVERT: B   74 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7872 (mm-40)
REVERT: B  191 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8114 (mt-10)
REVERT: B  325 ARG cc_start: 0.7762 (ptp-110) cc_final: 0.7485 (mtm180)
REVERT: B  465 MET cc_start: 0.7913 (mmm) cc_final: 0.7478 (mmm)
REVERT: B  472 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8409 (tmmm)
REVERT: C  310 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7766 (pm20)
REVERT: C  386 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.6882 (t0)
REVERT: C  396 ARG cc_start: 0.8053 (tpp-160) cc_final: 0.7120 (mpp80)
  outliers start: 61
  outliers final: 39
  residues processed: 219
  average time/residue: 1.1147
  time to fit residues: 271.2551
Evaluate side-chains
  218 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 172
  time to evaluate  : 1.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  152 GLU
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  433 SER
Chi-restraints excluded: chain A residue  550 GLN
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  605 LEU
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  831 TYR
Chi-restraints excluded: chain A residue  858 THR
Chi-restraints excluded: chain A residue  885 THR
Chi-restraints excluded: chain A residue 1057 MET
Chi-restraints excluded: chain A residue 1063 SER
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1141 VAL
Chi-restraints excluded: chain A residue 1163 MET
Chi-restraints excluded: chain A residue 1168 LEU
Chi-restraints excluded: chain A residue 1193 VAL
Chi-restraints excluded: chain A residue 1206 MET
Chi-restraints excluded: chain A residue 1218 LEU
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   72 ILE
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue  268 MET
Chi-restraints excluded: chain B residue  352 ASP
Chi-restraints excluded: chain B residue  371 VAL
Chi-restraints excluded: chain B residue  386 ASP
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  472 LYS
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   80 SER
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  278 CYS
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  329 LYS
Chi-restraints excluded: chain C residue  331 VAL
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain C residue  335 VAL
Chi-restraints excluded: chain C residue  338 VAL
Chi-restraints excluded: chain C residue  377 CYS
Chi-restraints excluded: chain C residue  386 ASP
Chi-restraints excluded: chain C residue  413 VAL
Chi-restraints excluded: chain C residue  459 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 69 optimal weight:    8.9990
   chunk 82 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 116 optimal weight:    0.9980
   chunk 60 optimal weight:    7.9990
   chunk 107 optimal weight:    0.9980
   chunk 126 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   chunk 104 optimal weight:    6.9990
   chunk 43 optimal weight:    0.3980
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
A  84 HIS
** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 740 ASN
** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.152839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.120970 restraints weight = 26905.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 3.42
r_work: 0.3600 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3609
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3609 r_free = 0.3609    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       20 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3609 r_free = 0.3609    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       20 |
|-----------------------------------------------------------------------------|
r_final: 0.3609
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.2433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  14516  Z= 0.172
  Angle     :  0.716  13.991  19832  Z= 0.354
  Chirality :  0.044   0.172   2138
  Planarity :  0.005   0.052   2416
  Dihedral  : 15.088 150.905   2209
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.49 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 26.90 %
    Favored  : 68.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.21), residues: 1643
  helix:  1.06 (0.21), residues: 623
  sheet:  0.09 (0.36), residues: 201
  loop : -1.29 (0.22), residues: 819

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A 607 
 HIS   0.010   0.001   HIS A  84 
 PHE   0.011   0.001   PHE C 403 
 TYR   0.018   0.002   TYR B 193 
 ARG   0.005   0.000   ARG A 853 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03503 (  582)
  hydrogen bonds       : angle       4.49257 ( 1616)
  covalent geometry    : bond        0.00397 (14516)
  covalent geometry    : angle       0.71620 (19832)

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

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

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 173
  time to evaluate  : 1.573 
Fit side-chains
REVERT: A  228 LEU cc_start: 0.5937 (OUTLIER) cc_final: 0.5184 (tp)
REVERT: A  536 GLU cc_start: 0.8119 (tp30) cc_final: 0.7398 (pt0)
REVERT: A  540 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7723 (mp10)
REVERT: A  544 MET cc_start: 0.8486 (ppp) cc_final: 0.8271 (pp-130)
REVERT: A  546 ARG cc_start: 0.8293 (ttp80) cc_final: 0.7962 (ttp80)
REVERT: A  550 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.6908 (mp10)
REVERT: A  552 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7810 (mp)
REVERT: A  934 LYS cc_start: 0.8897 (ttmm) cc_final: 0.8630 (ttmm)
REVERT: A 1098 ASN cc_start: 0.9006 (m-40) cc_final: 0.8518 (m-40)
REVERT: A 1144 GLU cc_start: 0.8499 (pt0) cc_final: 0.8135 (pm20)
REVERT: B   74 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7862 (mm-40)
REVERT: B  191 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8162 (mt-10)
REVERT: B  325 ARG cc_start: 0.7756 (ptp-110) cc_final: 0.7481 (mtm180)
REVERT: B  386 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8333 (t70)
REVERT: B  465 MET cc_start: 0.7965 (mmm) cc_final: 0.7706 (mmt)
REVERT: B  472 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8488 (tmmm)
REVERT: C  309 HIS cc_start: 0.7987 (t-90) cc_final: 0.7735 (t-90)
REVERT: C  310 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7691 (pm20)
REVERT: C  329 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.6851 (pmtt)
REVERT: C  386 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.6946 (t0)
REVERT: C  396 ARG cc_start: 0.8078 (tpp-160) cc_final: 0.7099 (mpp80)
  outliers start: 60
  outliers final: 37
  residues processed: 212
  average time/residue: 1.1778
  time to fit residues: 277.0723
Evaluate side-chains
  214 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 169
  time to evaluate  : 1.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 GLU
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  433 SER
Chi-restraints excluded: chain A residue  550 GLN
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  605 LEU
Chi-restraints excluded: chain A residue  615 SER
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  858 THR
Chi-restraints excluded: chain A residue  885 THR
Chi-restraints excluded: chain A residue  948 ILE
Chi-restraints excluded: chain A residue  992 LEU
Chi-restraints excluded: chain A residue 1057 MET
Chi-restraints excluded: chain A residue 1063 SER
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1141 VAL
Chi-restraints excluded: chain A residue 1163 MET
Chi-restraints excluded: chain A residue 1168 LEU
Chi-restraints excluded: chain A residue 1193 VAL
Chi-restraints excluded: chain A residue 1206 MET
Chi-restraints excluded: chain A residue 1218 LEU
Chi-restraints excluded: chain B residue   72 ILE
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue  371 VAL
Chi-restraints excluded: chain B residue  386 ASP
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  429 TYR
Chi-restraints excluded: chain B residue  472 LYS
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   80 SER
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  278 CYS
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  329 LYS
Chi-restraints excluded: chain C residue  331 VAL
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain C residue  335 VAL
Chi-restraints excluded: chain C residue  338 VAL
Chi-restraints excluded: chain C residue  377 CYS
Chi-restraints excluded: chain C residue  386 ASP
Chi-restraints excluded: chain C residue  413 VAL
Chi-restraints excluded: chain C residue  459 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 92 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9980
   chunk 94 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9980
   chunk 81 optimal weight:    3.9990
   chunk 17 optimal weight:    6.9990
   chunk 54 optimal weight:    0.6980
   chunk 124 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 138 optimal weight:    6.9990
   chunk 155 optimal weight:    2.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A  84 HIS
** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 323 HIS
** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.152906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.120632 restraints weight = 28789.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.3736 rms_B_bonded: 3.60
r_work: 0.3601 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3592
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3592 r_free = 0.3592    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       20 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3592 r_free = 0.3592    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       20 |
|-----------------------------------------------------------------------------|
r_final: 0.3592
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.2488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  14516  Z= 0.149
  Angle     :  0.711  12.864  19832  Z= 0.350
  Chirality :  0.043   0.167   2138
  Planarity :  0.004   0.051   2416
  Dihedral  : 15.095 150.839   2209
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.18 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 27.46 %
    Favored  : 68.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.21), residues: 1643
  helix:  1.12 (0.21), residues: 617
  sheet:  0.11 (0.36), residues: 198
  loop : -1.27 (0.22), residues: 828

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A 607 
 HIS   0.012   0.001   HIS A  84 
 PHE   0.010   0.001   PHE C 403 
 TYR   0.029   0.001   TYR A 831 
 ARG   0.005   0.000   ARG A1148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03429 (  582)
  hydrogen bonds       : angle       4.46054 ( 1616)
  covalent geometry    : bond        0.00344 (14516)
  covalent geometry    : angle       0.71095 (19832)

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

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

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3286 Ramachandran restraints generated.
    1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 180
  time to evaluate  : 1.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 LEU cc_start: 0.5954 (OUTLIER) cc_final: 0.5187 (tp)
REVERT: A  536 GLU cc_start: 0.8078 (tp30) cc_final: 0.7323 (pt0)
REVERT: A  540 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7780 (mp10)
REVERT: A  544 MET cc_start: 0.8474 (ppp) cc_final: 0.8257 (pp-130)
REVERT: A  552 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7834 (mp)
REVERT: A  977 GLU cc_start: 0.7373 (tm-30) cc_final: 0.7156 (tm-30)
REVERT: A 1098 ASN cc_start: 0.8992 (m-40) cc_final: 0.8507 (m-40)
REVERT: A 1136 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7204 (tm-30)
REVERT: A 1144 GLU cc_start: 0.8481 (pt0) cc_final: 0.8127 (pm20)
REVERT: B   74 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7817 (mm-40)
REVERT: B  191 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8140 (mt-10)
REVERT: B  325 ARG cc_start: 0.7791 (ptp-110) cc_final: 0.7492 (mtm180)
REVERT: B  465 MET cc_start: 0.7952 (mmm) cc_final: 0.7508 (mmm)
REVERT: B  472 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8485 (tmmm)
REVERT: C  309 HIS cc_start: 0.7957 (t-90) cc_final: 0.7708 (t-90)
REVERT: C  310 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7731 (pm20)
REVERT: C  386 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7639 (t0)
REVERT: C  396 ARG cc_start: 0.8106 (tpp-160) cc_final: 0.7152 (mpp80)
  outliers start: 53
  outliers final: 40
  residues processed: 218
  average time/residue: 1.2984
  time to fit residues: 312.8821
Evaluate side-chains
  218 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 173
  time to evaluate  : 1.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 GLU
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  433 SER
Chi-restraints excluded: chain A residue  550 GLN
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  605 LEU
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  858 THR
Chi-restraints excluded: chain A residue  885 THR
Chi-restraints excluded: chain A residue  948 ILE
Chi-restraints excluded: chain A residue  992 LEU
Chi-restraints excluded: chain A residue 1057 MET
Chi-restraints excluded: chain A residue 1063 SER
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1079 ILE
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1141 VAL
Chi-restraints excluded: chain A residue 1163 MET
Chi-restraints excluded: chain A residue 1168 LEU
Chi-restraints excluded: chain A residue 1193 VAL
Chi-restraints excluded: chain A residue 1206 MET
Chi-restraints excluded: chain A residue 1218 LEU
Chi-restraints excluded: chain B residue   72 ILE
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue  371 VAL
Chi-restraints excluded: chain B residue  386 ASP
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  429 TYR
Chi-restraints excluded: chain B residue  472 LYS
Chi-restraints excluded: chain C residue   80 SER
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  278 CYS
Chi-restraints excluded: chain C residue  306 LEU
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  329 LYS
Chi-restraints excluded: chain C residue  331 VAL
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain C residue  335 VAL
Chi-restraints excluded: chain C residue  338 VAL
Chi-restraints excluded: chain C residue  377 CYS
Chi-restraints excluded: chain C residue  386 ASP
Chi-restraints excluded: chain C residue  413 VAL
Chi-restraints excluded: chain C residue  459 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 99 optimal weight:    0.9990
   chunk 121 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 128 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 93 optimal weight:    3.9990
   chunk 49 optimal weight:    7.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 740 ASN
** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 323 HIS
** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.152662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.121420 restraints weight = 27988.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.3722 rms_B_bonded: 3.41
r_work: 0.3591 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3599
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3599 r_free = 0.3599    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       20 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3599 r_free = 0.3599    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3599
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.2585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  14516  Z= 0.176
  Angle     :  0.728  13.809  19832  Z= 0.361
  Chirality :  0.044   0.197   2138
  Planarity :  0.005   0.054   2416
  Dihedral  : 15.155 151.243   2209
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.85 %
    Favored  : 92.09 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 27.81 %
    Favored  : 68.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.21), residues: 1643
  helix:  1.00 (0.21), residues: 623
  sheet: -0.00 (0.35), residues: 204
  loop : -1.30 (0.22), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A 607 
 HIS   0.005   0.001   HIS A  84 
 PHE   0.011   0.001   PHE A 389 
 TYR   0.019   0.001   TYR A 573 
 ARG   0.005   0.000   ARG A 853 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03601 (  582)
  hydrogen bonds       : angle       4.52939 ( 1616)
  covalent geometry    : bond        0.00408 (14516)
  covalent geometry    : angle       0.72837 (19832)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 13790.11 seconds
wall clock time: 239 minutes 11.14 seconds (14351.14 seconds total)